WO2012117324A1 - Plants having enhanced yield-related traits and producing methods thereof - Google Patents

Plants having enhanced yield-related traits and producing methods thereof Download PDF

Info

Publication number
WO2012117324A1
WO2012117324A1 PCT/IB2012/050878 IB2012050878W WO2012117324A1 WO 2012117324 A1 WO2012117324 A1 WO 2012117324A1 IB 2012050878 W IB2012050878 W IB 2012050878W WO 2012117324 A1 WO2012117324 A1 WO 2012117324A1
Authority
WO
WIPO (PCT)
Prior art keywords
plant
nucleic acid
polypeptide
plants
seq
Prior art date
Application number
PCT/IB2012/050878
Other languages
French (fr)
Inventor
Marieke Louwers
Christophe Reuzeau
Ana Isabel Sanz Molinero
Yves Hatzfeld
Original Assignee
Basf Plant Science Company Gmbh
Basf (China) Company Limited
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Priority to US14/001,804 priority Critical patent/US20130340120A1/en
Priority to DE112012001017T priority patent/DE112012001017T5/en
Priority to EA201391243A priority patent/EA201391243A1/en
Priority to MX2013009749A priority patent/MX2013009749A/en
Priority to BR112013021836A priority patent/BR112013021836A2/en
Priority to EP12751992.4A priority patent/EP2681323A4/en
Application filed by Basf Plant Science Company Gmbh, Basf (China) Company Limited filed Critical Basf Plant Science Company Gmbh
Priority to AU2012222993A priority patent/AU2012222993A1/en
Priority to CN201280020339.7A priority patent/CN103492573A/en
Priority to CA2826591A priority patent/CA2826591A1/en
Publication of WO2012117324A1 publication Critical patent/WO2012117324A1/en
Priority to ZA2013/07172A priority patent/ZA201307172B/en
Priority to US15/877,863 priority patent/US20180291393A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/415—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from plants
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
    • C12N15/79—Vectors or expression systems specially adapted for eukaryotic hosts
    • C12N15/82—Vectors or expression systems specially adapted for eukaryotic hosts for plant cells, e.g. plant artificial chromosomes (PACs)
    • C12N15/8241—Phenotypically and genetically modified plants via recombinant DNA technology
    • C12N15/8261—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield
    • C12N15/8271—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • C12N15/8273—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for drought, cold, salt resistance
    • Y—GENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y02—TECHNOLOGIES OR APPLICATIONS FOR MITIGATION OR ADAPTATION AGAINST CLIMATE CHANGE
    • Y02A—TECHNOLOGIES FOR ADAPTATION TO CLIMATE CHANGE
    • Y02A40/00—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production
    • Y02A40/10—Adaptation technologies in agriculture, forestry, livestock or agroalimentary production in agriculture
    • Y02A40/146—Genetically Modified [GMO] plants, e.g. transgenic plants

Definitions

  • the present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a DUF642 (Protein containing a Domain of Unknown Function) polypeptide.
  • the present invention also concerns plants having modulated expression of a nucleic acid encoding a DUF642 polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants.
  • the invention also provides constructs useful in the methods of the invention.
  • the present invention furthermore concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding an epimerase-related like polypeptide.
  • the present invention also concerns plants having modulated expression of a nucleic acid encoding an epimerase-related like polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants.
  • the invention also provides constructs useful in the methods of the invention.
  • the present invention also concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a Phospholipase/carboxylesterase (PLPCase) polypeptide.
  • the present invention also concerns plants having modulated expression of a nucleic acid encoding a PLPCase polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants.
  • the invention also provides constructs useful in the methods of the invention.
  • Such technology has the capacity to deliver crops or plants having various improved economic, agronomic or horticultural traits.
  • a trait of particular economic interest is increased yield.
  • Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on several factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence and more. Root development, nutrient uptake, stress tolerance and early vigour may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.
  • Seed yield is a particularly important trait, since the seeds of many plants are important for human and animal nutrition.
  • Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the sou rce of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from the roots, leaves and stems into the growing seed. The endosperm, in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain.
  • a further important trait is that of improved abiotic stress tolerance.
  • Abiotic stress is a primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50% (Wang et al., Planta 218, 1 -14, 2003).
  • Abiotic stresses may be caused by drought, salinity, extremes of temperature, chemical toxicity and oxidative stress.
  • the ability to improve plant tolerance to abiotic stress would be of great economic advantage to farmers worldwide and would allow for the cultivation of crops during adverse conditions and in territories where cultivation of crops may not otherwise be possible.
  • Crop yield may therefore be increased by optimising one of the above-mentioned factors.
  • DUF642 polypeptides the family of DUF642 proteins represents a conserved region found in a number of uncharacterised plant proteins. DU F642 proteins were identified e.g. by Irshad et al., BMC Plant Biology 2008, 8:94.
  • Epimerases can be defined as isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules.
  • Arabidopsis epimerase gene Ascencio-lbanez et al. (2008, Plant Physiology 148(1 ):436-454) have reported amongst genes that are significantly changed during CalCuV injection an Arabodopsis epimerase gene, which is listed in a supplemental table (Table 2) of this paper. In this paper, the Arabidopsis gene is called a "Putative protein Isopenicillin-N-epimerase".
  • PLPCase polypeptides the PLPCase polypeptide fami ly contai ns both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases.
  • Members of the PLPCase superfamily are present in plants, but also in other organisms such as yeast and bacteria.
  • SOBER1 gene encoding a PLPCase is involved in resistance to plant pathogen P. synringae pv tomato DC3000 (Kirik and Mudgett (2009), PNAS 106 (48): 20532-20537).
  • Recent studies showed that PLPCase might have arisen from rare horizontal gene transfer from fungi to plant (Richards et al. (2009), The Plant Cell, 21 (7): 1897-191 1 ).
  • the modification of certain yield traits may be favoured over others.
  • an increase in the vegetative parts of a plant may be desirable, and for applications such as flour, starch or oil production, an increase in seed parameters may be particularly desirable. Even amongst the seed parameters, some may be favoured over others, depending on the application.
  • Various mechanisms may contribute to increasing seed yield, whether that is in the form of increased seed size or increased seed number.
  • the present invention shows that modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide gives plants having enhanced yield-related traits relative to control plants.
  • the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide and optionally selecting for plants having enhanced yield-related traits.
  • the present invention provides a method for producing plants having enhanced yield-related traits relative to control plants, wherein said method comprises the steps of modulating expression in said plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as described herein and optionally selecting for plants having enhanced yield-related traits.
  • a preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide is by introducing and expressing in a plant a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
  • any reference hereinafter to a "protein useful in the methods of the invention” is taken to mean a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein.
  • Any reference hereinafter to a "nucleic acid useful in the methods of the invention” is taken to mean a nucleic acid capable of encoding such a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
  • the nucleic acid to be introduced into a plant is any nucleic acid encoding the type of protein which will now be described, hereafter also named "DUF642 nucleic acid”, or “epimerase-related like nucleic acid”, or “PLPCase nucleic acid” or “DUF642 gene”, or “epimerase-related like gene", or "PLPCase gene”.
  • a "DUF642 polypeptide” as defined herein refers to any polypeptide comprising an InterPro accession IPR006946 DUF642 domain, preferably said DUF642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
  • DUF642 or "DUF642 polypeptide” as used herein also intends to include homologues as defined hereunder of "DUF642 polypeptide".
  • the DUF642 polypeptide polypeptide comprises one or more of the following motifs:
  • the DUF642 polypeptide comprises one or more of the following motifs: (i) Motif 4: N[ML][LV][KR]NG[DG]FEEGPY[IF][FLI]P[GND][TA][SPR]WGVL[VI]P[PS] [MN][DIV][EV] (SEQ ID NO: 184),
  • the DU F642 polypeptide comprises in increasi ng order of preference, at least 2, at least 3, at least 4, at least 5, or all 6 motifs.
  • Motifs 1 to 6 were derived using the MEME algorithm (Bailey and Elkan, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAA I Press, Menlo Park, California, 1994). At each position within a M EME motif, the residues are shown that are present in the query set of sequences with a frequency higher than 0.2. Residues within square brackets represent alternatives.
  • the homologue of a DUF642 protein has in increasing order of preference at least 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO
  • the overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides).
  • GAP GAP
  • sequence identity level is determined by comparison of the polypeptide sequences over the entire length of the sequence of SEQ ID NO: 2 or SEQ ID NO: 4.
  • the sequence identity will generally be higher when only conserved domains or motifs are considered.
  • the motifs in a DUF642 polypeptide have, in increasing order of preference, at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of the motifs represented by SEQ ID NO: 181 to SEQ ID NO: 186 (Motifs 1 to 6).
  • said DUF642 polypeptide comprises a conserved domain (or motif) with at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the conserved motifs starting with amino acid 202 up to amino acid 241 (motif 1 ), amino acid 108 up to amino acid 132 (motif 2), amino acid 78 up to amino acid 191 (motif 3) in SEQ ID NO:2; the conserved motifs starting with amino acid 202 up to amino acid 230 (motif 4), amino acid 130 up to amino acid 159 (motif 5), amino acid 1 14 up to amino acid 128 (motif 6) in SEQ ID NO:2; the conserved motifs starting with amino acid 202 up to amino acid
  • an "epimerase-related like polypeptide” or “epimerase-related like protein” as defined herein refers to any polypeptide having an amino acid sequence which comprises one or more of the following motifs:
  • Motif 8 EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK][RN]WQ [LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
  • the epimerase-related like polypeptide comprises in increasing order of preference, at least 1 , at least 2, or all 3 motifs.
  • an epimerase-related like polypeptide as used herein comprises a polypeptide having one or more of the domains as listed in Table C, and in particular having one or more of the following domains:
  • an epimerase-related like polypeptide as used herein comprises a conserved domain (or motif) with at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to or consists of a conserved domain as represented by any one of:
  • epoxyrase-related like polypeptide as used herein also intends to include homologues as defined hereunder of an "epimerase-related like polypeptide”.
  • the homologue of an epimerase-related like protein has in increasing order of preference at least 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 198, provided that the homologous protein comprises any one or more of the conserved motifs or domains as outlined above.
  • the overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides).
  • GAP GCG Wisconsin Package, Accelrys
  • sequence identity level is determined by comparison of the polypeptide sequences over the entire length of the sequence of SEQ ID NO: 198.
  • sequence identity will generally be higher when only conserved domains or motifs are considered.
  • motifs in an epimerase- related like polypeptide have, in increasing order of preference, at least 70%, 71 %, 72%,
  • PLAse polypeptide refers to any polypeptide comprising an InterPro accession IPR003140 corresponding to PFAM accession number PF022030 Phospholipase/carboxylesterase (PLPCase) domain.
  • PLPCase or "PLPCase polypeptide” as used herein also intends to include homologues as defined hereunder of "PLPCase polypeptide”.
  • the PLPCase polypeptide comprises one or more of the following motifs:
  • M otif 1 4 E[FY] G[KR]T[HY]WRPKG[K ]HQATIVWLHGLGDNG[LSA]S[SW]SQLL [ED][ST]LPLPNIKWICPTA (SEQ ID NO: 348),
  • the PLPCase polypeptide comprises one or more of the following motifs:
  • the PLPCase polypeptide comprises one or more of the following motifs:
  • the PLPCase polypeptide comprises one or more of the following motifs:
  • Motif 24 SEDG[PH]DDWEGLDASA[AS]HIANLLSTEPADV (SEQ ID NO: 358)
  • Motif 25 G[IT]SDDVV[LP]Y[KR][YF]GEKSAQSLS[SM]AGFRY[VI][AMT]FK[SP]Y
  • the PLPCase polypeptide comprises in increasing order of preference, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 1 1 , or all 12 motifs.
  • the homologue of a PLPCase protein has in increasing order of preference at least 25%, 26%, 27%, 28%, 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99%
  • the overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall seq uence identity, the sequence identity will generally be h igher when only conserved domains or motifs are considered.
  • GAP GAP
  • the motifs in a PLPCase polypeptide have, in increasing order of preference, at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of the motifs represented by SEQ ID NO: 348 to SEQ ID NO: 359 (Motifs 14 to 25).
  • a method wherein said PLPCase polypeptide comprises a conserved domain (or motif) with at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the conserved domain starting with amino acid 20 up to amino acid 69 and/or amino acid 92 to amino acid 1 18 and/or amino acid 194 to amino acid 225 in SEQ ID NO:285).
  • domain domain
  • th e polypeptid e seq uence whi ch when used i n the constru ction of a phylogenetic tree, such as the one depicted in Figure 5, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4 rather than with any other group.
  • DUF642 polypeptides when expressed in rice according to the methods of the present invention as outlined in Examples 6 and 7, give plants having increased yield related traits, in particular when grown under non-stress conditions, total seed yield (Totalwgseeds), number of seeds (nrfilledseed), seed fill rate (fillrate), harvest index, greenness before flowering, total number of seeds (nrtotalseed) and for aboveground biomass (AreaMax).
  • polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one depicted in Figure 9, clusters with the group of epimerase-related like polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group.
  • epimerase-related like polypeptides when expressed in rice according to the methods of the present invention as outlined in Examples 6 and 7, give plants having increased yield related traits, in particular increased biomass and/or increase seed yield, and more particularly any one or more of increased total weight of seeds, harvest index, fill rate, thousand kernel weight (TKW), above ground biomass, and number of filled seeds.
  • th e polypeptid e seq uence whi ch when used i n the constru ction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group.
  • PLPCase polypeptides typically have phospholipase and/or carboxylesterase activity. Tools and techniques for measuring phospholipase and/or carboxylesterase activity are well known in the art, as e.g. Kirik and Mudgett (2009), PNAS 106 (48): 20532-20537.
  • PLPCase polypeptides when expressed in rice according to the methods of the present invention as outlined in Examples 6 and 7, give plants having increased yield related traits, in particular increased root biomass and greenness index.
  • the function of the nucleic acid sequences of the invention is to confer information for a protein that increases yield or yield related traits, when a nucleic acid sequence of the invention is transcribed and translated in a living plant cell.
  • the function of the nucleic acid sequences of the invention is to confer information for synthesis of the PLPCase polypeptides that increases yield or yield related traits, when such a nucleic acid sequence of the invention is transcribed and translated in a living plant cell.
  • the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ I D NO: 1 , encoding the polypeptide sequence of SEQ ID NO: 2.
  • performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any DUF642-encoding nucleic acid or DUF642 polypeptide as defined herein.
  • nucleic acids encoding DUF642 polypeptides are given in Table A1 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention.
  • the amino acid sequences given in Table A1 of the Examples section are example sequences of orthologues and paralogues of the DUF642 polypeptide represented by SEQ I D NO: 2, the terms "orthologues” and "paralogues” being as defined herein.
  • orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search as described in the definitions section; where the query sequence is SEQ I D NO: 1 or SEQ ID NO: 2; or SEQ I D NO: 3 or SEQ ID NO: 4, the second BLAST (back-BLAST) would be against rice sequences.
  • the invention also provides hitherto unknown DUF642-encoding nucleic acids and DUF642 polypeptides useful for conferring enhanced yield-related traits in plants relative to control plants.
  • nucleic acid molecule selected from:
  • nucleic acid encoding a DUF642 polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 34, 40, 92, 170,
  • motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs given in SEQ ID NO: 181 to SEQ I D NO: 186, and further preferably conferring enhanced yield-related traits relative to control plants.
  • nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
  • polypeptide selected from:
  • an amino acid sequence represented by SEQ ID NO: 34, 40, 92, 170, 172, 176 (ii) an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 34, 40, 92, 170, 172, 176, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%,
  • the present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 197, encoding the polypeptide sequence of SEQ ID NO: 198.
  • performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any n ucleic acid encod ing epimerase-related like polypeptides or any epimerase-related like polypeptide as defined herein.
  • nucleic acids encoding epimerase-related like polypeptides are given in Table A2 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention.
  • the amino acid sequences given in Table A2 of the Examples section are example sequences of orthologues and paralogues of the epimerase-related like polypeptide represented by SEQ ID NO: 198, the terms "orthologues” and “paralogues” being as defined herein.
  • Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search as described in the definitions section; where the query sequence is SEQ ID NO: 197 or SEQ I D NO: 198, the second BLAST (back- BLAST) would be against poplar sequences.
  • the invention also provides hitherto unknown epimerase-related like-encoding nucleic acids and epimerase-related like polypeptides useful for conferring enhanced yield-related traits in plants relative to control plants.
  • nucleic acid molecule selected from:
  • nucleic acid encoding epimerase-related like polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96% , 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having i n increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, or 99% sequence identity to
  • nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
  • polypeptide selected from:
  • an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more
  • nucleic acids encoding PLPCase polypeptides are given in Table A3 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention.
  • the amino acid sequences given in Table A3 of the Examples section are example sequences of orthologues and paralogues of the PLPCase polypeptide represented by SEQ I D NO: 285, the terms "orthologues” and "paralogues” being as defined herein.
  • orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search as described in the definitions section; where the query sequence is SEQ ID NO: 284 or SEQ ID NO: 285, the second BLAST (back-BLAST) would be against Medicago truncatula sequences.
  • the invention also provides hitherto unknown PLPCase-encodi ng nucleic acids and PLPCase polypeptides useful for conferring enhanced yield-related traits in plants relative to control plants.
  • nucleic acid molecule selected from:
  • nucleic acid represented by any one of SEQ ID NO: 298, 302, 304, 312, 316, 336 or 346;
  • nucleic acid encoding a PLPCase polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,
  • nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
  • polypeptide selected from:
  • amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%,
  • Nucleic acid variants may also be useful in practising the methods of the invention.
  • Examples of such variants include nucleic acids encoding homologues and derivatives of any one of the amino acid sequences given in Table A1 to A3 of the Examples section, the terms "homologue” and “derivative” being as defined herein.
  • Also useful in the methods of the invention are nucleic acids encoding homologues and derivatives of orthologues or paralogues of any one of the amino acid seq uences given in Table A1 to A3 of the Examples section.
  • Homologues and derivatives useful in the methods of the present invention have substantially the same biological and functional activity as the unmodified protein from which they are derived.
  • Further variants useful in practising the methods of the invention are variants in which codon usage is optimised or in which imiRNA target sites are removed.
  • nucleic acid variants useful in practising the methods of the invention include portions of n ucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides, nucleic acids hybridising to nucleic acids encoding POI polypeptides, splice variants of nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides, allelic variants of nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides and variants of nucleic acids encoding DUF642 polypeptides, or epimerase- related like polypeptides, or PLPCase polypeptides obtained by gene shuffling.
  • the terms hybridising sequence, splice variant, allelic variant and gene shuffling are as described herein.
  • Nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full-length nucleic acid sequences.
  • a method for enhancing yield-related traits in plants comprising introducing and expressing in a plant a portion of any one of the nucleic acid sequences given in Table A1 to A3 of the Examples section, or a portion of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A1 to A3 of the Examples section.
  • a portion of a nucleic acid may be prepared, for example, by making one or more deletions to the nucleic acid.
  • the portions may be used in isolated form or they may be fused to other coding (or non-coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the protein portion.
  • portions useful in the methods of the invention encode a DUF642 polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A1 of the Examples section.
  • the portion is a portion of any one of the nucleic acids given in Table A1 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section.
  • the portion is at least 250, 300, 350, 400, 450 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A1 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section.
  • the portion is a portion of the nucleic acid of SEQ ID NO: 1.
  • the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one depicted in Figure 5, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 or 4 rather than with any other group, and/or comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
  • portions useful in the methods of the invention encode an epimerase-related like polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A2 of the Examples section.
  • the portion is a portion of any one of the nucleic acids given in Table A2 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section.
  • the portion is at least 850, 900, 950, 1000, 1050, 1100, 1 150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A2 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section.
  • the portion is a portion of the nucleic acid of SEQ ID NO: 197.
  • the portion encodes a fragment of an amino acid sequence which has one or more of the following characteristics:
  • motifs 7 to 13 comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
  • portions useful in the methods of the invention encode a PLPCase polypeptide as defined herein, and have substantially the same biological activity as the ami no acid seq uences given in Table A3 of the Examples section.
  • the portion is a portion of any one of the nucleic acids given in Table A3 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A3 of the Examples section.
  • the portion is at least 350, 400, 450, 500, 550, 600, 650, 700, 750, 780 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A3 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A3 of the Examples section.
  • the portion is a portion of the nucleic acid of SEQ ID NO: 284.
  • the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
  • nucleic acid variant useful in the methods of the invention is a nucleic acid capable of hybridising, under reduced stringency conditions, preferably under stringent conditions, with a n ucl ei c aci d encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, or with a portion as defined herein.
  • a method for enhancing yield-related traits in plants comprising introducing and expressing in a plant a nucleic acid capable of hybridizing to the complement of a nucleic acid encoding any one of the proteins given in Table A of the Examples section, or to the complement of a nucleic acid encoding an orthologue, paralogue or homologue of any one of the proteins given in Table A of the Examples section.
  • the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding any one of the proteins given in Table A of the Examples section, or to a portion of any of these sequences, a portion being as defined herein, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A of the Examples section.
  • the hybridising sequence is most preferably capable of hybridising to the complement of a nucleic acid encoding the polypeptide as represented by SEQ ID NO: 1 or to a portion thereof.
  • the hybridising sequence encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
  • the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ I D NO: 1 or SEQ ID NO: 3 or to a portion thereof under conditions of medium or high stringency, preferably high stringency as defined above.
  • the hybrid isi ng seq uence is capable of hybrid isi ng to the complement of a nucleic acid as represented by SEQ ID NO: 1 or SEQ ID NO: 3 under stringent conditions.
  • the hybridising sequence is most preferably capable of hybridising to the complement of a n ucleic acid encoding the polypeptide as represented by SEQ ID NO: 197 or to a portion thereof.
  • the hybridising sequence encodes a polypeptide with an amino acid sequence which has one or more of the following characteristics:
  • - comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
  • hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 197 or to a portion thereof under conditions of medium or high stringency, preferably high stringency as defined above. In another embodiment the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 197 under stringent conditions.
  • the hybridising sequence is most preferably capable of hybridising to the complement of a nucleic acid encoding the polypeptide as represented by SEQ I D NO: 284 or to a portion thereof.
  • the hybridization conditions are of medium stringency, preferably of high stringency, as defined herein.
  • the hybridising sequence encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/ or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
  • nucleic acid variant useful in the methods of the invention is a splice variant encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined hereinabove, a splice variant being as defined herein.
  • a method for enhancing yield-related traits in plants comprising introducing and expressing in a plant a splice variant of any one of the nucleic acid sequences given in Table A of the Examples section, or a splice variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section.
  • preferred splice variants are splice variants of a nucleic acid represented by SEQ I D NO: 1 , or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2.
  • the amino acid sequence encoded by the splice variant when used in the construction of a phylogenetic tree, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
  • preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 197, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 198.
  • the amino acid sequence encoded by the splice variant has one or more of the following characteristics:
  • - comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
  • preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 284, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 285.
  • the amino acid sequence encoded by the splice variant when used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
  • nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, an allelic variant being as defined herein.
  • a method for enhancing yield-related traits in plants comprising introducing and expressing in a plant an allelic variant of any one of the nucleic acids given in Table A of the Examples section, or comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section.
  • the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the DUF642 polypeptide of SEQ ID NO: 2 and any of the amino acids depicted in Table A1 of the Examples section.
  • Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles.
  • the allelic variant is an allelic variant of S EQ I D NO: 1 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2.
  • the amino acid sequence encoded by the allelic variant when used in the construction of a phylogenetic tree, clusters with the DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
  • allelic variants useful in the methods of the present invention have substantially the same biological activity as the epimerase-related like polypeptide of SEQ ID NO: 198 and any of the amino acids depicted in Table A2 of the Examples section.
  • Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles.
  • the allelic variant is an allelic variant of SEQ ID NO: 197 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ I D NO: 198.
  • the amino acid sequence encoded by the allelic variant has one or more of the following characteristics:
  • - comprises any one or more of the motifs 7 to 13 (as represented by SED ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
  • allelic variants useful in the methods of the present invention have substantially the same biological activity as the PLPCase polypeptide of SEQ ID NO: 285 and any of the amino acids depicted in Table A3 of the Examples section.
  • Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles.
  • the allelic variant is an allelic variant of SEQ ID NO: 284 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 285.
  • the amino acid sequence encoded by the allelic variant when used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the PLPCase polypeptides comprising the amino acid sequence represented by SEQ I D NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
  • Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding DUF642 polypeptides, o r epimerase-related like polypeptides, or PLPCase polypeptides as defined herein; the term “gene shuffling” being as defined herein.
  • a method for enhancing yield-related traits in plants comprising introducing and expressing in a plant a variant of any one of the nucleic acid sequences given in Table A of the Examples section, or comprising introducing and expressing in a plant a variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section, which variant nucleic acid is obtained by gene shuffling.
  • the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling when used in the construction of a phylogenetic tree, preferably clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ I D NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
  • the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling preferably is an amino acid sequence which has one or more of the following characteristics:
  • - comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
  • PLPCase polypeptides the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, when used in the construction of a phylogenetic tree such as the one depicted in Figure 14, preferably clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 1 7 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
  • nucleic acid variants may also be obtained by site-directed mutagenesis.
  • site-directed mutagenesis Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley Eds.).
  • nucleic acids encoding DUF642 polypeptides may be derived from any natural or artificial source.
  • the nucleic acid may be modified from its native form in composition and/or genomic envi ron ment th rough del iberate human manipulation.
  • the DUF642 polypeptide-encoding nucleic acid is from a plant, further preferably from a monocotyledonous plant, more preferably from the family Poaceae, most preferably the nucleic acid is from Oryza sativa.
  • the nucleic acid encoding the DUF642 polypeptide of SEQ ID NO:2 can be generated from the nucleic acid encoding the DUF642 polypeptide of SEQ ID NO:2 by alteration of several nucleotides, e.g. by site-directed mutagenesis using PCR based methods (see Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates)).
  • DUF642 polypeptides differing from the sequence of SEQ ID NO: 2 or SEQ ID NO: 4 by one or several amino acids may be used to increase the yield of plants in the methods and constructs and plants of the invention.
  • nucleic acids encoding epimerase-related like polypeptides may be derived from any natural or artificial source.
  • the nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation.
  • the epimerase-related like polypeptide-encoding nucleic acid is from a plant, further preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably the nucleic acid is from the genus Populus, and most preferably the nucleic acid is from Populus trichocarpa.
  • nucleic acids encoding PLPCase polypeptides may be derived from any natural or artificial source.
  • the nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate h uman manipulation.
  • the PLPCase polypeptide-encoding nucleic acid is from a plant, further preferably from a dicotyledonous plant, more preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably the n ucleic acid is from Medicago truncatula.
  • PLPCase polypeptides differing from the sequence of SEQ ID NO: 285 by one or several amino acids (substitution(s), insertion(s) and/or deletion(s) as defined above) may equally be useful to increase the yield of plants in the methods and constructs and plants of the invention.
  • the present invention extends to recombinant chromosomal DNA comprising a nucleic acid sequence useful in the methods of the invention, wherein said nucleic acid is present in the chromosomal DNA as a result of recombinant methods, i.e. said nucleic acid is not in the chromosomal DNA in its native surrounding.
  • Said recombinant chromosomal DNA may be a chromosome of native origin, with said nucleic acid inserted by recombinant means, or it may be a mini-chromosome or a non-native chromosomal structure, e.g. or an artificial chromosome.
  • the nature of the chromosomal DNA may vary, as long as it allows for stable passing on to successive generations of the recombinant nucleic acid useful in the methods of the invention, and allows for expression of said nucleic acid in a living plant cell resulting in increased yield or increased yield related traits of the plant cell or a plant comprising the plant cell.
  • the recombinant chromosomal DNA of the invention is comprised in a plant cell.
  • Performance of the methods of the invention gives plants having enhanced yield-related traits.
  • performance of the methods of the invention gives plants having increased yield, especially increased seed yield relative to control plants.
  • Reference herein to enhanced yield-related traits is taken to mean an increase of early vigour and/or in biomass (weight) of one or more parts of a plant, which may include (i) aboveground parts and preferably aboveground harvestable parts and/or (ii) parts below ground and preferably harvestable below ground.
  • harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants.
  • the present invention provides a method for increasing yield, especially seed yield of plants, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide as defined herein.
  • the present invention also provides a method for increasing yield, and more particularly increased seed yield and/or increased biomass, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide as defined herein.
  • the present invention also provides a method for increasing yield, especially enhancing root biomass of plants, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding a PLPCase polypeptide as defined herein.
  • performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein.
  • Performance of the methods of the invention gives plants grown u nder non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
  • Performance of the methods of the invention gives plants grown under conditions of drought, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of drought which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase- related like polypeptide, or a PLPCase polypeptide.
  • Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield-related traits in plants grown under conditions of nutrient deficiency, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
  • Performance of the methods of the invention gives plants grown under conditions of salt stress, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of salt stress, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase- related like polypeptide, or a PLPCase polypeptide.
  • the invention also provides genetic constructs and vectors to facilitate introduction and/or expression in plants of nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides.
  • the gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants or host cells and suitable for expression of the gene of interest in the transformed cells.
  • the invention also provides use of a gene construct as defined herein in the methods of the invention.
  • the present invention provides a construct comprising:
  • the nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide is as defined herein.
  • control sequence and terminal sequence are as defined herein.
  • the present invention provides a construct comprising:
  • the genetic construct of the invention may be comprised in a host cell, plant cell, seed, agricultural product or plant.
  • Plants or host cells are transformed with a genetic construct such as a vector or an expression cassette comprising any of the nucleic acids described herein.
  • the invention furthermore provides plants or host cells transformed with a construct as described above.
  • the invention provides plants transformed with a construct as described above, which plants have increased yield-related traits as described herein.
  • the genetic construct of the invention confers increased yield or yield related traits(s) to a living plant cell when it has been introduced into said plant cell and express the nucleic acid encoding the DUF642 polypeptide, or the epimerase-related like polypeptide, or the PLPCase polypeptide, comprised in the genetic construct.
  • sequence of interest is operably linked to one or more control sequences (at least to a promoter).
  • the promoter in such a genetic construct may be a non-native promoter to the nucleic acid described above, i .e. a promoter which does not regulate the expression of the herein disclosed polynucleotides in its native surrounding.
  • any type of promoter may be used to drive expression of the nucleic acid sequence, but preferably the promoter is of plant origin.
  • a constitutive promoter is particularly useful in the methods.
  • the constitutive promoter is a ubiquitous constitutive promoter of medium strength. See the "Definitions" section herein for definitions of the various promoter types.
  • the constitutive promoter is preferably a ubiquitous constitutive promoter of medium strength . More preferably it is a plant derived promoter, e. g. a promoter of plant chromosomal origin, such as a GOS2 promoter or a promoter of substantially the same strength and having substantially the same expression pattern (a functionally equivalent promoter), more preferably the promoter is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 189, or SEQ ID NO: 278, or SEQ ID NO: 361 , most preferably the constitutive promoter is as represented by SEQ ID NO: 189, or SEQ ID NO: 278, or SEQ ID NO: 361 . See the "Definitions" section herein for further examples of constitutive promoters.
  • DUF642 polypeptides are not restricted to the DUF642 polypeptide-encoding nucleic acid represented by SEQ I D NO: 1 or 3, nor is the applicability of the invention restricted to expression of a DUF642 polypeptide-encoding nucleic acid when driven by a constitutive promoter.
  • epimerase-related like polypeptides it should be clear that the applicability of the present invention is not restricted to the epimerase-related like polypeptide-encoding nucleic acid represented by SEQ I D NO: 197, nor is the applicability of the invention restricted to expression of an epimerase-related like polypeptide-encoding nucleic acid when driven by a constitutive promoter, or when driven by a root-specific promoter.
  • one or more terminator sequences may be used in the construct introduced into a plant.
  • the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 189, operably linked to the nucleic acid encoding the DUF642 polypeptide.
  • the construct comprises a zein terminator (t-zein) linked to the 3' end of the DUF642 coding sequence.
  • the expression cassette comprises a sequence having in increasing order of preference at least 95%, at least 96%, at least 97%, at least 98%, at l ea st 99% i d e nti ty to th e seq u e n ce re presen ted by S EQ I D N O : 1 87 o r 1 88 (pPRO::DUF642::t-zein sequence).
  • one or more sequences encoding selectable markers may be present on the construct introduced into a plant.
  • one or more terminator sequences may be used in the construct introduced into a plant.
  • the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 278, operably linked to the nucleic acid encoding the epimerase-related like polypeptide.
  • the construct comprises a zein terminator (t-zein) linked to the 3' end of the cod i ng seq uence of an epi merase-related like polypeptide.
  • the expression cassette comprises a sequence having in increasing order of preference at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identity to the seq u ence represented by S E Q I D NO : 279 (pP RO : : E RL : :t-zein sequence).
  • sequences encoding selectable markers may be present on the construct introduced into a plant.
  • one or more terminator sequences may be used in the construct introduced into a plant.
  • the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 361 , operably linked to the nucleic acid encoding the PLPCase polypeptide.
  • the expression cassette comprises the sequence represented by SEQ I D NO: 360 (pGOS2:: PLPCase::t-zein sequence).
  • sequences encoding selectable markers may be present on the construct introduced into a plant.
  • the modulated expression is increased expression.
  • Methods for increasing expression of nucleic acids or genes, or gene products are well documented in the art and examples are provided in the definitions section.
  • a preferred method for modulating expression of a nucleic acid encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide is by introducing and expressing in a plant a nucleic acid encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide; however the effects of performing the method, i.e. enhancing yield-related traits may also be achieved using other well known techniques, including but not limited to T-DNA activation tagging, TILLING, homologous recombination. A description of these techniques is provided in the definitions section.
  • the invention also provides a method for the production of transgenic plants having enhanced yield-related traits relative to control plants, comprising introduction and expression in a plant of any nucleic acid encoding a DUF642 polypeptide, or a epimerase- related like polypeptide, or a PLPCase polypeptide as defined herein.
  • the present invention provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased yield, more particularly increased seed yield, which method comprises:
  • the nucleic acid of (i) may be any of the nucleic acids capable of encoding a DUF642 polypeptide as defined herein. More specifically, the present invention also provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased yield, and more particuarly increased seed yield and/or increased biomass, which method comprises:
  • the nucleic acid of (i) may be any of the nucleic acids capable of encoding an epimerase- related like polypeptide as defined herein.
  • the present invention also provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased root biomass, which method comprises:
  • the nucleic acid of (i) may be any of the nucleic acids capable of encoding a PLPCase polypeptide as defined herein.
  • the plant cell transformed by the method according to the invention is regenerable into a transformed plant.
  • the plant cell transformed by the method according to the invention is not regenerable into a transformed plant, i.e. cells that are not capable to regenerate into a plant using cell culture techniques known i n the art.
  • Wh ile plants cells generally have the characteristic of totipotency, some plant cells can not be used to regenerate or propagate intact plants from said cells.
  • the plant cells of the invention are such cells.
  • the plant cells of the invention are plant cells that do not sustain themselves in an autotrophic way.
  • the nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant or plant cell by transformation.
  • transformation is described in more detail in the "definitions” section herein.
  • the present invention extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof.
  • the present invention encompasses plants or parts thereof (including seeds) obtainable by the methods according to the present invention.
  • the plants or plant parts or plant cells comprise a nucleic acid transgene encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, preferably in a genetic construct such as an expression cassette.
  • the present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.
  • I n a further embodi ment the invention extends to seeds comprising the expression cassettes of the invention, the genetic constructs of the invention, or the nucleic acids encoding the DUF642 polypeptides, or the epimerase-related like polypeptides, or the PLPCase polypeptides and/or the DUF642 polypeptides, or the epimerase-related like polypeptides, or the PLPCase polypeptides as described above.
  • the invention also includes host cells containing an isolated nucleic acid encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein.
  • host cells according to the invention are plant cells, yeasts, bacteria or fungi.
  • Host plants for the nucleic acids, construct, expression cassette or the vector used in the method according to the invention are, in principle, advantageously all plants which are capable of synthesizing the polypeptides used in the inventive method.
  • the plant cells of the invention overexpress the nucleic acid molecule of the invention.
  • Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and d icotyledonous plants incl uding fodder or forage legumes, ornamental plants, food crops, trees or shrubs.
  • the plant is a crop plant. Examples of crop plants include but are not limited to chicory, carrot, cassava, trefoil, soybean, beet, sugar beet, sunflower, canola, alfalfa, rapeseed, linseed, cotton, tomato, potato and tobacco.
  • th e p resen t i n ven ti on th e pl a nt i s a m o n ocotyl ed o n o us p l a nt.
  • Exam pl es of monocotyledonous plants include sugarcane.
  • the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn , teff, milo and oats.
  • the plants used in the methods of the invention are selected from the group consisting of maize, wheat, rice, soybean, cotton, oilseed rape including canola, sugarcane, sugar beet and alfalfa.
  • the methods of the invention are more efficient than the known methods, because the plants of the invention have increased yield and/or tolerance to an environmental stress compared to control plants used in comparable methods.
  • the plants of the invention and the plants used in the methods of the invention are sugarcane plants with increased biomass and/or increased sugar content of the shoot.
  • the plants of the invention and the plants used in the methods of the invention are sugarbeet plants with increased biomass and/or increased sugar content of the beets.
  • the invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, roots, rhizomes, tubers and bulbs, which harvestable parts comprise a recombinant nucleic acid encoding a DUF642 polypeptide, or a epimerase- related like polypeptide, or a PLPCase polypeptide.
  • the invention furthermore relates to products derived or produced, preferably directly derived or produced, from a harvestable part of such a plant, such as dry pellets, meal or powders, oil, fat and fatty acids, starch or proteins.
  • the invention also includes methods for manufacturing a product comprising a) growing the plants of the invention and b) producing said product from or by the plants of the invention or parts thereof, including seeds.
  • the methods comprise the steps of a) growing the plants of the invention, b) removing the harvestable parts as described herein from the plants and c) producing said product from, or with the harvestable parts of plants according to the invention.
  • Examples of such methods would be growing corn plants of the invention, harvesting the corn cobs and remove the kernels. These may be used as feedstuff or processed to starch and oil as agricultural products.
  • the product may be produced at the site where the plant has been grown, or the plants or parts thereof may be removed from the site where the plants have been grown to produce the product.
  • the plant is grown, the desired harvestable parts are removed from the plant, if feasible in repeated cycles, and the product made from the harvestable parts of the plant.
  • the step of growing the plant may be performed only once each time the methods of the invention is performed, while allowing repeated times the steps of product production e.g. by repeated removal of harvestable parts of the plants of the invention and if necessary further processing of these parts to arrive at the product.
  • the step of growing the plants of the invention is repeated and plants or harvestable parts are stored until the production of the product is then performed once for the accumulated plants or plant parts.
  • the steps of growing the plants and producing the product may be performed with an overlap in time, even simultaneously to a large extent, or sequentially. Generally the plants are grown for some time before the product is produced.
  • the products produced by the methods of the invention are plant products such as, but not li mited to, a foodstuff, feedstuff, a food su pplement, feed supplement, fiber, cosmetic or pharmaceutical.
  • the methods for production are used to make agricultural products such as, but not limited to, plant extracts, proteins, amino acids, carbohydrates, fats, oils, polymers, vitamins, and the like.
  • the polynucleotides or the polypeptides of the invention are comprised in an agricultural product.
  • the nucleic acid sequences and protein sequences of the invention may be used as product markers, for example where an agricultural product was produced by the methods of the invention.
  • Such a marker can be used to identify a product to have been produced by an advantageous process resulting not only in a greater efficiency of the process but also improved quality of the product due to increased quality of the plant material and harvestable parts used in the process.
  • markers can be detected by a variety of methods known in the art, for example but not limited to PCR based methods for nucleic acid detection or antibody based methods for protein detection.
  • the present invention also encompasses use of nucleic acids encoding DUF642 polypeptides, epimerase-related like polypeptides, or PLPCase polypeptides polypeptides as described herein and use of these DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides in enhancing any of the aforementioned yield- related traits in plants.
  • nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides described herein, or the DUF642 polypeptides, o r th e epimerase-related like polypeptides, or the PLPCase polypeptides themselves may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a DUF642 polypeptide-encoding gene, or an epimerase-related like polypeptide-encoding gene, or a PLPCase polypeptide-encoding gene.
  • nucleic acids/genes or the DUF642 polypeptides, or the epimerase-related like polypeptides, or the PLPCase polypeptides themselves may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having enhanced yield-related traits as defined herein in the methods of the invention. Furthermore, allelic variants of a DUF642 polypeptide-encoding nucleic acid/gene, or an epimerase-related like polypeptide-encoding nucleic acid/gene, o r a PLPCase polypeptide-encoding nucleic acid/gene may find use in marker-assisted breeding programmes.
  • Nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes.
  • a sequence identity of 50% sequence identity in this embodiment means that over the entire coding region of SEQ I D NO: 1 , 50 percent of all bases are identical between the sequence of SEQ I D NO: 1 and the related sequence.
  • a polypeptide sequence is 50 % identical to the polypeptide sequence of SEQ ID NO: 2, when 50 percent of the amino acids residues of the sequence as represented in SEQ I D NO: 2, are found in the polypeptide tested when comparing from the starting methionine to the end of the sequence of SEQ ID NO: 2.
  • any comparison to determine sequence identity percentages is performed
  • a sequence identity of 50% sequence identity in this embodiment means that over the entire coding region of SEQ ID NO: 197, 50 percent of all bases are identical between the sequence of SEQ ID NO: 197 and the related sequence.
  • a polypeptide sequence is 50 % identical to the polypeptide sequence of SEQ ID NO: 198, when 50 percent of the amino acids residues of the sequence as represented in SEQ ID NO: 198, are found in the polypeptide tested when comparing from the starting methionine to the end of the sequence of SEQ ID NO: 198.
  • the present invention relates to the following specific embodiments:
  • a method for enhancing yield-related traits in plants relative to control plants comprising modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, wherein said DUF642 polypeptide comprises an InterPro accession IPR006946 DU F642 domain , preferably said DU F642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
  • nucleic acid encoding a DUF642 encodes any one of the polypeptides listed in Table A1 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
  • nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
  • Plant, plant part thereof, including seeds, or plant cell obtainable by a method according to any one of embodiments 1 to 10, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9.
  • nucleic acid encoding a DUF642 as defined in any of embodiments 1 and 5 to 9; (ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
  • one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9 or a transgenic plant cell derived from said transgenic plant.
  • Transgenic plant according to embodiment 1 1 , 15 or 17, or a transgenic plant cell derived therefrom wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn, teff, milo or oats. 19.
  • Harvestable parts of a plant according to embodiment 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
  • nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9 for enhanci ng yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
  • a method for the production of a product comprising the steps of growing the plants of the invention and producing said product from or by
  • a dicot such as sugar beet, alfalfa, trefoil, chicory, carrot, cassava, cotton, soybean, canola
  • a monocot such as sugarcane
  • a cereal such as rice, maize, wheat, barley, millet, rye, triticale, sorghum emmer, spelt,
  • Construct according to embodiment 12 or 13 comprised in a plant cell.
  • Recombinant chromosomal DNA comprising the construct according to embodiment 12 or 13.
  • the present invention relates to the following specific items:
  • a m ethod for enhancing yield-related traits in plants relative to control plants comprising modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide, wherein said epimerase-related like polypeptide comprises one or more of the following motifs:
  • Motif 8 EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK] [RN] WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
  • n ucleic acid encodes a polypeptide having at least 40 % overal l sequence identity to the ami no acid represented by SEQ ID NO: 198.
  • nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa.
  • A2 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
  • nucleic acid is operably lin ked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
  • Plant, plant part thereof, including seeds, or plant cell obtainable by a method according to any one of items 1 to 1 1 , wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8.
  • Plant according to item 12 or a plant cell derived therefrom wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal , such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • a crop plant such as beet, sugarbeet or alfalfa
  • a monocotyledonous plant such as sugarcane
  • a cereal such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8;
  • one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
  • Plant according to item 17 or a plant cell derived therefrom wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • a crop plant such as beet, sugarbeet or alfalfa
  • a monocotyledonous plant such as sugarcane
  • a cereal such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8; or a transgenic plant cell derived from said transgenic plant.
  • Harvestable parts of a plant according to any of items 12-13, 17-18 or 20-21 wherein said harvestable parts are preferably shoot biomass and/or seeds.
  • Isolated nucleic acid molecule selected from:
  • nucleic acid encoding epimerase-related like polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90% , 91 %, 92%, 93%, 94%, 95%, 96% , 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, or
  • nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
  • Isolated polypeptide selected from:
  • an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more
  • nucleic acid as defined in item 24 and encoding an epimerase-related like polypeptide for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield in plants relative to control plants.
  • nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8 and 25; as molecular marker.
  • nucleic acid as defined in item 24 and encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8 and 25 as molecular marker Use of a nucleic acid as defined in item 24 and encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8 and 25 as molecular marker.
  • a method for the production of a product comprising the steps of growing the plants according to item 12, 18 or 20 and producing said product from or by
  • Recombinant chromosomal DNA comprising the construct according to item 14 or 15 comprised.
  • the invention is in particular characterized by any one or more of the following embodiments:
  • a method for enhancing yield-related traits in plants relative to control plants comprising modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide by introducing and expressing in a plant said nucleic acid encoding said epimerase-related like polypeptide, wherein said epimerase-related like polypeptide has at least 80 % overall sequence identity to the amino acid represented by SEQ ID NO: 198.
  • epimerase-related like polypeptide comprises one or more of the following motifs:
  • Motif 8 EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK] [RN]WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
  • said epimerase-related like polypeptide as used herein comprises at least two conserved domains selected from th e g rou p com pri si n g PyrdxlP-dep_Trfase_major (SSF53383), PTHR1 1601 , Aminotran_5 (PF00266) and PyrdxlP-dep_Trfase_major_sub1 (G3DSA:3.40.640.10), and preferably comprises i) an Aminotran_5 conserved domain and ii) at least one other co n s erved d om a i n se l e cted from th e g ro u p co m p ri si n g PyrdxIP- dep_Trfase_major (SSF53383), PTHR1 1601 , and PyrdxIP- dep_Trfase_
  • nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa.
  • nucleic acid encoding said epimerase-related like polypeptide encodes any one of the polypeptides listed in Table A2 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
  • nucleic acid is operably linked to a GOS2 promoter, preferably to a GOS2 promoter from rice.
  • nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments I and V to IX;
  • control sequences capable of driving expression of the nucleic acid sequence of (i), and preferably a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice, and optionally
  • XII Plant, plant part or plant cell transformed with a construct according to embodiment XI.
  • XIII Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from the introduction and expression therein of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodi ments I and V to IX; or a transgenic plant cell derived from said transgenic plant.
  • XV Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments I and V to IX; for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
  • the present invention relates to the following specific embodiments:
  • a method for enhancing yield-related traits in plants relative to control plants comprising m o d u l a t i n g e x p r e s s i o n i n a plant of a nucleic acid encoding a Phospholipase/carboxylesterase (PLPCase) polypeptide, wherein said PLPCase polypeptide comprises an I nterPro accession IPR003140 corresponding to PFAM accession number PF022030 Phospholipase/carboxylesterase (PLPCase) domain.
  • said modulated expression is effected by introduci ng and expressing in a plant said nucleic acid encodi ng said PLPCase polypeptide.
  • Motif 14 E[FY]G[KR]T[HY]WRPKG[KR]HQATIVWLHGLGDNG[LSA]S[SW]SQLL [ED][ST]LPLPNIKWICPTA (SEQ ID NO: 348),
  • nucleic acid encoding a PLPCase is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably from Medicago truncatula.
  • nucleic acid encoding a PLPCase encodes any one of the polypeptides listed in Table A3 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
  • nucleic acid encodes the polypeptide represented by SEQ ID NO: 285.
  • nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
  • Plant, plant part thereof, including seeds, or plant cell obtainable by a method according to any one of embodiments 1 to 1 1 , wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10.
  • nucleic acid encoding a PLPCase as defined in any of embodiments 1 and 6 to 10;
  • one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
  • Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants, comprising:
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10 or a transgenic plant cell derived from said transgenic plant.
  • Transgenic plant according to embodiment 12, 16 or 18, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal , such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • a crop plant such as beet, sugarbeet or alfalfa
  • a monocotyledonous plant such as sugarcane
  • a cereal such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for root biomass, increased greenness index and/or increased seed yield in plants relative to control plants.
  • a method for the production of a product comprising the steps of growing the plants according to embodiment 16, 18 or 19 and producing said product from or by
  • Construct according to embodiment 13 or 14 comprised in a plant cell.
  • a method for enhancing yield-related traits in plants relative to control plants comprising introducing and expressing in a plant of a nucleic acid encoding a DUF642 polypeptide, wherein said DUF642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
  • nucleic acid encodes the polypeptide represented by S EQ I D NO: 2 or SEQ I D NO: 4 or a nucleic acid encodi ng a polypeptide having at least 90% sequence identity to SEQ ID NO: 2 and/or SEQ I D NO: 4.
  • nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
  • Plant, plant part thereof, including seeds, or plant cell obtainable by a method according to any one of embodiments 1 to 3, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 to 3.
  • (iii) a transcription termination sequence (iii) a transcription termination sequence.
  • one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
  • a construct according to embodiment 5 or 6 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants.
  • DUF642 polypeptide as defined in any of embodiments 1 to 3;
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 to 3 or a transgenic plant cell derived from said transgenic plant.
  • a crop plant such as beet, sugarbeet or alfalfa
  • a monocotyledonous plant such as sugarcane
  • a cereal such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn, teff, milo or oats.
  • Harvestable parts of a plant according to embodiment 1 1 wherein said harvestable parts are preferably shoot biomass and/or seeds.
  • n u cl e ic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 to 3 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
  • a method for enhancing yield-related traits in plants relative to control plants comprising modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide by introducing and expressing in a plant said nucleic acid encoding said epimerase-related like polypeptide, wherein said epimerase-related like polypeptide has at least 80 % overall sequence identity to the amino acid represented by SEQ ID NO: 198.
  • said epimerase-related like polypeptide comprises one or more of the following motifs:
  • Motif 8 EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK] [RN]WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
  • said epimerase-related like polypeptide as used herein comprises at least two conserved domains selected from the group comprising PyrdxIP-dep Trfase major (SSF53383), PTHR1 1601 , A m i n o t r a n _ 5 ( PF00266) and PyrdxlP-dep_Trfase_major_sub1 (G3DSA:3.40.640.1 0), and preferably com prises an Am inotra n_5 conserved domain and at least one other conserved domai ns selected from the group comprising PyrdxlP-dep_Trfase_major (SSF53383), PTHR1 1601 , and PyrdxIP- dep_Trfase_major_sub1 (G3DSA:3.40.640.10), Method according to any of embodiments 15 to 18, wherein said epimerase-related like
  • nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa.
  • nucleic acid encoding said epimerase-related like polypeptide encodes any one of the polypeptides listed in Table A or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
  • nucleic aci sequence encodes an orthologue or paralogue of any of the polypeptides given i Table A2.
  • nucleic acid is operably linked to a GOS2 promoter, preferably to a GOS2 promoter from rice.
  • nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 5 and 19 to 23;
  • control sequences capable of driving expression of the nucleic acid sequence of (i), and preferably a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice, and optionally
  • Plant, plant part or plant cell transformed with a construct according to embodiment 25 Plant, plant part or plant cell transformed with a construct according to embodiment 25.
  • Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from the introduction and expression therein of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 15 and 19 to 23; or a transgenic plant cell derived from said transgenic plant.
  • nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 15 and 19 to 23; for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
  • a method for enhancing yield-related traits in plants relative to control plants comprising introducing and expressing in a plant of a nucleic acid encoding SEQ I D NO: 285 or homologues having 80% sequence identity to SEQ ID NO: 285.
  • Method according to embodiment 30, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased root biomass and/or increased seed yield relative to control plants.
  • Method according to any one of embodiments 30 to 31 wherein said enhanced yield- related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
  • said nucleic acid encoding a PLPCase is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably from Medicago truncatula. 35.
  • nucleic acid encoding a PLPCase encodes any one of the polypeptides listed in Table A3 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid, provided said nucleic acid has 80% sequence identity to SEQ ID NO: 285.
  • nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
  • nucleic acid encoding a PLPCase as defined in any of embodiments 30 and 34 to 36;
  • control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
  • Plant, plant part or plant cell transformed with a construct according to embodiment 38 or 39 Plant, plant part or plant cell transformed with a construct according to embodiment 38 or 39.
  • Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants, comprising:
  • Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 30 and 34 to 36 or a transgenic plant cell derived from said transgenic plant.
  • Transgenic plant according to embodiment 37, 41 or 43, or a transgenic plant cell derived therefrom wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
  • n ucleic acid encod i ng a PLPCase polypeptide as defined in any of embodiments 30 and 34 to 36 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for root biomass, increased greenness index and/or increased seed yield in plants relative to control plants.
  • peptides amino acids in a polymeric form of any length, linked together by peptide bonds, unless mentioned herein otherwise.
  • nucleic acid sequence(s) refers to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both , in a polymeric unbranched form of any length.
  • Homologue(s) refers to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both , in a polymeric unbranched form of any length.
  • Homologues of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes havi ng ami no acid su bstitutions, deletions and/or i nsertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived.
  • Orthologues and paralogues are two d ifferent forms of homologues and encompass evolutionary concepts used to describe the ancestral relationships of genes.
  • Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organ isms that have origi nated th rough speciation, and are also derived from a common ancestral gene.
  • a “deletion” refers to removal of one or more amino acids from a protein.
  • An “insertion” refers to one or more amino acid residues being introduced into a predetermined site in a protein. Insertions may comprise N-terminal and/or C-terminal fusions as well as intra-sequence insertions of single or multiple amino acids. Generally, insertions within the amino acid sequence will be smaller than N- or C-terminal fusions, of the order of about 1 to 1 0 residues.
  • N- or C-terminal fusion proteins or peptides include the binding domain or activation domain of a transcriptional activator as used in the yeast two-hybrid system, phage coat proteins, (histidine)-6-tag, glutathione S- transferase-tag, protein A, maltose-binding protein, dihydrofolate reductase, Tag*100 epitope, c-myc epitope, FLAG ® -epitope, lacZ, CMP (calmodulin-binding peptide), HA epitope, protein C epitope and VSV epitope.
  • a transcriptional activator as used in the yeast two-hybrid system
  • phage coat proteins phage coat proteins
  • glutathione S- transferase-tag glutathione S- transferase-tag
  • protein A maltose-binding protein
  • dihydrofolate reductase Tag*100 epitope
  • c-myc epitope FL
  • substitution refers to replacement of amino acids of the protein with other amino acids having similar properties (such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break a-helical structures or ⁇ -sheet structures).
  • Amino acid substitutions are typically of single residues, but may be clustered depending upon functional constraints placed upon the polypeptide and may range from 1 to 10 amino acids.
  • the amino acid substitutions are preferably conservative amino acid substitutions. Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company (Eds) and Table 1 below).
  • Amino acid substitutions, deletions and/or insertions may readily be made using peptide synthetic techniques known in the art, such as solid phase peptide synthesis and the like, or by recombinant DNA manipulation. Methods for the manipulation of DNA sequences to produce substitution, insertion or deletion variants of a protein are well known in the art.
  • substitution mutations at predetermined sites in DNA are well known to those skilled in the art and include M 13 mutagenesis, T7-Gen in vitro mutagenesis (USB, Cleveland, OH), QuickChange Site Directed mutagenesis (Stratagene, San Diego, CA), PCR-mediated site-directed mutagenesis or other site-directed mutagenesis protocols (see Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates)).
  • “Derivatives” include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the protein of interest, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues.
  • “Derivatives” of a protein also encompass peptides, oligopeptides, polypeptides which comprise naturally occurring altered (glycosylated, acylated , prenylated, phosphorylated , myristoylated , sulphated etc.) or non-naturally altered amino acid residues compared to the amino acid sequence of a naturally-occurring form of the polypeptide.
  • a derivative may also comprise on e or more non-amino acid substituents or additions compared to the amino acid sequence from which it is derived, for example a reporter molecule or other ligand, covalently or non-covalently bound to the amino acid sequence, such as a reporter molecule which is bound to facilitate its detection, and non-naturally occurring amino acid residues relative to the amino acid sequence of a naturally-occurring protein.
  • reporter molecule or other ligand covalently or non-covalently bound to the amino acid sequence, such as a reporter molecule which is bound to facilitate its detection, and non-naturally occurring amino acid residues relative to the amino acid sequence of a naturally-occurring protein.
  • derivatives also include fusions of the naturally-occurring form of the protein with tagging peptides such as FLAG, HIS6 or thioredoxin (for a review of tagging peptides, see Terpe, Appl. Microbiol. Biotechnol. 60, 523-533, 2003
  • domain refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide family.
  • motif or "consensus sequence” or “signature” refers to a short conserved region in the sequence of evolutionarily related proteins. Motifs are frequently highly conserved parts of domains, but may also include only part of the domain, or be located outside of conserved domain (if all of the amino acids of the motif fall outside of a defined domain).
  • GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (i.e. spanning the complete sequences) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps.
  • the BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences.
  • the software for performing BLAST analysis is publicly available through the National Centre for Biotechnology I nformation (NCBI).
  • Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1 .83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determ in ed usin g one of the methods available in the MatGAT software package (Campanella et al. , BMC Bioinformatics. 2003 Jul 10;4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. Furthermore, instead of using full-length sequences for the identification of homologues, specific domains may also be used.
  • sequence identity values may be determined over the entire nucleic acid or amino acid sequence or over selected domains or conserved motif(s), using the programs mentioned above using the default parameters.
  • Smith-Waterman algorithm is particularly useful (Smith TF, Waterman MS (1981 ) J. Mol. Biol 147(1 );195-7). Reciprocal BLAST
  • BLASTN or TBLASTX (using standard default values) are general ly used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence.
  • the BLAST results may optionally be filtered.
  • the full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived.
  • the results of the first and second BLASTs are then compared.
  • a paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
  • High-ranking hits are those having a low E-value.
  • Computation of the E-value is well known i n the art.
  • comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.
  • hybridisation is a process wherein substantially homologous complementary nucleotide sequences anneal to each other.
  • the hybridisation process can occur entirely in solution, i .e. both complementary nucleic acids are in solution.
  • the hybridisation process can also occur with one of the complementary nucleic acids immobilised to a matrix such as magnetic beads, Sepharose beads or any other resin.
  • the hybridisation process can furthermore occur with one of the complementary nucleic acids immobilised to a solid support such as a nitro-cellulose or nylon membrane or immobilised by e.g. photolithography to, for example, a siliceous glass support (the latter known as nucleic acid arrays or microarrays or as nucleic acid chips).
  • the nucleic acid molecules are generally thermally or chemically denatured to melt a double strand into two single strands and/or to remove hairpi ns or other secondary structures from single stranded nucleic acids.
  • stringency refers to the conditions under which a hybridisation takes place.
  • the stri ngency of hybridisation is influenced by conditions such as temperature, salt concentration, ionic strength and hybridisation buffer composition.
  • low stringency conditions are selected to be about 30°C lower than the thermal melting point (T m ) for the specific sequence at a defined ionic strength and pH.
  • Medium stringency conditions are when the temperature is 20°C below T m
  • high stringency conditions are when the temperature is 10°C below T m .
  • High stringency hybridisation conditions are typically used for isolating hybridising sequences that have high sequence similarity to the target nucleic acid seq uence.
  • Tm is the temperature under defined ionic strength and pH, at which 50% of the target sequence hybridises to a perfectly matched probe.
  • the T m is dependent upon the solution conditions and the base composition and length of the probe. For example, longer sequences hybridise specifically at higher temperatures.
  • the maximum rate of hybridisation is obtained from about 16°C up to 32°C below T m .
  • Formamide reduces the melting temperature of DNA-DNA and DNA-RNA duplexes with 0.6 to 0.7°C for each percent formamide, and addition of 50% formamide allows hybridisation to be performed at 30 to 45°C, though the rate of hybridisation will be lowered.
  • Base pair mismatches reduce the hybridisation rate and the thermal stability of the duplexes.
  • the Tm decreases about 1 °C per % base mismatch. The T m may be calculated using the following equations, depending on the types of hybrids:
  • T m 79.8°C+ 18.5 (logio[Na + ] a ) + 0.58 (%G/C b ) + 1 1 .8 (%G/C b ) 2 - 820/L c
  • T m 22 + 1 .46 (l n )
  • c L length of duplex in base pairs.
  • Non-specific binding may be controlled using any one of a number of known techniques such as, for example, blocking the membrane with protein containing solutions, additions of heterologous RNA, DNA, and SDS to the hybridisation buffer, and treatment with Rnase.
  • a series of hybridizations may be performed by varying one of (i) progressively lowering the annealing temperature (for example from 68°C to 42°C) or (ii) progressively lowering the formamide concentration (for example from 50% to 0%) .
  • annealing temperature for example from 68°C to 42°C
  • formamide concentration for example from 50% to 0%
  • hybridisation typically also depends on the fu nction of post-hybridisation washes.
  • samples are washed with dilute salt solutions.
  • Critical factors of such washes include the ionic strength and temperature of the final wash solution: the lower the salt concentration and the higher the wash temperature, the higher the stringency of the wash .
  • Wash conditions are typical ly performed at or below hybridisation stringency. A positive hybridi sation gives a signal that is at least twice of that of the backgrou nd .
  • suitable stringent cond itions for nucleic acid hybridisation assays or gene amplification detection procedures are as set forth above. More or less stringent conditions may also be selected. The skilled artisan is aware of various parameters which may be altered during washing and which will either maintain or change the stringency conditions.
  • typical high stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 65°C in 1x SSC or at 42°C in 1x SSC and 50% formamide, followed by washing at 65°C in 0.3x SSC.
  • Examples of medium stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 50°C in 4x SSC or at 40°C in 6x SSC and 50% formamide, followed by washing at 50°C in 2x SSC.
  • the length of the hybrid is the anticipated length for the hybridising nucleic acid. When nucleic acids of known sequence are hybridised, the hybrid length may be determined by aligning the sequences and identifying the conserved regions described herein .
  • 1 xSSC is 0.1 5M NaCI and 1 5mM sodium citrate; the hybridisation solution and wash solutions may additionally include 5x Denhardt's reagent, 0.5-1.0% SDS, 100 ⁇ g/ml denatured, fragmented salmon sperm DNA, 0.5% sodium pyrophosphate.
  • splice variant encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the biological activity of the protein is substantially retained; this may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for predicting and isolating such splice variants are well known in the art (see for example Foissac and Schiex (2005) BMC Bioinformatics 6: 25). Allelic variant
  • Allelic variants are alternative forms of a given gene, located at the same chromosomal position . Allelic variants encompass Single Nucleotide Polymorphisms (SNPs), as well as Small Insertion/Deletion Polymorphisms (INDELs). The size of INDELs is usually less than 100 bp. SNPs and INDELs form the largest set of sequence variants in naturally occurring polymorphic strains of most organisms.
  • an "endogenous" gene not only refers to the gene in question as found in a plant in its natural form (i.e. , without there being any human intervention), but also refers to that same gene (or a substantially homologous nucleic acid/gene) in an isolated form subsequently (re)introduced into a plant (a transgene).
  • a transgenic plant containing such a transgene may encounter a substantial reduction of the transgene expression and/or substantial reduction of expression of the endogenous gene.
  • the isolated gene may be isolated from an organism or may be manmade, for example by chemical synthesis.
  • Gene shuffling or “directed evolution” consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of nucleic acids or portions thereof encoding proteins having a modified biological activity (Castle et al., (2004) Science 304(5674): 1 151 -4; US patents 5,81 1 ,238 and 6,395,547).
  • Artificial DNA (such as but, not limited to plasmids or viral DNA) capable of replication in a host cell and used for introduction of a DNA sequence of interest into a host cell or host organism.
  • Host cells of the invention may be any cell selected from bacterial cells, such as Escherichia coli or Agrobacterium species cells, yeast cells, fungal, algal or cyanobacterial cells or plant cells.
  • the skilled artisan is well aware of the genetic elements that must be present on the genetic construct in order to successfully transform, select and propagate host cells containing the sequence of interest.
  • the sequence of interest is operably linked to one or more control sequences (at least to a promoter) as described herein. Additional regulatory elements may include transcriptional as well as translational enhancers.
  • an intron sequence may also be added to the 5' untranslated region (UTR) or in the coding sequence to increase the amount of the mature message that accumulates in the cytosol, as described in the definitions section.
  • Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3'UTR and/or 5'UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.
  • the genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type.
  • an origin of replication sequence that is required for maintenance and/or replication in a specific cell type.
  • Preferred origins of replication include, but are not limited to, the f1 -ori and colEl
  • marker genes or reporter genes. Therefore, the genetic construct may optionally comprise a selectable marker gene. Selectable markers are described in more detail in the "definitions" section herein.
  • the marker genes may be removed or excised from the transgenic cell once they are no longer needed. Techniques for marker removal are known in the art, useful techniques are described above in the definitions section. Regulatory element/Control sequence/Promoter
  • regulatory element control sequence
  • promoter typically refers to a nucleic acid control sequence located upstream from the transcriptional start of a gene and which is involved in recognising and binding of RNA polymerase and other proteins, thereby directing transcription of an operably linked nucleic acid.
  • transcriptional regulatory sequences derived from a classical eukaryotic genomic gene (including the TATA box which is required for accurate transcription initiation , with or without a CCAAT box sequence) and additional regulatory elements (i.e. upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli , or in a tissue-specific manner.
  • additional regulatory elements i.e. upstream activating sequences, enhancers and silencers
  • transcriptional regulatory sequence of a classical prokaryotic gene in which case it may include a -35 box sequence and/or -10 box transcriptional regulatory sequences.
  • regulatory element also encompasses a synthetic fusion molecule or derivative that confers, activates or enhances expression of a nucleic acid molecule in a cell, tissue or organ.
  • a “plant promoter” comprises regulatory elements, which mediate the expression of a coding sequence segment in plant cells. Accordingly, a plant promoter need not be of plant origin, but may originate from viruses or micro-organisms, for example from viruses which attack plant cells. The "plant promoter” can also originate from a plant cell, e.g. from the plant which is transformed with the nucleic acid sequence to be expressed in the inventive process and described herein. This also applies to other “plant” regulatory signals, such as "plant” terminators.
  • the promoters upstream of the nucleotide sequences useful in the methods of the present invention can be modified by one or more nucleotide substitution(s), insertion(s) and/or deletion(s) without interfering with the functionality or activity of either the promoters, the open reading frame (ORF) or the 3'-regulatory region such as terminators or other 3' regulatory regions which are located away from the ORF. It is furthermore possible that the activity of the promoters is increased by modification of their sequence, or that they are replaced completely by more active promoters, even promoters from heterologous organisms.
  • the nucleic acid molecule must, as described above, be linked operably to or comprise a suitable promoter which expresses the gene at the right point in time and with the required spatial expression pattern.
  • the promoter strength and/or expression pattern of a candidate promoter may be analysed for example by operably linking the promoter to a reporter gene and assaying the expression level and pattern of the reporter gene in various tissues of the plant.
  • Suitable well-known reporter genes include for example beta-glucuronidase or beta-galactosidase.
  • the promoter activity is assayed by measuring the enzymatic activity of the beta-glucuronidase or beta-galactosidase.
  • the promoter strength and/or expression pattern may then be compared to that of a reference promoter (such as the one used in the methods of the present invention).
  • promoter strength may be assayed by quantifying mRNA levels or by comparing mRNA levels of the nucleic acid used in the methods of the present invention, with mRNA levels of housekeeping genes such as 18S rRNA, using methods known in the art, such as Northern blotting with densitometric analysis of autoradiograms, quantitative real-time PCR or RT- PCR (Heid et al., 1996 Genome Methods 6: 986-994).
  • weak promoter is intended a promoter that drives expression of a coding sequence at a low level.
  • low level is intended at levels of about 1/10,000 transcripts to about 1/100,000 transcripts, to about 1/500,0000 transcripts per cell.
  • a “strong promoter” drives expression of a coding sequence at high level, or at about 1 /10 transcripts to about 1/100 transcripts to about 1/1000 transcripts per cell.
  • “medium strength promoter” is intended a promoter that drives expression of a coding sequence at a lower level than a strong promoter, in particular at a level that is in all instances below that obtained when under the control of a 35S CaMV promoter.
  • operably linked refers to a functional linkage between the promoter sequence and the gene of interest, such that the promoter sequence is able to initiate transcription of the gene of interest.
  • a “constitutive promoter” refers to a promoter that is transcriptionally active during most, but not necessarily all, phases of growth and development and under most environmental cond itions, in at least one cel l , tissue or organ .
  • Table 2a below gives examples of constitutive promoters.
  • a "ubiquitous promoter” is active in substantially all tissues or cells of an organism. Developmentally-regulated promoter
  • a "developmentally-regulated promoter” is active during certain developmental stages or in parts of the plant that undergo developmental changes.
  • inducible promoter has induced or increased transcription initiation in response to a chemical (for a review see Gatz 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:89- 108), environmental or physical stimulus, or may be "stress-inducible", i.e. activated when a plant is exposed to various stress conditions, or a “pathogen-inducible” i.e. activated when a plant is exposed to exposure to various pathogens.
  • organ-specific or tissue-specific promoter is one that is capable of preferentially initiating transcription in certain organs or tissues, such as the leaves, roots, seed tissue etc.
  • a "root-specific promoter” is a promoter that is transcriptionally active predominantly in plant roots, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Promoters able to initiate transcription in certain cells only are referred to herein as "cell-specific”.
  • root-specific promoters examples are listed in Table 2b below:
  • ALF5 (Arabidopsis) Diener et al. (2001 , Plant Cell 13:1625)
  • NRT2;1 Np N. Quesada et al. (1997, Plant Mol. Biol. 34:265)
  • seed-specific promoter is transcriptionally active predominantly in seed tissue, but not necessarily exclusively in seed tissue (in cases of leaky expression).
  • the seed-specific promoter may be active during seed development and/or during germination.
  • the seed specific promoter may be endosperm/aleurone/embryo specific. Examples of seed-specific promoters (endosperm/aleurone/embryo specific) are shown in Table 2c to Table 2f below. Further examples of seed-specific promoters are given in Qing Qu and Takaiwa (Plant Biotechnol. J. 2, 1 13-125, 2004), which disclosure is incorporated by reference herein as if fully set forth.
  • a-amylase (Amy32b) Lanahan et al, Plant Cell 4:203-21 1 , 1992; Skriver et al,
  • a-amylase (Amy32b) Lanahan et al, Plant Cell 4:203-21 1 , 1992;
  • green tissue-specific promoter as defined herein is a promoter that is transcriptionally active predominantly in green tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Examples of green tissue-specific promoters which may be used to perform the methods of the invention are shown in Table 2g below.
  • tissue-specific promoter is a meristem-specific promoter, which is transcriptionally active predominantly in meristematic tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts.
  • Examples of green meristem-specific promoters which may be used to perform the methods of the invention are shown in Table 2h below.
  • terminal encompasses a control sequence which is a DNA sequence at the end of a transcriptional unit which signals 3' processing and polyadenylation of a primary transcript and termination of transcription.
  • the terminator can be derived from the natural gene, from a variety of other plant genes, or from T-DNA.
  • the terminator to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
  • “Selectable marker”, “selectable marker gene” or “reporter gene” includes any gene that confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells that are transfected or transformed with a nucleic acid construct of the invention. These marker genes enable the identification of a successful transfer of the nucleic acid molecules via a series of different principles. Suitable markers may be selected from markers that confer antibiotic or herbicide resistance, that introduce a new metabolic trait or that allow visual selection.
  • selectable marker genes include genes conferring resistance to antibiotics (such as nptl l that phosphorylates neomycin and kanamycin, or hpt, phosphorylating hygromycin, or genes conferring resistance to, for example, bleomycin, streptomycin, tetracyclin, chloramphenicol, ampicillin, gentamycin, geneticin (G41 8), spectinomycin or blasticidin), to herbicides (for example bar which provides resistance to Basta ® ; aroA or gox providing resistance against glyphosate, or the genes conferri ng resistance to, for exampl e, i midazolinone, phosph inoth rici n or sulfonylurea), or genes that provide a metabolic trait (such as manA that allows plants to use mannose as sole carbon source or xylose isomerase for the utilisation of xylose, or antinutritive markers such as the resistance to 2-deoxyglucos
  • Visual marker genes results in the formation of colour (for example ⁇ -glucuronidase, GUS or ⁇ - galactosidase with its coloured substrates, for example X-Gal), luminescence (such as the luciferin/luceferase system) or fluorescence (Green Fluorescent Protein , GFP, and derivatives thereof).
  • colour for example ⁇ -glucuronidase, GUS or ⁇ - galactosidase with its coloured substrates, for example X-Gal
  • luminescence such as the luciferin/luceferase system
  • fluorescence Green Fluorescent Protein
  • nucleic acid molecules encoding a selectable marker can be introduced into a host cell on the same vector that comprises the sequence encoding the polypeptides of the invention or used in the methods of the invention, or else in a separate vector. Cells which have been stably transfected with the introduced nucleic acid can be identified for example by selection (for example, cells which have integrated the selectable marker survive whereas the other cells die).
  • the process according to the invention for introducing the nucleic acids advantageously employs techniques which enable the removal or excision of these marker genes.
  • One such a method is what is known as co-transformation.
  • the co- transformation method employs two vectors simultaneously for the transformation, one vector bearing the nucleic acid according to the invention and a second bearing the marker gene(s).
  • a large proportion of transformants receives or, in the case of plants, comprises (up to 40% or more of the transformants), both vectors.
  • the transformants usually receive only a part of the vector, i.e.
  • the marker genes can subsequently be removed from the transformed plant by performing crosses.
  • marker genes integrated into a transposon are used for the transformation together with desired nucleic acid (known as the Ac/Ds technology).
  • the transformants can be crossed with a transposase source or the transformants are transformed with a nucleic acid construct conferring expression of a transposase, transiently or stable.
  • the transposon jumps out of the genome of the host cell once transformation has taken place successfully and is lost.
  • the transposon jumps to a different location. In these cases the marker gene must be eliminated by performing crosses.
  • Cre/lox system Cre1 is a recombinase that removes the sequences located between the loxP sequences. If the marker gene is integrated between the loxP sequences, it is removed once transformation has taken place successfully, by expression of the recombinase.
  • Cre1 is a recombinase that removes the sequences located between the loxP sequences. If the marker gene is integrated between the loxP sequences, it is removed once transformation has taken place successfully, by expression of the recombinase.
  • Further recombination systems are the HIN/HIX, FLP/FRT and REP/STB system (Tribble et al. , J. Biol.
  • transgenic means with regard to, for example, a nucleic acid sequence, an expression cassette, gene construct or a vector comprising the nucleic acid sequence or an organism transformed with the nucleic acid sequences, expression cassettes or vectors according to the invention, all those constructions brought about by recombinant methods in which either
  • genetic control sequence(s) which is operably linked with the nucleic acid sequence according to the invention, for example a promoter, or
  • the natural genetic environment is understood as meaning the natural genomic or chromosomal locus in the original plant or the presence in a genomic library.
  • the natural genetic environment of the nucleic acid sequence is preferably retained, at least in part.
  • the environment flanks the nucleic acid sequence at least on one side and has a sequence length of at least 50 bp, preferably at least 500 bp, especially preferably at least 1000 bp, most preferably at least 5000 bp.
  • transgenic plant for the purposes of the invention is thus understood as meaning, as above, that the nucleic acids used in the method of the invention are not present in, or originating from, the genome of said plant, or are present in the genome of said plant but not at their natural locus in the genome of said plant, it being possible for the nucleic acids to be expressed homologously or heterologously.
  • transgenic also means that, while the nucleic acids according to the invention or used in the inventive method are at their natural position in the genome of a plant, the sequence has been modified with regard to the natural sequence, and/or that the regulatory sequences of the natural sequences have been modified.
  • Transgenic is preferably understood as meaning the expression of the nucleic acids according to the invention at an unnatural locus in the genome, i.e. homologous or, preferably, heterologous expression of the nucleic acids takes place.
  • Preferred transgenic plants are mentioned herein.
  • isolated nucleic acid or isolated polypeptide
  • isolated polypeptide may in some instances be considered as a synonym for a "recombinant nucleic acid” or a “recombinant polypeptide”, respectively and refers to a nucleic acid or polypeptide that is not located in its natural genetic environment and/or that has been modified by recombinant methods. Modulation
  • modulation means in relation to expression or gene expression, a process in which the expression level is changed by said gene expression in comparison to the control plant, the expression level may be increased or decreased.
  • the original, unmodulated expression may be of any kind of expression of a structural RNA (rRNA, tRNA) or mRNA with subsequent translation.
  • the original unmodulated expression may also be absence of any expression.
  • modulating the activity shall mean any change of the expression of the inventive nucleic acid sequences or encoded proteins, which leads to increased yield and/or increased growth of the plants.
  • the expression can increase from zero (absence of, or immeasurable expression) to a certain amount, or can decrease from a certain amount to immeasurable small amounts or zero.
  • expression means the transcription of a specific gene or specific genes or specific genetic construct.
  • expression in particular means the transcription of a gene or genes or genetic construct into structural RNA (rRNA, tRNA) or imRNA with or without subsequent translation of the latter into a protein. The process includes transcription of DNA and processing of the resulting mRNA product.
  • the term "increased expression” or “overexpression” as used herein means any form of expression that is additional to the original wild-type expression level.
  • the original wild-type expression level might also be zero, i.e. absence of expression or immeasurable expression.
  • Isolated nucleic acids which serve as promoter or enhancer elements may be introduced in an appropriate position (typically upstream) of a non-heterologous form of a polynucleotide so as to upregulate expression of a nucleic acid encoding the polypeptide of interest.
  • endogenous promoters may be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, US 5,565,350; Zarling et al., W09322443), or isolated promoters may be introduced into a plant cell in the proper orientation and distance from a gene of the present invention so as to control the expression of the gene.
  • polypeptide expression it is generally desirable to include a polyadenylation region at the 3'-end of a polynucleotide coding region.
  • the polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA.
  • the 3' end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
  • An intron sequence may also be added to the 5' untranslated region (UTR) or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol.
  • UTR 5' untranslated region
  • coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol.
  • Inclusion of a spliceable intron in the transcription unit in both plant and animal expression constructs has been shown to increase gene expression at both the mRNA and protein levels up to 1000-fold (Buchman and Berg (1988) Mol. Cell biol. 8: 4395-4405; Callis et al. (1987) Genes Dev 1 :1 183-1200).
  • Such intron enhancement of gene expression is typically greatest when placed near the 5' end of the transcription unit.
  • Reference herein to "decreased expression” or “reduction or substantial elimination” of expression is taken to mean a decrease in endogenous gene expression and/or polypeptide levels and/or polypeptide activity relative to control plants.
  • the reduction or substantial elimination is in increasing order of preference at least 10%, 20%, 30%, 40% or 50%, 60%, 70%, 80%, 85%, 90%, or 95%, 96%, 97%, 98%, 99% or more reduced compared to that of control plants.
  • substantially contiguous nucleotides of a nucleic acid sequence is required. In order to perform gene silencing, this may be as little as 20, 19, 18, 17, 16, 15, 14, 13, 12, 1 1 , 10 or fewer nucleotides, alternatively this may be as much as the entire gene (including the 5' and/or 3' UTR, either in part or in whole).
  • the stretch of substantially contiguous nucleotides may be derived from the nucleic acid encoding the protein of interest (target gene), or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest.
  • the stretch of substantially contiguous nucleotides is capable of forming hydrogen bonds with the target gene (either sense or antisense strand), more preferably, the stretch of substantially contiguous nucleotides has, in increasing order of preference, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97% , 98% , 99% , 100% seq uence identity to the target gene (either sense or antisense strand).
  • a nucleic acid sequence encoding a (functional) polypeptide is not a requirement for the various methods discussed herein for the reduction or substantial elimination of expression of an endogenous gene. This reduction or substantial elimination of expression may be achieved using routine tools and techn iques.
  • a preferred method for the reduction or substantial elimination of endogenous gene expression is by introducing and expressing in a plant a genetic construct into which the nucleic acid (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of any one of the protein of interest) is cloned as an inverted repeat (in part or completely), separated by a spacer (non-coding DNA).
  • the nucleic acid in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of any one of the protein of interest
  • expression of the endogenous gene is reduced or substantially eliminated through RNA-mediated silencing using an inverted repeat of a nucleic acid or a part thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), preferably capable of forming a hairpin structure.
  • the inverted repeat is cloned in an expression vector comprising control sequences.
  • a non- coding DNA nucleic acid sequence (a spacer, for example a matrix attachment region fragment (MAR), an intron, a polylinker, etc.) is located between the two inverted nucleic acids forming the inverted repeat.
  • MAR matrix attachment region fragment
  • a chimeric RNA with a self-complementary structure is formed (partial or complete).
  • This double-stranded RNA structure is referred to as the hairpin RNA (hpRNA).
  • the hpRNA is processed by the plant into siRNAs that are incorporated into an RNA-induced silencing complex (RISC).
  • RISC RNA-induced silencing complex
  • the RISC further cleaves the mRNA transcripts, thereby substantially reducing the number of imRNA transcripts to be translated into polypeptides.
  • RISC RNA-induced silencing complex
  • Performance of the methods of the invention does not rely on introducing and expressing in a plant a genetic construct into which the nucleic acid is cloned as an inverted repeat, but any one or more of several well-known "gene silencing" methods may be used to achieve the same effects.
  • RNA-mediated silencing of gene expression is triggered in a plant by a double stranded RNA sequence (dsRNA) that is substantially similar to the target endogenous gene.
  • dsRNA double stranded RNA sequence
  • This dsRNA is further processed by the plant into about 20 to about 26 nucleotides called short interfering RNAs (siRNAs).
  • the siRNAs are incorporated into an RNA-i nd uced silencing complex (RI SC) that cleaves the m RNA transcript of the endogenous target gene, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide.
  • RI SC RNA-i nd uced silencing complex
  • the double stranded RNA sequence corresponds to a target gene.
  • RNA silencing method involves the introduction of nucleic acid sequences or parts thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest) in a sense orientation into a plant.
  • Sense orientation refers to a DNA sequence that is homologous to an mRNA transcript thereof. Introduced into a plant would therefore be at least one copy of the nucleic acid sequence.
  • the additional nucleic acid sequence wi ll reduce expression of the endogenous gene, giving rise to a phenomenon known as co-suppression. The reduction of gene expression will be more pronounced if several additional copies of a nucleic acid sequence are introduced into the plant, as there is a positive correlation between high transcript levels and the triggering of co-suppression.
  • RNA silencing method involves the use of antisense nucleic acid sequences.
  • An "antisense" nucleic acid sequence comprises a nucleotide sequence that is complementary to a "sense" nucleic acid sequence encoding a protein, i.e. complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA transcript sequence.
  • the antisense nucleic acid sequence is preferably complementary to the endogenous gene to be silenced.
  • the complementarity may be located in the "coding region” and/or in the "non-coding region" of a gene.
  • the term “coding region” refers to a region of the nucleotide sequence comprising codons that are translated into amino acid residues.
  • non-coding region refers to 5' and 3' sequences that flank the coding region that are transcribed but not translated into amino acids (also referred to as 5' and 3' untranslated regions).
  • Antisense nucleic acid sequences can be designed according to the rules of Watson and Crick base pairing.
  • the antisense nucleic acid sequence may be complementary to the entire nucleic acid sequence (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), but may also be an oligonucleotide that is antisense to only a part of the nucleic acid sequence (including the mRNA 5' and 3' UTR).
  • the antisense oligonucleotide sequence may be complementary to the region surrounding the translation start site of an mRNA transcript encoding a polypeptide.
  • an antisense nucleic acid sequence according to the invention may be constructed using chemical synthesis and enzymatic ligation reactions using methods known in the art.
  • an antisense nucleic acid sequence e.g., an antisense oligonucleotide sequence
  • an antisense nucleic acid sequence may be chemically synthesized usi ng naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acid sequences, e.g.
  • nucleotide modifications include methylation, cyclization and 'caps' and substitution of one or more of the naturally occurring nucleotides with an analogue such as inosine. Other modifications of nucleotides are well known in the art.
  • the antisense nucleic acid sequence can be produced biologically using an expression vector into which a nucleic acid sequence has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest).
  • an expression vector into which a nucleic acid sequence has been subcloned in an antisense orientation i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest.
  • production of antisense nucleic acid sequences in plants occurs by means of a stably integrated nucleic acid construct comprising a promoter, an operably linked antisense oligonucleotide, and a terminator.
  • the nucleic acid molecules used for silencing in the methods of the invention hybridize with or bind to mRNA transcripts and/or genomic DNA encoding a polypeptide to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation.
  • the hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid sequence which binds to DNA duplexes, through specific interactions in the major groove of the double helix.
  • Antisense nucleic acid sequences may be introduced into a plant by transformation or direct injection at a specific tissue site.
  • antisense nucleic acid sequences can be modified to target selected cells and then administered systemically.
  • antisense nucleic acid sequences can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid sequence to peptides or antibodies which bind to cell surface receptors or antigens.
  • the antisense nucleic acid sequences can also be delivered to cells using the vectors described herein.
  • the antisense nucleic acid sequence is an a-anomeric nucleic acid seq uence.
  • An a-anomeric nucleic acid sequence forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gaultier et al. (1987) Nucl Ac Res 15: 6625-6641 ).
  • the antisense nucleic acid sequence may also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987) Nucl Ac Res 15, 6131 -6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett.
  • Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid sequence, such as an mRNA, to which they have a complementary region.
  • ribozymes e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334, 585-591) can be used to catalytically cleave mRNA transcripts encoding a polypeptide, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide.
  • a ribozyme having specificity for a nucleic acid sequence can be designed (see for example: Cech et al. U.S. Patent No. 4,987,071 ; and Cech et al. U.S. Patent No. 5, 1 16,742).
  • mRNA transcripts corresponding to a nucleic acid sequence can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules (Bartel and Szostak (1993) Science 261 , 141 1 -1418).
  • the use of ribozymes for gene silencing in plants is known in the art (e.g., Atkins et al. (1994) WO 94/00012; Lenne et al. (1995) WO 95/03404; Lutziger et al. (2000) WO 00/00619; Prinsen et al. (1997) WO 97/13865 and Scott et al. (1997) WO 97/381
  • Gene silencing may also be achieved by insertion mutagenesis (for example, T-DNA insertion or transposon insertion) or by strategies as described by, among others, Angell and Bau lcombe ((1999) Plant J 20(3): 357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).
  • insertion mutagenesis for example, T-DNA insertion or transposon insertion
  • strategies as described by, among others, Angell and Bau lcombe ((1999) Plant J 20(3): 357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).
  • Gene silencing may also occur if there is a mutation on an endogenous gene and/or a mutation on an isolated gene/nucleic acid subsequently introduced into a plant.
  • the reduction or substantial elimination may be caused by a non-functional polypeptide.
  • the polypeptide may bind to various interacting proteins; one or more mutation(s) and/or truncation(s) may therefore provide for a polypeptide that is still able to bind interacting proteins (such as receptor proteins) but that cannot exhibit its normal function (such as signalling ligand).
  • a further approach to gene silencing is by targeting nucleic acid sequences complementary to the regulatory region of the gene (e.g., the promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells.
  • nucleic acid sequences complementary to the regulatory region of the gene e.g., the promoter and/or enhancers
  • the regulatory region of the gene e.g., the promoter and/or enhancers
  • miRNAs Artificial and/or natural microRNAs
  • Endogenous miRNAs are single stranded small RNAs of typically 19-24 nucleotides long. They function primarily to regulate gene expression and/ or mRNA translation.
  • Most plant microRNAs have perfect or near-perfect complementarity with their target sequences. However, there are natural targets with up to five mismatches. They are processed from longer non-coding RNAs with characteristic fold-back structures by double-strand specific RNases of the Dicer family. Upon processing, they are incorporated i n th e RNA-induced silencing complex (RISC) by binding to its main component, an Argonaute protein.
  • RISC RNA-induced silencing complex
  • MiRNAs serve as the specificity components of RISC, since they base-pair to target nucleic acids, mostly mRNAs, in the cytoplasm. Subsequent regulatory events include target mRNA cleavage and destruction and/or translational inhibition. Effects of miRNA overexpression are thus often reflected in decreased mRNA levels of target genes.
  • ami RNAs which are typically 21 nucleotides in length , can be genetically engineered specifically to negatively regulate gene expression of single or multiple genes of interest. Determinants of plant microRNA target selection are well known in the art. Empirical parameters for target recognition have been defined and can be used to aid in the design of specific amiRNAs, (Schwab et al., Dev. Cell 8, 517-527, 2005). Convenient tools for design and generation of amiRNAs and their precursors are also available to the public (Schwab et al., Plant Cell 18, 1 121 -1 133, 2006).
  • the gene silencing techniques used for reducing expression in a plant of an endogenous gene requires the use of nucleic acid sequences from monocotyledonous plants for transformation of monocotyledonous plants, and from dicotyledonous plants for transformation of dicotyledonous plants.
  • a nucleic acid sequence from any given plant species is introduced into that same species.
  • a nucleic acid sequence from rice is transformed into a rice plant.
  • Described above are examples of various methods for the reduction or substantial elimination of expression in a plant of an endogenous gene.
  • a person skilled in the art would readily be able to adapt the aforementioned methods for silencing so as to achieve reduction of expression of an endogenous gene in a whole plant or in parts thereof through the use of an appropriate promoter, for example.
  • introduction or “transformation” as referred to herein encompasses the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for transfer.
  • Plant tissue capable of subsequent clonal propagation may be transformed with a genetic construct of the present invention and a whole plant regenerated there from.
  • the particular tissue chosen will vary depending on the clonal propagation systems available for, and best suited to, the particular species being transformed.
  • tissue targets include leaf disks, pollen, embryos, cotyledons, hypocotyls, megagametophytes, callus tissue, existing meristematic tissue (e.g., apical meristem, axillary buds, and root meristems), and induced meristem tissue (e.g., cotyledon meristem and hypocotyl meristem).
  • the polynucleotide may be transiently or stably introduced into a host cell and may be maintained non-integrated, for example, as a plasmid. Alternatively, it may be integrated into the host genome.
  • the resulting transformed plant cell may then be used to regenerate a transformed plant in a manner known to persons skilled in the art.
  • a plant cell that cannot be regenerated into a plant may be chosen as host cell, i.e. the resulting transformed plant cell does not have the capacity to regenerate into a (whole) plant.
  • Transformation of plant species is now a fairly routine technique.
  • any of several transformation methods may be used to introd uce the gene of interest into a suitable ancestor cell.
  • the methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. Methods may be selected from the calcium/polyethylene glycol method for protoplasts (Krens, F.A.
  • Transgenic plants including transgenic crop pla nts , a re prefera bly prod uced vi a transformation.
  • An advantageous transformation method is the transformation in planta.
  • Methods for Agrobacterium-medlated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1 198985 A1 , Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491 -506, 1993), Hiei et al. (Plant J 6 (2): 271 -282, 1994), which disclosures are incorporated by reference herein as if fully set forth.
  • the preferred method is as described in either Ishida et al. (Nat. Biotechnol 14(6): 745-50, 1996) or Frame et al.
  • the nucleic acids or the construct to be expressed is preferably cloned into a vector, wh ich is suitable for transforming Agrobacterium tumefaciens, for example pBin 19 (Bevan et al., Nucl. Acids Res. 12 (1984) 871 1 ).
  • Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model , like Arabidopsis (Arabidopsis thaliana is with in th e scope of the present i nvention not considered as a crop plant), or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then cu ltu ri ng them in suitable med ia .
  • the transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Hofgen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F.F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1 , Engineering and Utilization, eds. S.D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.
  • the genetically modified plant cells can be regenerated via all methods with which the skilled worker is fami liar. Suitable methods can be fou nd in the abovementioned publications by S.D. Kung and R. Wu, Potrykus or Hofgen and Willmitzer. Alternatively, the genetically modified plant cells are non-regenerable into a whole plant.
  • plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant.
  • the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants.
  • the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying.
  • a further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants.
  • the transformed plants are screened for the presence of a selectable marker such as the ones described above.
  • putatively transformed plants may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art.
  • the generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1 ) transformed plant may be selfed and homozygous second-generation (or T2) transformants selected, and the T2 plants may then further be propagated through classical breeding techniques.
  • the generated transformed organisms may take a variety of forms.
  • they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g. , all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion).
  • clonal transformants e.g. , all cells transformed to contain the expression cassette
  • grafts of transformed and untransformed tissues e.g., in plants, a transformed rootstock grafted to an untransformed scion.
  • T-DNA activation tagging involves insertion of T-DNA, usually containing a promoter (may also be a translation enhancer or an intron), in the genomic region of the gene of interest or 10 kb up- or downstream of the coding region of a gene in a configuration such that the promoter directs expression of the targeted gene.
  • a promoter may also be a translation enhancer or an intron
  • regulation of expression of the targeted gene by its natural promoter is disrupted and the gene falls under the control of the newly introduced promoter.
  • the promoter is typically embedded in a T-DNA. This T-DNA is randomly inserted into the plant genome, for example, through Agrobacterium infection and leads to modified expression of genes near the inserted T-DNA.
  • the resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.
  • TILLING is an abbreviation of "Targeted Induced Local Lesions In Genomes” and refers to a mutagenesis technology useful to generate and/or identify nucleic acids encoding proteins with modified expression and/or activity. TILLING also allows selection of plants carrying such mutant variants. These mutant variants may exhibit modified expression, either in strength or in location or in timing (if the mutations affect the promoter for example). These mutant variants may exhibit higher activity than that exhibited by the gene in its natural form. TILLING combines high-density mutagenesis with high-throughput screening methods.
  • Homologous recombination allows introduction in a genome of a selected nucleic acid at a defined selected position. Homologous recombination is a standard technology used routi nely in biologi ca l sci en ces for lower organ isms such as yeast or the moss Physcomitrella. Methods for performing homologous recombination in plants have been described not only for model plants (Offringa et al. (1990) EMBO J 9(10): 3077-84) but also for crop plants, for example rice (Terada et al.
  • a "Yield related trait” is a trait or feature which is related to plant yield. Yield-related traits may comprise one or more of the following non-limitative list of features: early flowering time, yield, biomass, seed yield, early vigour, greenness index, growth rate, agronomic traits, such as e.g. tolerance to submergence (which leads to yield in rice), Water Use Efficiency (WUE), Nitrogen Use Efficiency (NUE), etc.
  • WUE Water Use Efficiency
  • NUE Nitrogen Use Efficiency
  • Reference herein to enhanced yield-related traits, relative to of control plants is taken to mean one or more of an increase in early vigour and/or in biomass (weight) of one or more parts of a plant, which may include (i) aboveground parts and preferably aboveground harvestable parts and/or (ii) parts below ground and preferably harvestable below ground. In particular, such harvestable parts are seeds.
  • yield in general means a measurable produce of economic value, typically related to a specified crop, to an area, and to a period of time. Individual plant parts directly contribute to yield based on their number, size and/or weight, or the actual yield is the yield per square meter for a crop and year, which is determined by dividing total production (includes both harvested and appraised production) by planted square meters.
  • yield of a plant and “plant yield” are used interchangeably herein and are meant to refer to vegetative biomass such as root and/or shoot biomass, to reproductive organs, and/or to propagules such as seeds of that plant.
  • a yield increase in maize may be manifested as one or more of the following: increase in the number of plants established per square meter, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate, which is the number of filled florets (i.e. florets containing seed) divided by the total number of florets and multiplied by 100), among others.
  • Inflorescences in rice plants are named panicles.
  • the panicle bears spikelets, which are the basic units of the panicles, and which consist of a pedicel and a floret.
  • a yield increase may manifest itself as an increase in one or more of the following: number of plants per square meter, number of panicles per plant, panicle length, number of spikelets per panicle, number of flowers (or florets) per panicle; an increase in the seed filling rate which is the number of filled florets (i .e. florets containing seeds) divided by the total number of florets and multiplied by 100; an increase in thousand kernel weight, among others.
  • Plants having an "early flowering time” as used herein are plants which start to flower earlier than control plants. Hence this term refers to plants that show an earlier start of flowering.
  • Flowering time of plants can be assessed by counting the number of days ("time to flower") between sowing and the emergence of a first inflorescence.
  • the "flowering time" of a plant can for instance be determined using the method as described in WO 2007/093444.
  • Early vigour refers to active healthy well-balanced growth especially during early stages of plant growth, and may result from increased plant fitness due to, for example, the plants being better adapted to their environment (i.e. optimizing the use of energy resources and partitioning between shoot and root). Plants having early vigour also show increased seedling survival and a better establishment of the crop, which often results in highly uniform fields (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and often better and higher yield. Therefore, early vigour may be determined by measuring various factors, such as thousand kernel weight, percentage germination, percentage emergence, seedling growth, seedling height, root length, root and shoot biomass and many more.
  • the increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle.
  • the life cycle of a plant may be taken to mean the time needed to grow from a mature seed up to the stage where the plant has produced mature seeds, similar to the starting material. This life cycle may be influenced by factors such as speed of germination, early vigour, growth rate, greenness index, flowering time and speed of seed maturation.
  • the increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour.
  • the increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soybean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible.
  • Altering the harvest cycle of a plant may lead to an increase in annual biomass production per square meter (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested).
  • An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened.
  • the growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.
  • Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% , 30% or 25%, more preferably less than 20% or 15% in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture.
  • Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures.
  • Biotic stresses are typically those stresses caused by pathogens, such as bacteria, viruses, fungi, nematodes and insects.
  • the "abiotic stress” may be an osmotic stress caused by a water stress, e.g. due to drought, salt stress, or freezing stress.
  • Abiotic stress may also be an oxidative stress or a cold stress.
  • Freezing stress is intended to refer to stress due to freezing temperatures, i.e. temperatures at which available water molecules freeze and turn into ice.
  • Cold stress also called “chilling stress” is intended to refer to cold temperatures, e.g. temperatures below 10°, or preferably below 5°C, but at which water molecules do not freeze.
  • abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity.
  • Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms.
  • Rabbani et al. Plant Physiol (2003) 133: 1755-1767
  • drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell.
  • Oxidative stress which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins.
  • non-stress conditions are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil cond itions and climatic conditions for a given location. Plants with optimal growth conditions, (grown under non-stress conditions) typically yield in increasing order of preference at least 97%, 95%, 92%, 90%, 87%, 85%, 83%, 80%, 77% or 75% of the average production of such plant in a given environment. Average production may be calculated on harvest and/or season basis.
  • the methods of the present invention may be performed under non-stress conditions.
  • the methods of the present invention may be performed under non-stress conditions such as mild drought to give plants having increased yield relative to control plants.
  • the methods of the present invention may be performed under stress conditions.
  • the methods of the present invention may be performed under stress conditions such as drought to give plants having increased yield relative to control plants.
  • the methods of the present invention may be performed under stress conditions such as nutrient deficiency to give plants having increased yield relative to control plants.
  • Nutrient deficiency may result from a lack of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, magnesium, manganese, iron and boron, amongst others.
  • the methods of the present invention may be performed under stress conditions such as salt stress to give plants having increased yield relative to control plants.
  • salt stress is not restricted to common salt (NaCI), but may be any one or more of: NaCI, KCI, LiCI, MgCI 2 , CaCI 2 , amongst others.
  • the methods of the present invention may be performed under stress conditions such as cold stress or freezing stress to give plants having increased yield relative to control plants.
  • Increased seed yield may manifest itself as one or more of the following:
  • total seed weight an increase in seed biomass (total seed weight) which may be on an individual seed basis and/or per plant and/or per square meter;
  • TKW thousand kernel weight
  • filled florets and “filled seeds” may be considered synonyms.
  • An increase in seed yield may also be manifested as an increase in seed size and/or seed volume. Furthermore, an increase in seed yield may also manifest itself as an increase in seed area and/or seed length and/or seed width and/or seed perimeter.
  • the "greenness index” as used herein is calculated from digital images of plants. For each pixel belonging to the plant object on the image, the ratio of the green value versus the red value (i n the RGB model for encoding color) is calculated. The green ness index is expressed as the percentage of pixels for which the green-to-red ratio exceeds a given threshold. Under normal growth conditions, under salt stress growth conditions, and under reduced nutrient availability growth conditions, the greenness index of plants is measured in the last imaging before flowering. In contrast, under drought stress growth conditions, the greenness index of plants is measured in the first imaging after drought.
  • biomass as used herein is intended to refer to the total weight of a plant. Within the definition of biomass, a distinction may be made between the biomass of one or more parts of a plant, which may include any one or more of the following:
  • aboveground parts such as but not limited to shoot biomass, seed biomass, leaf biomass, etc.
  • - aboveground harvestable parts such as but not limited to shoot biomass, seed biomass, leaf biomass, etc.
  • parts below ground such as but not limited to root biomass, tubers, bulbs, etc.;
  • harvestable parts below ground such as but not limited to root biomass, tubers, bulbs, etc.;
  • harvestable parts partially below ground such as but not limited to beets and other hypocotyl areas of a plant, rhizomes, stolons or creeping rootstalks;
  • - vegetative biomass such as root biomass, shoot biomass, etc.
  • Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a col lection of a llelic variants of so called "natural" origi n caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.
  • nucleic acids encoding the protein of interest for genetically and physically mapping the genes requires only a nucleic acid sequence of at least 15 nucleotides in length. These nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch EF and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the nucleic acids encoding the protein of interest. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1 : 174-181 ) in order to construct a genetic map.
  • MapMaker Large et al. (1987) Genomics 1 : 174-181
  • the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the nucleic acid encoding the protein of interest in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331 ).
  • the nucleic acid probes may also be used for physical mapping (i .e. , placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).
  • the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991 ) Trends Genet. 7: 149-154).
  • FISH direct fluorescence in situ hybridisation
  • current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laa n et al . (1 995) Genome Res. 5: 1 3-20)
  • improvements i n sensitivity may allow performance of FISH mapping using shorter probes.
  • nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med 1 1 :95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241 : 1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671 ), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet.
  • plant as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, leaves, roots (including tubers), flowers, and tissues and organs, wherein each of the aforementioned comprise the gene/nucleic acid of interest.
  • plant also encompasses plant cells, suspension cultures, callus tissue, embryos, meristematic regions, gametophytes, sporophytes, pollen and microspores, again wherein each of the aforementioned comprises the gene/nucleic acid of interest.
  • Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs selected from the list comprising Acer spp., Actinidia spp., Abelmoschus spp., Agave sisalana, Agropyron spp., Agrostis stolonifera, Allium spp., Amaranthus spp., Ammophila arenaria, Ananas comosus, Annona spp., Apium graveolens, Arachis spp, Artocarpus spp., Asparagus officinalis, Avena spp.
  • Avena sativa e.g. Avena sativa, Avena fatua, Avena byzantina, Avena fatua var. sativa, Avena hybrida
  • Averrhoa carambola e.g. Bambusa sp.
  • Benincasa hispida Bertholletia excelsea
  • Beta vulgaris Brassica spp.
  • Brassica napus e.g. Brassica napus, Brassica rapa ssp.
  • control plants are routine part of an experimental setup and may include corresponding wild type plants or corresponding plants without the gene of interest.
  • the control plant is typically of the same plant species or even of the same variety as the plant to be assessed.
  • the control plant may also be a nullizygote of the plant to be assessed. Nullizygotes (or null control plants) are individuals missing the transgene by segregation.
  • control plants are grown under equal growing conditions to the growing conditions of the plants of the invention, i.e. in the vicinity of, and simultaneously with, the plants of the invention.
  • a "control plant” as used herein refers not only to whole plants, but also to plant parts, including seeds and seed parts.
  • Figure 1 represents the domain structure of SEQ ID NO: 2 with conserved motifs.
  • Figure 2 represents the domain structure of SEQ ID NO: 4 with conserved motifs.
  • Figure 3 represents a multiple alignment of various DU F642 polypeptides. These alignments can be used for defining further motifs or signature sequences, when using conserved amino acids.
  • the corresponding SEQ ID NO's for the aligned polypeptide sequences shown in Figure 3 are:
  • Figure 4 represents a multiple alignment of a selection (clade A) of DUF642 polypeptides from Figure 3.
  • the corresponding SEQ ID NO's for the aligned polypeptide sequences shown in Figure 4 are:
  • Figure 5 shows a phylogenetic tree of DUF642 polypeptides, as described in Example 2. Clade A is encircled, the remainder of the branches of the tree are grouped in clade B. Figure 6 shows the MATGAT table of Example 3.
  • Figure 7 represents the binary vector used for increased expression in Oryza sativa of a DUF642-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2).
  • Figure 8 represents the domain structure of SEQ ID NO: 198 with conserved motifs.
  • Figure 9 represents a multiple alignment of the epimerase-related like polypeptides as listed in table A. These alignments can be used for defining further motifs or signature sequences, when using conserved amino acids.
  • Figure 10 shows phylogenetic tree of epimerase-related like polypeptides.
  • protein sequences were aligned with MAFFT, a bootstrapped Neighbour Joining (NJ) tree was calculated with QuickTree (100 repeats, uncorrected), which was visualized with Dendroscope (for further details on the used techniques see example 2)
  • NJ Neighbour Joining
  • Figure 1 1 shows the MATGAT table of Example 3.
  • Figure 12 represents the binary vector used for increased expression in Oryza sativa of a nucleic acid encoding an epimerase-related like polypeptide under the control of a rice GOS2 promoter (pGOS2).
  • pGOS2 rice GOS2 promoter
  • Figure 13 represents the domain structure of SEQ ID NO: 285 with conserved motifs.
  • Figure 14 shows phylogenetic tree of PLPCase polypeptides, showing three clusters.
  • Figure 15 shows the MatGAT table of Example 3.
  • Figure 16 represents the binary vector used for increased expression in Oryza sativa of a PLPCase-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2). Examples
  • the present invention will now be described with reference to the following examples, which are by way of illustration only. The following examples are not intended to limit the scope of the invention. Unless otherwise indicated, the present invention employs conventional techniques and methods of plant biology, molecular biology, bioinformatics and plant breedings.
  • Example 1 Identification of sequences related to the nucleic acid sequence used in the methods of intervention
  • Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 1 and SEQ ID NO: 2; and SEQ ID NO: 3 and SEQ ID NO: 4 were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches.
  • BLAST Basic Local Alignment Tool
  • the program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches.
  • the polypeptide encoded by the nucleic acid of SEQ ID NO: 1 was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off.
  • the output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit).
  • E-value probability score
  • comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length.
  • the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
  • Table A1 provides a list of nucleic acid and protein sequences related to SEQ ID NO: 1 , SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4.
  • Table A1 Examples of DUF642 nucleic acids and polypeptides:
  • V.vinifera_GSVIVT00028751001 167 168

Landscapes

  • Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Molecular Biology (AREA)
  • Wood Science & Technology (AREA)
  • Biotechnology (AREA)
  • General Engineering & Computer Science (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • Biomedical Technology (AREA)
  • Zoology (AREA)
  • Biochemistry (AREA)
  • General Health & Medical Sciences (AREA)
  • Biophysics (AREA)
  • Microbiology (AREA)
  • Physics & Mathematics (AREA)
  • Plant Pathology (AREA)
  • Cell Biology (AREA)
  • Botany (AREA)
  • Gastroenterology & Hepatology (AREA)
  • Medicinal Chemistry (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Breeding Of Plants And Reproduction By Means Of Culturing (AREA)
  • Micro-Organisms Or Cultivation Processes Thereof (AREA)
  • Peptides Or Proteins (AREA)
  • Enzymes And Modification Thereof (AREA)

Abstract

Provided are a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a DUF642 (Protein containing a Domain of Unknown Function) polypeptide, or an epimerase-related like polypeptide, or a phospholipase/carboxylesterase (PLPCase) polypeptide, and plants having modulated expression of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide, which plants have enhanced yield-related traits relative to control plants. Also provided are DUF642-encoding nucleic acids, or epimerase-related like polypeptides, or PLPCase-encoding nucleic acids, and constructs comprising the same, useful in performing the methods for enhancing yield-related traits in plants.

Description

PLANTS HAVING ENHANCED YIELD-RELATED TRAITS AND PRODUCING METHODS THEREOF
Background
The present invention relates generally to the field of molecular biology and concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a DUF642 (Protein containing a Domain of Unknown Function) polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding a DUF642 polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.
The present invention furthermore concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding an epimerase-related like polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding an epimerase-related like polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.
The present invention also concerns a method for enhancing yield-related traits in plants by modulating expression in a plant of a nucleic acid encoding a Phospholipase/carboxylesterase (PLPCase) polypeptide. The present invention also concerns plants having modulated expression of a nucleic acid encoding a PLPCase polypeptide, which plants have enhanced yield-related traits relative to corresponding wild type plants or other control plants. The invention also provides constructs useful in the methods of the invention.
The ever-increasing world population and the dwindling supply of arable land available for agriculture fuels research towards increasing the efficiency of agriculture. Conventional means for crop and horticultural improvements utilise selective breeding techniques to identify plants having desi rable characteristics. However, such selective breeding techniques have several drawbacks, namely that these techniques are typically labour intensive and result in plants that often contain heterogeneous genetic components that may not always result in the desirable trait being passed on from parent plants. Advances in molecular biology have allowed mankind to modify the germplasm of animals and plants. Genetic engineering of plants entails the isolation and manipulation of genetic material (typically in the form of DNA or RNA) and the subsequent introduction of that genetic material into a plant. Such technology has the capacity to deliver crops or plants having various improved economic, agronomic or horticultural traits. A trait of particular economic interest is increased yield. Yield is normally defined as the measurable produce of economic value from a crop. This may be defined in terms of quantity and/or quality. Yield is directly dependent on several factors, for example, the number and size of the organs, plant architecture (for example, the number of branches), seed production, leaf senescence and more. Root development, nutrient uptake, stress tolerance and early vigour may also be important factors in determining yield. Optimizing the abovementioned factors may therefore contribute to increasing crop yield.
Seed yield is a particularly important trait, since the seeds of many plants are important for human and animal nutrition. Crops such as corn, rice, wheat, canola and soybean account for over half the total human caloric intake, whether through direct consumption of the seeds themselves or through consumption of meat products raised on processed seeds. They are also a source of sugars, oils and many kinds of metabolites used in industrial processes. Seeds contain an embryo (the sou rce of new shoots and roots) and an endosperm (the source of nutrients for embryo growth during germination and during early growth of seedlings). The development of a seed involves many genes, and requires the transfer of metabolites from the roots, leaves and stems into the growing seed. The endosperm, in particular, assimilates the metabolic precursors of carbohydrates, oils and proteins and synthesizes them into storage macromolecules to fill out the grain.
Another important trait for many crops is early vigour. Improving early vigour is an important objective of modern rice breeding programs in both temperate and tropical rice cultivars. Long roots are important for proper soil anchorage in water-seeded rice. Where rice is sown directly into flooded fields, and where plants must emerge rapidly through water, longer shoots are associated with vigour. Where drill-seeding is practiced, longer mesocotyls and coleoptiles are important for good seedling emergence. The ability to engineer early vigour into plants would be of great importance in agriculture. For example, poor early vigour has been a limitation to the introduction of maize (Zea mays L.) hybrids based on Corn Belt germplasm in the European Atlantic.
A further important trait is that of improved abiotic stress tolerance. Abiotic stress is a primary cause of crop loss worldwide, reducing average yields for most major crop plants by more than 50% (Wang et al., Planta 218, 1 -14, 2003). Abiotic stresses may be caused by drought, salinity, extremes of temperature, chemical toxicity and oxidative stress. The ability to improve plant tolerance to abiotic stress would be of great economic advantage to farmers worldwide and would allow for the cultivation of crops during adverse conditions and in territories where cultivation of crops may not otherwise be possible.
Crop yield may therefore be increased by optimising one of the above-mentioned factors.
Concerning DUF642 polypeptides, the family of DUF642 proteins represents a conserved region found in a number of uncharacterised plant proteins. DU F642 proteins were identified e.g. by Irshad et al., BMC Plant Biology 2008, 8:94. Concerning epimerase-related like polypeptides, the present invention relates to the use of epimerase-related like polynucleotides and polypeptides in the field of plant biotechnology. Epimerases can be defined as isomerase enzymes that catalyze the inversion of stereochemistry in biological molecules.
Ascencio-lbanez et al. (2008, Plant Physiology 148(1 ):436-454) have reported amongst genes that are significantly changed during CalCuV injection an Arabodopsis epimerase gene, which is listed in a supplemental table (Table 2) of this paper. In this paper, the Arabidopsis gene is called a "Putative protein Isopenicillin-N-epimerase". The authors described microarray analyses of the Arabidopsis {Arabidopsis thaliana) transcriptome in response to cabbage leaf curl virus (CaLCuV) infection, and indicated that they uncovered 5,365 genes (false discovery rate <0.005) differentially expressed in infected rosette leaves at 12days postinoculation, including an Arabidopsis isomerase gene (At3g62130). Mehta and Christen (1994 Biochem. Biophys. Res. Commun.14;198(1 ):138-43) described the homology of isopenicillin-N-epimerases to aminotransferases.
Concerning PLPCase polypeptides, the PLPCase polypeptide fami ly contai ns both phospholipases and carboxylesterases with broad substrate specificity, and is structurally related to alpha/beta hydrolases. Members of the PLPCase superfamily are present in plants, but also in other organisms such as yeast and bacteria. In Arabidopsis, SOBER1 gene encoding a PLPCase is involved in resistance to plant pathogen P. synringae pv tomato DC3000 (Kirik and Mudgett (2009), PNAS 106 (48): 20532-20537). Recent studies showed that PLPCase might have arisen from rare horizontal gene transfer from fungi to plant (Richards et al. (2009), The Plant Cell, 21 (7): 1897-191 1 ).
Depending on the end use, the modification of certain yield traits may be favoured over others. For example for applications such as forage or wood production , or bio-fuel resource, an increase in the vegetative parts of a plant may be desirable, and for applications such as flour, starch or oil production, an increase in seed parameters may be particularly desirable. Even amongst the seed parameters, some may be favoured over others, depending on the application. Various mechanisms may contribute to increasing seed yield, whether that is in the form of increased seed size or increased seed number. It has now been found that various yield-related traits may be improved in plants by modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide in a plant.
Detailed description of the invention
The present invention shows that modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide gives plants having enhanced yield-related traits relative to control plants. According to a first embodiment, the present invention provides a method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide and optionally selecting for plants having enhanced yield-related traits. According to another embodiment, the present invention provides a method for producing plants having enhanced yield-related traits relative to control plants, wherein said method comprises the steps of modulating expression in said plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as described herein and optionally selecting for plants having enhanced yield-related traits.
A preferred method for modulating (preferably, increasing) expression of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide is by introducing and expressing in a plant a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
Any reference hereinafter to a "protein useful in the methods of the invention" is taken to mean a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein. Any reference hereinafter to a "nucleic acid useful in the methods of the invention" is taken to mean a nucleic acid capable of encoding such a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide. The nucleic acid to be introduced into a plant (and therefore useful in performing the methods of the invention) is any nucleic acid encoding the type of protein which will now be described, hereafter also named "DUF642 nucleic acid", or "epimerase-related like nucleic acid", or "PLPCase nucleic acid" or "DUF642 gene", or "epimerase-related like gene", or "PLPCase gene".
A "DUF642 polypeptide" as defined herein refers to any polypeptide comprising an InterPro accession IPR006946 DUF642 domain, preferably said DUF642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
The term "DU F642" or "DUF642 polypeptide" as used herein also intends to include homologues as defined hereunder of "DUF642 polypeptide". Preferably, the DUF642 polypeptide polypeptide comprises one or more of the following motifs:
(i) Motif 1 : N[LAM][VL]KNG[DG]FEEGP[WYH][M I][FLI]P[NG][TS][STR][WL]GVL [LVI]P[PTS][NKM][LQDV][EDV][DE][ED][THY]S[PS]L[PS][GP]W[IMT][IV] (SEQ ID NO: 181 ),
(ii) Motif 2: [VLA][EKAT][KPR]G[SAM][LRH]Y[SA][LIV][TI]F[SG]A[AS]RTCAQ[DLAS] E[SVRL]L[NR][VI] (SEQ ID NO: 182),
(iii) Motif 3: D[PE][AT]CGP[LI][IL]D[AS][VIF]AI[KR] (SEQ ID NO: 183) More preferably, the DUF642 polypeptide comprises one or more of the following motifs: (i) Motif 4: N[ML][LV][KR]NG[DG]FEEGPY[IF][FLI]P[GND][TA][SPR]WGVL[VI]P[PS] [MN][DIV][EV] (SEQ ID NO: 184),
(ii) Motif 5: N[VI][ST][VAI][SAT][PG][EQ][SW][GA][VE][LI]P[IM]QT[VIM]Y[TGS]S[SN] GWDSY[SA]WA[FW] (SEQ ID NO: 185),
(iii) Motif 6: Y[SA][IL][TI]FSAARTCAQ[AS]E (SEQ ID NO: 186)
Even more preferably, the DU F642 polypeptide comprises in increasi ng order of preference, at least 2, at least 3, at least 4, at least 5, or all 6 motifs.
Motifs 1 to 6 were derived using the MEME algorithm (Bailey and Elkan, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAA I Press, Menlo Park, California, 1994). At each position within a M EME motif, the residues are shown that are present in the query set of sequences with a frequency higher than 0.2. Residues within square brackets represent alternatives.
Additionally or alternatively, the homologue of a DUF642 protein has in increasing order of preference at least 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 2 or 4, provided that the homologous protein comprises any one or more of the conserved motifs as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides).
I n one embodiment the sequence identity level is determined by comparison of the polypeptide sequences over the entire length of the sequence of SEQ ID NO: 2 or SEQ ID NO: 4.
Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered. Preferably the motifs in a DUF642 polypeptide have, in increasing order of preference, at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of the motifs represented by SEQ ID NO: 181 to SEQ ID NO: 186 (Motifs 1 to 6).
I n other words, in another embodiment a method is provided wherein said DUF642 polypeptide comprises a conserved domain (or motif) with at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the conserved motifs starting with amino acid 202 up to amino acid 241 (motif 1 ), amino acid 108 up to amino acid 132 (motif 2), amino acid 78 up to amino acid 191 (motif 3) in SEQ ID NO:2; the conserved motifs starting with amino acid 202 up to amino acid 230 (motif 4), amino acid 130 up to amino acid 159 (motif 5), amino acid 1 14 up to amino acid 128 (motif 6) in SEQ ID NO:2; the conserved motifs starting with amino acid 121 up to amino acid 160 (motif 1 ), amino acid 27 up to amino acid 51 (motif 2), amino acid 97 up to amino acid 1 10 (motif 3) in SEQ ID NO:4; the conserved motifs starting with amino acid 121 up to amino acid 149 (motif 4), amino acid 50 up to amino acid 78 (motif 5), amino acid 33 up to amino acid 47 (motif 6) in SEQ ID NO:4.
An "epimerase-related like polypeptide" or "epimerase-related like protein" as defined herein refers to any polypeptide having an amino acid sequence which comprises one or more of the following motifs:
(i) Motif 7: CREEGV[DE][QK]VFVD[AG]AH[AS]IG[QSC]V[PDE][VI][DN][VM][KR][ED]IGA DFY[TV]SNLHKWFFCPP[SA]VAFL[YH] (SEQ ID NO: 273),
(ii) Motif 8: EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK][RN]WQ [LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
(iii)Motif 9: S[LI]VDNATTAAAIVLQ[HQ][VAI][AG][WR][AS]FAEG[RKN]FA[KR][GN]D[AVT]V [LV]MLH[YC]AY[GQ][AS]VKKSI[EQH]AYV (SEQ ID NO: 275)
Motifs 7 to 9 were derived using the MEME algorithm (Bailey and Elkan, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAA I Press, Menlo Park, California, 1994). At each position within a MEME motif, the residues are shown that are present in the query set of sequences with a frequency higher than 0.2. Residues within square brackets represent alternatives.
More preferably, the epimerase-related like polypeptide comprises in increasing order of preference, at least 1 , at least 2, or all 3 motifs.
In another embodiment, an epimerase-related like polypeptide as used herein comprises a polypeptide having one or more of the domains as listed in Table C, and in particular having one or more of the following domains:
- a domai n as determined with the superfamily database and having accession number SSF53383;
- a domain as determined with the HMMPanther database and having accession number as PTHR1 1601
- a domain as determined with the HMMPfam database and having accession number PF00266; and
- a domain as determined with the Gene3D database and having accession number G3DSA:3.40.640.10 In another preferred embodiment, an epimerase-related like polypeptide as used herein comprises a conserved domain (or motif) with at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to or consists of a conserved domain as represented by any one of:
- amino acid coordinates 32 to 449 in SEQ ID NO: 198 (motif 10 -SEQ ID NO: 280);
- amino acid coordinates 47 to 276 in SEQ ID NO: 198 (motif 1 1 - SEQ ID NO: 281 ); - amino acid coordinates 92 to 364 in SEQ ID NO: 198 (motif 12 - SEQ ID NO: 282); and
- amino acid coordinates 59 to 323 in SEQ ID NO: 198 (motif 13 - SEQ ID NO: 283).
The term "epimerase-related like polypeptide" as used herein also intends to include homologues as defined hereunder of an "epimerase-related like polypeptide".
Additionally or alternatively, the homologue of an epimerase-related like protein has in increasing order of preference at least 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 198, provided that the homologous protein comprises any one or more of the conserved motifs or domains as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). In one embodiment the sequence identity level is determined by comparison of the polypeptide sequences over the entire length of the sequence of SEQ ID NO: 198.
Compared to overall sequence identity, the sequence identity will generally be higher when only conserved domains or motifs are considered. Preferably the motifs in an epimerase- related like polypeptide have, in increasing order of preference, at least 70%, 71 %, 72%,
73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of the motifs 1 to 7 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as described above.
A "PLPCase polypeptide" as defined herein refers to any polypeptide comprising an InterPro accession IPR003140 corresponding to PFAM accession number PF022030 Phospholipase/carboxylesterase (PLPCase) domain.
The term "PLPCase" or "PLPCase polypeptide" as used herein also intends to include homologues as defined hereunder of "PLPCase polypeptide".
In a preferred embodiment, the PLPCase polypeptide comprises one or more of the following motifs:
(i) M otif 1 4 : E[FY] G[KR]T[HY]WRPKG[K ]HQATIVWLHGLGDNG[LSA]S[SW]SQLL [ED][ST]LPLPNIKWICPTA (SEQ ID NO: 348),
(ii) Motif 15: PDD[WIVL]EGLDASAAH[IV]ANLLS[TS]EP[AS]D[VI]K[VL]G[IV]G (SEQ ID NO: 349),
(iii) Motif 16: FSMGAA[IT]ALYSA[TA]C[YF]A[MHL] (SEQ ID NO: 350)
In a more preferred embodiment, the PLPCase polypeptide comprises one or more of the following motifs:
(i) Motif 17: E[FY]G[KR]T[HY]VVRPKGKH[QK]ATIVWLHGLGDNG[LS]S[SW]SQL
LE[ST]LPLPNIKWICPTA (SEQ ID NO: 351 )
(ii) Motif 18: ED[GA]PDD[WLV]EGLDA[SA]AAH[IV]ANLLSTEPA[DN][VI]K (SEQ ID NO:
352)
(iii) Motif 19: [LF]GGFP[CS]TAWFD (SEQ ID NO: 353)
In an alternative preferred embodiment, the PLPCase polypeptide comprises one or more of the following motifs:
(i) Motif 20: T[HY]VVRPKG[KR]HQATIVWLHG[LI]GDNG[LAG]S[SW]SQLL[ED]SLP LPN[IV]KWICPTAP[TS]RP (SEQ ID NO: 354)
(ii) Motif 21 : FPCTAWFDV[GE][ED][LT]S[ELV]DG[PHR]DD[WI]EG[LM]DASA[AS]H
[IV]ANLLS[TS]EP[AS]DV[KS][VL]GIGGFSM (SEQ ID NO: 355)
(iii) Motif 22: FK[SP]Y[END]G[IL]GHYT[VI]P[RE]EM[GD][ED]V[SC][TKN] (SEQ I D NO: 356) In a most preferred embodiment, the PLPCase polypeptide comprises one or more of the following motifs:
(i) Motif 23: EFG[KR]T[HY]VVRPKGKHQATIVWLHGLGDNG[LS]SS[SY]QLLES LPLPNIKWICPTA (SEQ ID NO: 357)
(ii) Motif 24: SEDG[PH]DDWEGLDASA[AS]HIANLLSTEPADV (SEQ ID NO: 358) (iii) Motif 25: G[IT]SDDVV[LP]Y[KR][YF]GEKSAQSLS[SM]AGFRY[VI][AMT]FK[SP]Y
(SEQ ID NO: 259)
Motifs 14 to 25 were derived using the MEME algorithm (Bailey and Elkan, Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28- 36, AAAI Press, Menlo Park, California, 1994). At each position within a MEME motif, the residues are shown that are present in the query set of sequences with a frequency higher than 0.2. Residues within square brackets represent alternatives. More preferably, the PLPCase polypeptide comprises in increasing order of preference, at least 2, at least 3, at least 4, at least 5, at least 6, at least 7, at least 8, at least 9, at least 10, at least 1 1 , or all 12 motifs.
Additionally or alternatively, the homologue of a PLPCase protein has in increasing order of preference at least 25%, 26%, 27%, 28%, 29%, 30%, 31 %, 32%, 33%, 34%, 35%, 36%, 37%, 38%, 39%, 40%, 41 %, 42%, 43%, 44%, 45%, 46%, 47%, 48%, 49%, 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% overall sequence identity to the amino acid represented by SEQ ID NO: 285, provided that the homologous protein comprises any one or more of the conserved motifs as outlined above. The overall sequence identity is determined using a global alignment algorithm, such as the Needleman Wunsch algorithm in the program GAP (GCG Wisconsin Package, Accelrys), preferably with default parameters and preferably with sequences of mature proteins (i.e. without taking into account secretion signals or transit peptides). Compared to overall seq uence identity, the sequence identity will generally be h igher when only conserved domains or motifs are considered. Preferably the motifs in a PLPCase polypeptide have, in increasing order of preference, at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to any one or more of the motifs represented by SEQ ID NO: 348 to SEQ ID NO: 359 (Motifs 14 to 25). In another preferred embodiment a method is provided wherein said PLPCase polypeptide comprises a conserved domain (or motif) with at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the conserved domain starting with amino acid 20 up to amino acid 69 and/or amino acid 92 to amino acid 1 18 and/or amino acid 194 to amino acid 225 in SEQ ID NO:285).
The terms "domain", "signature" and "motif" are defined in the "definitions" section herein.
Preferably, th e polypeptid e seq uence whi ch when used i n the constru ction of a phylogenetic tree, such as the one depicted in Figure 5, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4 rather than with any other group.
In addition, DUF642 polypeptides, when expressed in rice according to the methods of the present invention as outlined in Examples 6 and 7, give plants having increased yield related traits, in particular when grown under non-stress conditions, total seed yield (Totalwgseeds), number of seeds (nrfilledseed), seed fill rate (fillrate), harvest index, greenness before flowering, total number of seeds (nrtotalseed) and for aboveground biomass (AreaMax).
Preferably, the polypeptide sequence which when used in the construction of a phylogenetic tree, such as the one depicted in Figure 9, clusters with the group of epimerase-related like polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group.
In addition, epimerase-related like polypeptides, when expressed in rice according to the methods of the present invention as outlined in Examples 6 and 7, give plants having increased yield related traits, in particular increased biomass and/or increase seed yield, and more particularly any one or more of increased total weight of seeds, harvest index, fill rate, thousand kernel weight (TKW), above ground biomass, and number of filled seeds. Preferably, th e polypeptid e seq uence whi ch when used i n the constru ction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group. Furthermore, PLPCase polypeptides (at least in their native form) typically have phospholipase and/or carboxylesterase activity. Tools and techniques for measuring phospholipase and/or carboxylesterase activity are well known in the art, as e.g. Kirik and Mudgett (2009), PNAS 106 (48): 20532-20537. In addition, PLPCase polypeptides, when expressed in rice according to the methods of the present invention as outlined in Examples 6 and 7, give plants having increased yield related traits, in particular increased root biomass and greenness index.
In one embodiment of the present invention the function of the nucleic acid sequences of the invention is to confer information for a protein that increases yield or yield related traits, when a nucleic acid sequence of the invention is transcribed and translated in a living plant cell.
In one embodiment of the present invention the function of the nucleic acid sequences of the invention is to confer information for synthesis of the PLPCase polypeptides that increases yield or yield related traits, when such a nucleic acid sequence of the invention is transcribed and translated in a living plant cell.
The present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ I D NO: 1 , encoding the polypeptide sequence of SEQ ID NO: 2. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any DUF642-encoding nucleic acid or DUF642 polypeptide as defined herein.
Examples of nucleic acids encoding DUF642 polypeptides are given in Table A1 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A1 of the Examples section are example sequences of orthologues and paralogues of the DUF642 polypeptide represented by SEQ I D NO: 2, the terms "orthologues" and "paralogues" being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search as described in the definitions section; where the query sequence is SEQ I D NO: 1 or SEQ ID NO: 2; or SEQ I D NO: 3 or SEQ ID NO: 4, the second BLAST (back-BLAST) would be against rice sequences.
The invention also provides hitherto unknown DUF642-encoding nucleic acids and DUF642 polypeptides useful for conferring enhanced yield-related traits in plants relative to control plants.
According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:
(i) a nucleic acid represented by SEQ ID NO: 33, 39, 91 , 169, 171 , 175;
(ii) the complement of a nucleic acid represented by SEQ ID NO: 33, 39, 91 , 169,
171 , 175;
(iii) a nucleic acid encoding a DUF642 polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 34, 40, 92, 170,
172, 176, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs given in SEQ ID NO: 181 to SEQ I D NO: 186, and further preferably conferring enhanced yield-related traits relative to control plants.
(iv) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:
(i) an amino acid sequence represented by SEQ ID NO: 34, 40, 92, 170, 172, 176; (ii) an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 34, 40, 92, 170, 172, 176, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs given in SEQ ID NO: 181 to SEQ ID NO: 186, and further preferably conferring enhanced yield-related traits relative to control plants;
(iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
The present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 197, encoding the polypeptide sequence of SEQ ID NO: 198. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any n ucleic acid encod ing epimerase-related like polypeptides or any epimerase-related like polypeptide as defined herein.
Examples of nucleic acids encoding epimerase-related like polypeptides are given in Table A2 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A2 of the Examples section are example sequences of orthologues and paralogues of the epimerase-related like polypeptide represented by SEQ ID NO: 198, the terms "orthologues" and "paralogues" being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search as described in the definitions section; where the query sequence is SEQ ID NO: 197 or SEQ I D NO: 198, the second BLAST (back- BLAST) would be against poplar sequences.
The invention also provides hitherto unknown epimerase-related like-encoding nucleic acids and epimerase-related like polypeptides useful for conferring enhanced yield-related traits in plants relative to control plants.
According to a further embodiment of the present invention, there is therefore provided an isolated nucleic acid molecule selected from:
(i) a nucleic acid represented by SEQ ID NO: 199;
(ii) the complement of a nucleic acid represented by SEQ ID NO: 199;
(iii) a nucleic acid encoding epimerase-related like polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96% , 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having i n increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs 7 to 13 as given herein, and further preferably conferring enhanced yield-related traits relative to control plants,
a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
According to a further embodiment of the present invention, there is also provided an isolated polypeptide selected from:
(i) an amino acid sequence represented by SEQ ID NO: 200;
(ii) an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs 7 to 13 as given herein, and further preferably conferring enhanced yield-related traits relative to control plants;
(iii) derivatives of any of the amino acid sequences given in (i) or (ii) above. The present invention is illustrated by transforming plants with the nucleic acid sequence represented by SEQ ID NO: 284, encoding the polypeptide sequence of SEQ ID NO: 285. However, performance of the invention is not restricted to these sequences; the methods of the invention may advantageously be performed using any PLPCase-encoding nucleic acid or PLPCase polypeptide as defined herein.
Examples of nucleic acids encoding PLPCase polypeptides are given in Table A3 of the Examples section herein. Such nucleic acids are useful in performing the methods of the invention. The amino acid sequences given in Table A3 of the Examples section are example sequences of orthologues and paralogues of the PLPCase polypeptide represented by SEQ I D NO: 285, the terms "orthologues" and "paralogues" being as defined herein. Further orthologues and paralogues may readily be identified by performing a so-called reciprocal blast search as described in the definitions section; where the query sequence is SEQ ID NO: 284 or SEQ ID NO: 285, the second BLAST (back-BLAST) would be against Medicago truncatula sequences.
The invention also provides hitherto unknown PLPCase-encodi ng nucleic acids and PLPCase polypeptides useful for conferring enhanced yield-related traits in plants relative to control plants.
According to a further embodiment of the present invention, there is therefore provided isolated nucleic acid molecule selected from:
(i) a nucleic acid represented by any one of SEQ ID NO: 298, 302, 304, 312, 316, 336 or 346;
(ii) the complement of a nucleic acid represented by any one of SEQ ID NO: 298, 302, 304, 312, 316, 336 or 346;
(iii) a nucleic acid encoding a PLPCase polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%,
60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 299, 303, 305, 313, 317, 337 or 347, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs given in SEQ ID NO: 348 to SEQ ID NO: 359, and further preferably conferring enhanced yield-related traits relative to control plants.
(iv) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
According to a further embodiment of the present invention, there is also provided isolated polypeptide selected from:
an amino acid sequence represented by any one of SEQ ID NO: 299, 303, 305, 313, 317, 337 or 347;
an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%,
65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by any one of SEQ ID NO: 299, 303, 305, 313, 317, 337 or 347, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs given in SEQ ID NO: 348 to SEQ I D NO: 359, and further preferably conferring enhanced yield-related traits relative to control plants;
derivatives of any of the amino acid sequences given in (i) or (ii) above.
Nucleic acid variants may also be useful in practising the methods of the invention. Examples of such variants include nucleic acids encoding homologues and derivatives of any one of the amino acid sequences given in Table A1 to A3 of the Examples section, the terms "homologue" and "derivative" being as defined herein. Also useful in the methods of the invention are nucleic acids encoding homologues and derivatives of orthologues or paralogues of any one of the amino acid seq uences given in Table A1 to A3 of the Examples section. Homologues and derivatives useful in the methods of the present invention have substantially the same biological and functional activity as the unmodified protein from which they are derived. Further variants useful in practising the methods of the invention are variants in which codon usage is optimised or in which imiRNA target sites are removed.
Further nucleic acid variants useful in practising the methods of the invention include portions of n ucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides, nucleic acids hybridising to nucleic acids encoding POI polypeptides, splice variants of nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides, allelic variants of nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides and variants of nucleic acids encoding DUF642 polypeptides, or epimerase- related like polypeptides, or PLPCase polypeptides obtained by gene shuffling. The terms hybridising sequence, splice variant, allelic variant and gene shuffling are as described herein.
Nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides need not be full-length nucleic acids, since performance of the methods of the invention does not rely on the use of full-length nucleic acid sequences. According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a portion of any one of the nucleic acid sequences given in Table A1 to A3 of the Examples section, or a portion of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A1 to A3 of the Examples section.
A portion of a nucleic acid may be prepared, for example, by making one or more deletions to the nucleic acid. The portions may be used in isolated form or they may be fused to other coding (or non-coding) sequences in order to, for example, produce a protein that combines several activities. When fused to other coding sequences, the resultant polypeptide produced upon translation may be bigger than that predicted for the protein portion.
Concerning DUF642 polypeptides, portions useful in the methods of the invention, encode a DUF642 polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A1 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A1 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section. Preferably the portion is at least 250, 300, 350, 400, 450 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A1 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A1 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 1. Preferably, the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one depicted in Figure 5, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 or 4 rather than with any other group, and/or comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
Concerning epimerase-related like polypeptides, portions useful in the methods of the invention, encode an epimerase-related like polypeptide as defined herein, and have substantially the same biological activity as the amino acid sequences given in Table A2 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A2 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section. Preferably the portion is at least 850, 900, 950, 1000, 1050, 1100, 1 150, 1200, 1250, 1300, 1350, 1400, 1450, 1500, 1550, consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A2 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A2 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 197.
Preferably, the portion encodes a fragment of an amino acid sequence which has one or more of the following characteristics:
- when used in the construction of a phylogenetic tree, such as the one depicted in Figure 10, clusters with the group of polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group;
- comprises one or more of the following domains SSF53383, PTHR1 1601 ; PF00266, and G3DSA:3.40.640.10
comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
- has at least 40% sequence identity to SEQ ID NO: 198.
Concerning PLPCase polypeptides, portions useful in the methods of the invention, encode a PLPCase polypeptide as defined herein, and have substantially the same biological activity as the ami no acid seq uences given in Table A3 of the Examples section. Preferably, the portion is a portion of any one of the nucleic acids given in Table A3 of the Examples section, or is a portion of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A3 of the Examples section. Preferably the portion is at least 350, 400, 450, 500, 550, 600, 650, 700, 750, 780 consecutive nucleotides in length, the consecutive nucleotides being of any one of the nucleic acid sequences given in Table A3 of the Examples section, or of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A3 of the Examples section. Most preferably the portion is a portion of the nucleic acid of SEQ ID NO: 284. Preferably, the portion encodes a fragment of an amino acid sequence which, when used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
Another nucleic acid variant useful in the methods of the invention is a nucleic acid capable of hybridising, under reduced stringency conditions, preferably under stringent conditions, with a n ucl ei c aci d encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, or with a portion as defined herein. According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a nucleic acid capable of hybridizing to the complement of a nucleic acid encoding any one of the proteins given in Table A of the Examples section, or to the complement of a nucleic acid encoding an orthologue, paralogue or homologue of any one of the proteins given in Table A of the Examples section.
Hybrid isi ng sequences usefu l i n the methods of the i nvention encode a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, having substantially the same biological activity as the DUF642, epimerase-related like or PLPCase amino acid sequences given in Table A of the Examples section . Preferably, the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding any one of the proteins given in Table A of the Examples section, or to a portion of any of these sequences, a portion being as defined herein, or the hybridising sequence is capable of hybridising to the complement of a nucleic acid encoding an orthologue or paralogue of any one of the amino acid sequences given in Table A of the Examples section.
Concerning DUF642 polypeptides, the hybridising sequence is most preferably capable of hybridising to the complement of a nucleic acid encoding the polypeptide as represented by SEQ ID NO: 1 or to a portion thereof. Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
In one embodiment the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ I D NO: 1 or SEQ ID NO: 3 or to a portion thereof under conditions of medium or high stringency, preferably high stringency as defined above. I n another embodi ment the hybrid isi ng seq uence is capable of hybrid isi ng to the complement of a nucleic acid as represented by SEQ ID NO: 1 or SEQ ID NO: 3 under stringent conditions. Concerning epimerase-related like polypeptides, the hybridising sequence is most preferably capable of hybridising to the complement of a n ucleic acid encoding the polypeptide as represented by SEQ ID NO: 197 or to a portion thereof.
Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which has one or more of the following characteristics:
- when used in the construction of a phylogenetic tree, such as the one depicted in Figure 10, clusters with the group of polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group;
- comprises one or more of the following domains SSF53383, PTHR1 1601 ; PF00266, and G3DSA:3.40.640.10
- comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
- has at least 40% sequence identity to SEQ ID NO: 198. In one embodiment the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 197 or to a portion thereof under conditions of medium or high stringency, preferably high stringency as defined above. In another embodiment the hybridising sequence is capable of hybridising to the complement of a nucleic acid as represented by SEQ ID NO: 197 under stringent conditions.
Concerning PLPCase polypeptides, the hybridising sequence is most preferably capable of hybridising to the complement of a nucleic acid encoding the polypeptide as represented by SEQ I D NO: 284 or to a portion thereof. In one embodiment, the hybridization conditions are of medium stringency, preferably of high stringency, as defined herein.
Preferably, the hybridising sequence encodes a polypeptide with an amino acid sequence which, when full-length and used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/ or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
Another nucleic acid variant useful in the methods of the invention is a splice variant encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined hereinabove, a splice variant being as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a splice variant of any one of the nucleic acid sequences given in Table A of the Examples section, or a splice variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section.
Concerning DUF642 polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ I D NO: 1 , or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2. Preferably, the amino acid sequence encoded by the splice variant, when used in the construction of a phylogenetic tree, clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
Concerning epimerase-related like polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 197, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 198. Preferably, the amino acid sequence encoded by the splice variant, has one or more of the following characteristics:
- when used in the construction of a phylogenetic tree, such as the one depicted in Figure 10, cl usters with the group of polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group;
- comprises one or more of the following domains SSF53383, PTHR1 1601 ; PF00266, and G3DSA:3.40.640.10
- comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
- has at least 40% sequence identity to SEQ ID NO: 198. Concerning PLPCase polypeptides, preferred splice variants are splice variants of a nucleic acid represented by SEQ ID NO: 284, or a splice variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 285. Preferably, the amino acid sequence encoded by the splice variant, when used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
Another nucleic acid variant useful in performing the methods of the invention is an allelic variant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, an allelic variant being as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant an allelic variant of any one of the nucleic acids given in Table A of the Examples section, or comprising introducing and expressing in a plant an allelic variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section.
Concerning DUF642 polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the DUF642 polypeptide of SEQ ID NO: 2 and any of the amino acids depicted in Table A1 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of S EQ I D NO: 1 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 2. Preferably, the amino acid sequence encoded by the allelic variant, when used in the construction of a phylogenetic tree, clusters with the DUF642 polypeptides comprising the amino acid sequence represented by SEQ ID NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4.
Concerning epimerase-related like polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the epimerase-related like polypeptide of SEQ ID NO: 198 and any of the amino acids depicted in Table A2 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 197 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ I D NO: 198. Preferably, the amino acid sequence encoded by the allelic variant has one or more of the following characteristics:
- when used in the construction of a phylogenetic tree, such as the one depicted in Figure 10, clusters with the group of polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group;
- comprises one or more of the following domains SSF53383, PTHR1 1601 ; PF00266, and G3DSA:3.40.640.10
- comprises any one or more of the motifs 7 to 13 (as represented by SED ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
- has at least 40% sequence identity to SEQ ID NO: 198.
Concerning PLPCase polypeptides, the polypeptides encoded by allelic variants useful in the methods of the present invention have substantially the same biological activity as the PLPCase polypeptide of SEQ ID NO: 285 and any of the amino acids depicted in Table A3 of the Examples section. Allelic variants exist in nature, and encompassed within the methods of the present invention is the use of these natural alleles. Preferably, the allelic variant is an allelic variant of SEQ ID NO: 284 or an allelic variant of a nucleic acid encoding an orthologue or paralogue of SEQ ID NO: 285. Preferably, the amino acid sequence encoded by the allelic variant, when used in the construction of a phylogenetic tree, such as the one depicted in Figure 14, clusters with the PLPCase polypeptides comprising the amino acid sequence represented by SEQ I D NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 17 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
Gene shuffling or directed evolution may also be used to generate variants of nucleic acids encoding DUF642 polypeptides, o r epimerase-related like polypeptides, or PLPCase polypeptides as defined herein; the term "gene shuffling" being as defined herein.
According to the present invention, there is provided a method for enhancing yield-related traits in plants, comprising introducing and expressing in a plant a variant of any one of the nucleic acid sequences given in Table A of the Examples section, or comprising introducing and expressing in a plant a variant of a nucleic acid encoding an orthologue, paralogue or homologue of any of the amino acid sequences given in Table A of the Examples section, which variant nucleic acid is obtained by gene shuffling. Concerning DUF642 polypeptides, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, when used in the construction of a phylogenetic tree, preferably clusters with the group of DUF642 polypeptides comprising the amino acid sequence represented by SEQ I D NO: 2 and/or 4, rather than with any other group, comprises at least one of the motifs 1 to 6 (SEQ ID NO: 181 to 186), and/or has at least 50% sequence identity to SEQ ID NO: 2 or 4. Concerning epimerase-related like polypeptides, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, preferably is an amino acid sequence which has one or more of the following characteristics:
- when used in the construction of a phylogenetic tree, such as the one depicted in Figure 10, clusters with the group of polypeptides comprising the amino acid sequence represented by SEQ ID NO: 198 rather than with any other group;
- comprises one or more of the following domains SSF53383, PTHR1 1601 ; PF00266, and G3DSA:3.40.640.10
- comprises any one or more of the motifs 7 to 13 (as represented by SEQ ID NO 273, 274, 275, 280, 281 , 282, 283, respectively) as provided herein, and
- has at least 40% sequence identity to SEQ ID NO: 198.
Concerning PLPCase polypeptides, the amino acid sequence encoded by the variant nucleic acid obtained by gene shuffling, when used in the construction of a phylogenetic tree such as the one depicted in Figure 14, preferably clusters with the group of PLPCase polypeptides comprising the amino acid sequence represented by SEQ ID NO: 285 rather than with any other group, and/or comprises motifs any of the motifs 14 to 16, preferably any of the motifs 1 7 to 19, or preferably any of the motifs 20 to 22, more preferably comprises any of the motifs 23 to 25, and/or has phospholipase and/or carboxylesterase biological activity, and/or has at least 60% sequence identity to SEQ ID NO: 285.
Furthermore, nucleic acid variants may also be obtained by site-directed mutagenesis. Several methods are available to achieve site-directed mutagenesis, the most common being PCR based methods (Current Protocols in Molecular Biology. Wiley Eds.).
Concerning DUF642 polypeptides, nucleic acids encoding DUF642 polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic envi ron ment th rough del iberate human manipulation. Preferably the DUF642 polypeptide-encoding nucleic acid is from a plant, further preferably from a monocotyledonous plant, more preferably from the family Poaceae, most preferably the nucleic acid is from Oryza sativa.
For example, the nucleic acid encoding the DUF642 polypeptide of SEQ ID NO:2 can be generated from the nucleic acid encoding the DUF642 polypeptide of SEQ ID NO:2 by alteration of several nucleotides, e.g. by site-directed mutagenesis using PCR based methods (see Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates)). DUF642 polypeptides differing from the sequence of SEQ ID NO: 2 or SEQ ID NO: 4 by one or several amino acids may be used to increase the yield of plants in the methods and constructs and plants of the invention.
Concerning epimerase-related like polypeptides, nucleic acids encoding epimerase-related like polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate human manipulation. Preferably the epimerase-related like polypeptide-encoding nucleic acid is from a plant, further preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably the nucleic acid is from the genus Populus, and most preferably the nucleic acid is from Populus trichocarpa.
Concerning PLPCase polypeptides, nucleic acids encoding PLPCase polypeptides may be derived from any natural or artificial source. The nucleic acid may be modified from its native form in composition and/or genomic environment through deliberate h uman manipulation. Preferably the PLPCase polypeptide-encoding nucleic acid is from a plant, further preferably from a dicotyledonous plant, more preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably the n ucleic acid is from Medicago truncatula. PLPCase polypeptides differing from the sequence of SEQ ID NO: 285 by one or several amino acids (substitution(s), insertion(s) and/or deletion(s) as defined above) may equally be useful to increase the yield of plants in the methods and constructs and plants of the invention. In another embodiment the present invention extends to recombinant chromosomal DNA comprising a nucleic acid sequence useful in the methods of the invention, wherein said nucleic acid is present in the chromosomal DNA as a result of recombinant methods, i.e. said nucleic acid is not in the chromosomal DNA in its native surrounding. Said recombinant chromosomal DNA may be a chromosome of native origin, with said nucleic acid inserted by recombinant means, or it may be a mini-chromosome or a non-native chromosomal structure, e.g. or an artificial chromosome. The nature of the chromosomal DNA may vary, as long as it allows for stable passing on to successive generations of the recombinant nucleic acid useful in the methods of the invention, and allows for expression of said nucleic acid in a living plant cell resulting in increased yield or increased yield related traits of the plant cell or a plant comprising the plant cell. In a further embodiment the recombinant chromosomal DNA of the invention is comprised in a plant cell.
Performance of the methods of the invention gives plants having enhanced yield-related traits. In particular performance of the methods of the invention gives plants having increased yield, especially increased seed yield relative to control plants. The terms "yield" and "seed yield" are described in more detail in the "definitions" section herein.
Reference herein to enhanced yield-related traits is taken to mean an increase of early vigour and/or in biomass (weight) of one or more parts of a plant, which may include (i) aboveground parts and preferably aboveground harvestable parts and/or (ii) parts below ground and preferably harvestable below ground. In particular, such harvestable parts are seeds, and performance of the methods of the invention results in plants having increased seed yield relative to the seed yield of control plants.
The present invention provides a method for increasing yield, especially seed yield of plants, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide as defined herein.
The present invention also provides a method for increasing yield, and more particularly increased seed yield and/or increased biomass, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide as defined herein.
The present invention also provides a method for increasing yield, especially enhancing root biomass of plants, relative to control plants, which method comprises modulating expression in a plant of a nucleic acid encoding a PLPCase polypeptide as defined herein.
According to a preferred feature of the present invention, performance of the methods of the invention gives plants having an increased growth rate relative to control plants. Therefore, according to the present invention, there is provided a method for increasing the growth rate of plants, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein.
Performance of the methods of the invention gives plants grown u nder non-stress conditions or under mild drought conditions increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under non-stress conditions or under mild drought conditions, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
Performance of the methods of the invention gives plants grown under conditions of drought, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of drought which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase- related like polypeptide, or a PLPCase polypeptide.
Performance of the methods of the invention gives plants grown under conditions of nutrient deficiency, particularly under conditions of nitrogen deficiency, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield-related traits in plants grown under conditions of nutrient deficiency, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide.
Performance of the methods of the invention gives plants grown under conditions of salt stress, increased yield relative to control plants grown under comparable conditions. Therefore, according to the present invention, there is provided a method for increasing yield in plants grown under conditions of salt stress, which method comprises modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, or an epimerase- related like polypeptide, or a PLPCase polypeptide.
The invention also provides genetic constructs and vectors to facilitate introduction and/or expression in plants of nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides. The gene constructs may be inserted into vectors, which may be commercially available, suitable for transforming into plants or host cells and suitable for expression of the gene of interest in the transformed cells. The invention also provides use of a gene construct as defined herein in the methods of the invention.
More specifically, the present invention provides a construct comprising:
(a) a nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein;
(b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
(c) a transcription termination sequence.
Preferably, the nucleic acid encoding a DUF642 polypeptide, or an epimerase-related like polypeptide, or a PLPCase polypeptide is as defined herein. The term "control sequence" and "termination sequence" are as defined herein. In a preferred embodiment, the present invention provides a construct comprising:
(a) a nucleic acid encoding a PLPCase polypeptide as represented by any of SEQ ID NO: 299, 303, 305, 313, 317, 337 or 347;
(b) one or more control sequences capable of driving expression of the nucleic acid sequence of (a); and optionally
(c) a transcription termination sequence.
The genetic construct of the invention may be comprised in a host cell, plant cell, seed, agricultural product or plant. Plants or host cells are transformed with a genetic construct such as a vector or an expression cassette comprising any of the nucleic acids described herein. Thus the invention furthermore provides plants or host cells transformed with a construct as described above. In particular, the invention provides plants transformed with a construct as described above, which plants have increased yield-related traits as described herein. In one embodiment the genetic construct of the invention confers increased yield or yield related traits(s) to a living plant cell when it has been introduced into said plant cell and express the nucleic acid encoding the DUF642 polypeptide, or the epimerase-related like polypeptide, or the PLPCase polypeptide, comprised in the genetic construct.
The skilled artisan is well aware of the genetic elements that must be present on the genetic construct in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter).
The promoter in such a genetic construct may be a non-native promoter to the nucleic acid described above, i .e. a promoter which does not regulate the expression of the herein disclosed polynucleotides in its native surrounding.
Advantageously, any type of promoter, whether natural or synthetic, may be used to drive expression of the nucleic acid sequence, but preferably the promoter is of plant origin. A constitutive promoter is particularly useful in the methods. Preferably the constitutive promoter is a ubiquitous constitutive promoter of medium strength. See the "Definitions" section herein for definitions of the various promoter types.
The constitutive promoter is preferably a ubiquitous constitutive promoter of medium strength . More preferably it is a plant derived promoter, e. g. a promoter of plant chromosomal origin, such as a GOS2 promoter or a promoter of substantially the same strength and having substantially the same expression pattern (a functionally equivalent promoter), more preferably the promoter is the promoter GOS2 promoter from rice. Further preferably the constitutive promoter is represented by a nucleic acid sequence substantially similar to SEQ ID NO: 189, or SEQ ID NO: 278, or SEQ ID NO: 361 , most preferably the constitutive promoter is as represented by SEQ ID NO: 189, or SEQ ID NO: 278, or SEQ ID NO: 361 . See the "Definitions" section herein for further examples of constitutive promoters.
Concerning DUF642 polypeptides, it should be clear that the applicability of the present invention is not restricted to the DUF642 polypeptide-encoding nucleic acid represented by SEQ I D NO: 1 or 3, nor is the applicability of the invention restricted to expression of a DUF642 polypeptide-encoding nucleic acid when driven by a constitutive promoter.
Concerning epimerase-related like polypeptides, it should be clear that the applicability of the present invention is not restricted to the epimerase-related like polypeptide-encoding nucleic acid represented by SEQ I D NO: 197, nor is the applicability of the invention restricted to expression of an epimerase-related like polypeptide-encoding nucleic acid when driven by a constitutive promoter, or when driven by a root-specific promoter. Concerning PLPCase polypeptides, it should be clear that the applicability of the present invention is not restricted to the PLPCase polypeptide-encoding nucleic acid represented by SEQ ID NO: 284, nor is the applicability of the invention restricted to expression of a PLPCase polypeptide-encoding nucleic acid when driven by a constitutive promoter.
Concerning DUF642 polypeptides, optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 189, operably linked to the nucleic acid encoding the DUF642 polypeptide. More preferably, the construct comprises a zein terminator (t-zein) linked to the 3' end of the DUF642 coding sequence. Most preferably, the expression cassette comprises a sequence having in increasing order of preference at least 95%, at least 96%, at least 97%, at least 98%, at l ea st 99% i d e nti ty to th e seq u e n ce re presen ted by S EQ I D N O : 1 87 o r 1 88 (pPRO::DUF642::t-zein sequence). Furthermore, one or more sequences encoding selectable markers may be present on the construct introduced into a plant.
Concerning epimerase-related l ike polypeptides, optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 278, operably linked to the nucleic acid encoding the epimerase-related like polypeptide. More preferably, the construct comprises a zein terminator (t-zein) linked to the 3' end of the cod i ng seq uence of an epi merase-related like polypeptide. Most preferably, the expression cassette comprises a sequence having in increasing order of preference at least 95%, at least 96%, at least 97%, at least 98%, at least 99% identity to the seq u ence represented by S E Q I D NO : 279 (pP RO : : E RL : :t-zein sequence). Furthermore, one or more sequences encoding selectable markers may be present on the construct introduced into a plant.
Concerning PLPCase polypeptides, optionally, one or more terminator sequences may be used in the construct introduced into a plant. Preferably, the construct comprises an expression cassette comprising a GOS2 promoter, substantially similar to SEQ ID NO: 361 , operably linked to the nucleic acid encoding the PLPCase polypeptide. More preferably, the expression cassette comprises the sequence represented by SEQ I D NO: 360 (pGOS2:: PLPCase::t-zein sequence). Furthermore, one or more sequences encoding selectable markers may be present on the construct introduced into a plant.
According to a preferred feature of the invention, the modulated expression is increased expression. Methods for increasing expression of nucleic acids or genes, or gene products, are well documented in the art and examples are provided in the definitions section.
As mentioned above, a preferred method for modulating expression of a nucleic acid encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide is by introducing and expressing in a plant a nucleic acid encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide; however the effects of performing the method, i.e. enhancing yield-related traits may also be achieved using other well known techniques, including but not limited to T-DNA activation tagging, TILLING, homologous recombination. A description of these techniques is provided in the definitions section.
The invention also provides a method for the production of transgenic plants having enhanced yield-related traits relative to control plants, comprising introduction and expression in a plant of any nucleic acid encoding a DUF642 polypeptide, or a epimerase- related like polypeptide, or a PLPCase polypeptide as defined herein.
More specifically, the present invention provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased yield, more particularly increased seed yield, which method comprises:
(i) introducing and expressing in a plant or plant cell a DU F642 polypeptide- encoding nucleic acid or a genetic construct comprising a DUF642 polypeptide- encoding nucleic acid; and
(ii) cultivati ng the plant cell un der cond itions promoti ng pl ant growth an d development.
The nucleic acid of (i) may be any of the nucleic acids capable of encoding a DUF642 polypeptide as defined herein. More specifically, the present invention also provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased yield, and more particuarly increased seed yield and/or increased biomass, which method comprises:
(i) introducing and expressing in a plant or plant cell an epimerase-related like polypeptide-encodi ng n ucleic acid or a genetic construct comprising an epimerase-related like polypeptide-encoding nucleic acid; and
(ii) cu ltivati ng th e plant cel l u nd er cond itions promoti ng plant growth and development.
The nucleic acid of (i) may be any of the nucleic acids capable of encoding an epimerase- related like polypeptide as defined herein.
More specifically, the present invention also provides a method for the production of transgenic plants having enhanced yield-related traits, particularly increased root biomass, which method comprises:
(i) introducing and expressing in a plant or plant cell a PLPCase polypeptide- encoding nucleic acid or a genetic construct comprising a PLPCase polypeptide- encoding nucleic acid; and (ii) cultivating the plant cell under conditions promoting plant growth and development.
The nucleic acid of (i) may be any of the nucleic acids capable of encoding a PLPCase polypeptide as defined herein.
Cultivating the plant cell under conditions promoting plant growth and development, may or may not include regeneration and/or growth to maturity. Accordingly, in a particular embodiment of the invention, the plant cell transformed by the method according to the invention is regenerable into a transformed plant. In another particular embodiment, the plant cell transformed by the method according to the invention is not regenerable into a transformed plant, i.e. cells that are not capable to regenerate into a plant using cell culture techniques known i n the art. Wh ile plants cells generally have the characteristic of totipotency, some plant cells can not be used to regenerate or propagate intact plants from said cells. In one embodiment of the invention the plant cells of the invention are such cells. In another embodiment the plant cells of the invention are plant cells that do not sustain themselves in an autotrophic way.
The nucleic acid may be introduced directly into a plant cell or into the plant itself (including introduction into a tissue, organ or any other part of a plant). According to a preferred feature of the present invention, the nucleic acid is preferably introduced into a plant or plant cell by transformation. The term "transformation" is described in more detail in the "definitions" section herein. In one embodiment the present invention extends to any plant cell or plant produced by any of the methods described herein, and to all plant parts and propagules thereof.
The present invention encompasses plants or parts thereof (including seeds) obtainable by the methods according to the present invention. The plants or plant parts or plant cells comprise a nucleic acid transgene encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein, preferably in a genetic construct such as an expression cassette. The present invention extends further to encompass the progeny of a primary transformed or transfected cell, tissue, organ or whole plant that has been produced by any of the aforementioned methods, the only requirement being that progeny exhibit the same genotypic and/or phenotypic characteristic(s) as those produced by the parent in the methods according to the invention.
I n a further embodi ment the invention extends to seeds comprising the expression cassettes of the invention, the genetic constructs of the invention, or the nucleic acids encoding the DUF642 polypeptides, or the epimerase-related like polypeptides, or the PLPCase polypeptides and/or the DUF642 polypeptides, or the epimerase-related like polypeptides, or the PLPCase polypeptides as described above. The invention also includes host cells containing an isolated nucleic acid encoding a DUF642 polypeptide, or a epimerase-related like polypeptide, or a PLPCase polypeptide as defined herein. In one embodiment host cells according to the invention are plant cells, yeasts, bacteria or fungi. Host plants for the nucleic acids, construct, expression cassette or the vector used in the method according to the invention are, in principle, advantageously all plants which are capable of synthesizing the polypeptides used in the inventive method. In a particular embodiment the plant cells of the invention overexpress the nucleic acid molecule of the invention.
The methods of the invention are advantageously applicable to any plant, in particular to any plant as defined herein . Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and d icotyledonous plants incl uding fodder or forage legumes, ornamental plants, food crops, trees or shrubs. According to an embodiment of the present invention, the plant is a crop plant. Examples of crop plants include but are not limited to chicory, carrot, cassava, trefoil, soybean, beet, sugar beet, sunflower, canola, alfalfa, rapeseed, linseed, cotton, tomato, potato and tobacco. According to another embodiment of th e p resen t i n ven ti on , th e pl a nt i s a m o n ocotyl ed o n o us p l a nt. Exam pl es of monocotyledonous plants include sugarcane. According to another embodiment of the present invention, the plant is a cereal. Examples of cereals include rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn , teff, milo and oats. In a particular embodiment the plants used in the methods of the invention are selected from the group consisting of maize, wheat, rice, soybean, cotton, oilseed rape including canola, sugarcane, sugar beet and alfalfa. Advantageously the methods of the invention are more efficient than the known methods, because the plants of the invention have increased yield and/or tolerance to an environmental stress compared to control plants used in comparable methods. In another embodiment of the present invention the plants of the invention and the plants used in the methods of the invention are sugarcane plants with increased biomass and/or increased sugar content of the shoot. In yet another embodiment of the present invention the plants of the invention and the plants used in the methods of the invention are sugarbeet plants with increased biomass and/or increased sugar content of the beets.
The invention also extends to harvestable parts of a plant such as, but not limited to seeds, leaves, fruits, flowers, stems, roots, rhizomes, tubers and bulbs, which harvestable parts comprise a recombinant nucleic acid encoding a DUF642 polypeptide, or a epimerase- related like polypeptide, or a PLPCase polypeptide. The invention furthermore relates to products derived or produced, preferably directly derived or produced, from a harvestable part of such a plant, such as dry pellets, meal or powders, oil, fat and fatty acids, starch or proteins. The invention also includes methods for manufacturing a product comprising a) growing the plants of the invention and b) producing said product from or by the plants of the invention or parts thereof, including seeds. In a further embodiment the methods comprise the steps of a) growing the plants of the invention, b) removing the harvestable parts as described herein from the plants and c) producing said product from, or with the harvestable parts of plants according to the invention.
Examples of such methods would be growing corn plants of the invention, harvesting the corn cobs and remove the kernels. These may be used as feedstuff or processed to starch and oil as agricultural products. The product may be produced at the site where the plant has been grown, or the plants or parts thereof may be removed from the site where the plants have been grown to produce the product. Typically, the plant is grown, the desired harvestable parts are removed from the plant, if feasible in repeated cycles, and the product made from the harvestable parts of the plant. The step of growing the plant may be performed only once each time the methods of the invention is performed, while allowing repeated times the steps of product production e.g. by repeated removal of harvestable parts of the plants of the invention and if necessary further processing of these parts to arrive at the product. It is also possible that the step of growing the plants of the invention is repeated and plants or harvestable parts are stored until the production of the product is then performed once for the accumulated plants or plant parts. Also, the steps of growing the plants and producing the product may be performed with an overlap in time, even simultaneously to a large extent, or sequentially. Generally the plants are grown for some time before the product is produced. In one embodiment the products produced by the methods of the invention are plant products such as, but not li mited to, a foodstuff, feedstuff, a food su pplement, feed supplement, fiber, cosmetic or pharmaceutical. In another embodiment the methods for production are used to make agricultural products such as, but not limited to, plant extracts, proteins, amino acids, carbohydrates, fats, oils, polymers, vitamins, and the like.
In yet another embodiment the polynucleotides or the polypeptides of the invention are comprised in an agricultural product. In a particular embodiment the nucleic acid sequences and protein sequences of the invention may be used as product markers, for example where an agricultural product was produced by the methods of the invention. Such a marker can be used to identify a product to have been produced by an advantageous process resulting not only in a greater efficiency of the process but also improved quality of the product due to increased quality of the plant material and harvestable parts used in the process. Such markers can be detected by a variety of methods known in the art, for example but not limited to PCR based methods for nucleic acid detection or antibody based methods for protein detection. The present invention also encompasses use of nucleic acids encoding DUF642 polypeptides, epimerase-related like polypeptides, or PLPCase polypeptides polypeptides as described herein and use of these DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides in enhancing any of the aforementioned yield- related traits in plants. For example, nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides described herein, or the DUF642 polypeptides, o r th e epimerase-related like polypeptides, or the PLPCase polypeptides themselves, may find use in breeding programmes in which a DNA marker is identified which may be genetically linked to a DUF642 polypeptide-encoding gene, or an epimerase-related like polypeptide-encoding gene, or a PLPCase polypeptide-encoding gene. The nucleic acids/genes, or the DUF642 polypeptides, or the epimerase-related like polypeptides, or the PLPCase polypeptides themselves may be used to define a molecular marker. This DNA or protein marker may then be used in breeding programmes to select plants having enhanced yield-related traits as defined herein in the methods of the invention. Furthermore, allelic variants of a DUF642 polypeptide-encoding nucleic acid/gene, or an epimerase-related like polypeptide-encoding nucleic acid/gene, o r a PLPCase polypeptide-encoding nucleic acid/gene may find use in marker-assisted breeding programmes. Nucleic acids encoding DUF642 polypeptides, or epimerase-related like polypeptides, or PLPCase polypeptides may also be used as probes for genetically and physically mapping the genes that they are a part of, and as markers for traits linked to those genes. Such information may be useful in plant breeding in order to develop lines with desired phenotypes.
Concerning DU F642 polypeptides, in one embodiment any comparison to determine sequence identity percentages is performed
in the case of a comparison of nucleic acids over the entire coding region of SEQ ID NO: 1 or SEQ ID NO: 3, or
in the case of a comparison of polypeptide sequences over the entire length of SEQ ID NO: 2 or SEQ ID NO: 4.
For example, a sequence identity of 50% sequence identity in this embodiment means that over the entire coding region of SEQ I D NO: 1 , 50 percent of all bases are identical between the sequence of SEQ I D NO: 1 and the related sequence. Similarly, in this embodiment a polypeptide sequence is 50 % identical to the polypeptide sequence of SEQ ID NO: 2, when 50 percent of the amino acids residues of the sequence as represented in SEQ I D NO: 2, are found in the polypeptide tested when comparing from the starting methionine to the end of the sequence of SEQ ID NO: 2.
Concerning epimerase-related like polypeptides, in one embodiment any comparison to determine sequence identity percentages is performed
- in the case of a comparison of nucleic acids over the entire coding region of
SEQ ID NO: 197, or
in the case of a comparison of polypeptide sequences over the entire length of SEQ ID NO: 198.
For example, a sequence identity of 50% sequence identity in this embodiment means that over the entire coding region of SEQ ID NO: 197, 50 percent of all bases are identical between the sequence of SEQ ID NO: 197 and the related sequence. Similarly, in this embodiment a polypeptide sequence is 50 % identical to the polypeptide sequence of SEQ ID NO: 198, when 50 percent of the amino acids residues of the sequence as represented in SEQ ID NO: 198, are found in the polypeptide tested when comparing from the starting methionine to the end of the sequence of SEQ ID NO: 198. Moreover concerning DUF642 polypeptides, the present invention relates to the following specific embodiments:
1 . A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, wherein said DUF642 polypeptide comprises an InterPro accession IPR006946 DU F642 domain , preferably said DU F642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
2. Method according to embodiment 1 , wherein said modulated expression is effected by introd ucing and expressing i n a plant said nucleic acid encoding said DU F642 polypeptide.
3. Method according to embodiment 1 or 2, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased biomass and/or increased seed yield relative to control plants.
4. Method according to any one of embodiments 1 to 3, wherein said enhanced yield- related traits are obtained under non-stress conditions.
5. Method according to any of embodiments 1 to 4, wherein said DUF642 polypeptide comprises one or more of the following motifs:
(i) Motif 1 : N[LAM][VL]KNG[DG]FEEGP[WYH][MI][FLI]P[NG][TS][STR][WL]GVL [LVI]P[PTS][NKM][LQDV][EDV][DE][ED][THY]S[PS]L[PS][GP]W[IMT][IV] (SEQ ID NO: 181 ),
(ii) Motif 2: [VLA][EKAT][KPR]G[SAM][LRH]Y[SA][LIV][TI]F[SG]A[AS]RTCAQ[DLAS] E[SVRL]L[NR][VI] (SEQ ID NO: 182),
(iii) Motif 3: D[PE][AT]CGP[LI][IL]D[AS][VIF]AI[KR] (SEQ ID NO: 183)
6. Method according to any one of embodiments 1 to 5, wherein said nucleic acid encoding a D U F642 i s of pl ant ori gin, preferably from a monocotyledonous plant, further preferably from the family Poaceae, more preferably from the genus Oryza, most preferably from Oryza sativa.
7. Method according to any one of embodiments 1 to 6, wherein said nucleic acid encoding a DUF642 encodes any one of the polypeptides listed in Table A1 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
8. Method accordi ng to any one of embodi ments 1 to 7, wherein said n ucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A1. 9. Method according to any one of embodiments 1 to 8, wherein said nucleic acid encodes the polypeptide represented by SEQ I D NO: 2 or S EQ I D NO: 4 or a nucleic acid encoding a polypeptide having at least 90% sequence identity to SEQ ID NO: 2 and/or SEQ ID NO: 4.
10. Method according to any one of embodiments 1 to 9 wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
1 1 . Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of embodiments 1 to 10, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9.
12. Construct comprising:
(i) nucleic acid encoding a DUF642 as defined in any of embodiments 1 and 5 to 9; (ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence.
13. Construct according to embodiment 12, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
14. Use of a construct according to embodiment 12 or 13 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants.
15. Plant, plant part or plant cell transformed with a construct according to embodiment 12 or 13.
16. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
17. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9 or a transgenic plant cell derived from said transgenic plant.
18. Transgenic plant according to embodiment 1 1 , 15 or 17, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn, teff, milo or oats. 19. Harvestable parts of a plant according to embodiment 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
20. Products derived from a plant according to embodiment 18 and/or from harvestable parts of a plant according to embodiment 19.
21 . Use of a nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 and 5 to 9 for enhanci ng yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
22. Plant having increased yield, particularly increased biomass and/or increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide, or a transgenic plant cell originating from or being part of said transgenic plant.
23. A method for the production of a product comprising the steps of growing the plants of the invention and producing said product from or by
a. the plants of the invention; or
b. parts, including seeds, of these plants.
24. Plant according to embodiment 1 1 , 15, or 21 , or a transgenic plant cell originating thereof, or a method according to embodiment 22, wherein said plant is a crop plant, preferably a dicot such as sugar beet, alfalfa, trefoil, chicory, carrot, cassava, cotton, soybean, canola or a monocot, such as sugarcane, or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
25. Construct according to embodiment 12 or 13 comprised in a plant cell.
26. Recombinant chromosomal DNA comprising the construct according to embodiment 12 or 13.
Moreover concerning epimerase-related like polypeptides, the present invention relates to the following specific items:
1. A m ethod for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide, wherein said epimerase-related like polypeptide comprises one or more of the following motifs:
(i) Motif 7: CREEGV[DE][QK]VFVD[AG]AH[AS]IG[QSC]V[PDE][VI][DN][VM][KR]
[ED]IGADFY[TV]SNLHKWFFCPP[SA]VAFL[YH] (SEQ ID NO: 273),
(ii) Motif 8: EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK] [RN] WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
(iii) Motif 9: S[LI]VDNATTAAAIVLQ[HQ][VAI][AG][WR][AS]FAEG[RKN]FA[KR][GN] D[AVT]V[LV]MLH[YC]AY[GQ][AS]VKKSI[EQH]AYV (SEQ ID NO: 275)
2. Method accord ing to item 1 , wherein said modulated expression is effected by introducing and expressing in a plant said nucleic acid encoding said epimerase- related like polypeptide.
3. Method according to item 1 or 2, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased biomass and/or increased seed yield relative to control plants.
4. Method accordi ng to any of items 1 to 3, wherein said epimerase-related like polypeptide as used herein comprises a conserved domain with at least 50% sequence identity to a conserved domain as represented by any one of:
amino acid coordinates 32 to 449 in SEQ ID NO:198 (motif 10);
- amino acid coordinates 47 to 276 in SEQ ID NO:198 (motif 1 1 );
- amino acid coordinates 92 to 364 in SEQ ID NO:198 (motif 12); and
amino acid coordinates 59 to 323 in SEQ ID NO: 198 (motif 13).
5. Method according to any of items 1 or 4, wherein said n ucleic acid encodes a polypeptide having at least 40 % overal l sequence identity to the ami no acid represented by SEQ ID NO: 198.
6. Method according to any of items 1 to 5, wherein said nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa.
7. Method according to any one of items 1 to 6, wherein said nucleic acid encoding said epimerase-related like polypeptide encodes any one of the polypeptides listed in Table
A2 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
8. Method according to any one of items 1 to 7, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A2. 9. Method according to any one of items 1 to 8, wherein said enhanced yield-related traits are obtained under non-stress conditions.
10. Method according to any one of items 1 to 8, wherein said enhanced yield-related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
1 . Method according to any one of items 1 to 0, wherein said nucleic acid is operably lin ked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
12. Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of items 1 to 1 1 , wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8.
13. Plant according to item 12 or a plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal , such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
14. Construct comprising:
(i) nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence.
15. Construct according to item 14, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
16. Use of a construct according to item 14 or 15 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants.
17. Plant, plant part or plant cell transformed with a construct according to item 14 or 15.
18. Plant according to item 17 or a plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
19. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
20. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8; or a transgenic plant cell derived from said transgenic plant.
21. Transgenic plant according to item 20 or a transgenic plant cell derived therefrom, wh erei n said plant is a crop pl ant, such as beet, sugarbeet or alfa lfa ; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats. 22. Harvestable parts of a plant according to any of items 12-13, 17-18 or 20-21 , wherein said harvestable parts are preferably shoot biomass and/or seeds.
23. Products derived from a plant according to any of items 12-13, 17-18 or 20-21 and/or from harvestable parts of a plant according to item 22.
24. Isolated nucleic acid molecule selected from:
(i) a nucleic acid represented by SEQ ID NO: 199 ;
(ii) the complement of a nucleic acid represented by SEQ ID NO: 199;
(iii) a nucleic acid encoding epimerase-related like polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90% , 91 %, 92%, 93%, 94%, 95%, 96% , 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs 7 to 13, and further preferably conferring enhanced yield- related traits relative to control plants.
(iv) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
25. Isolated polypeptide selected from:
(i) an amino acid sequence represented by SEQ ID NO: 200;
(ii) an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs 7 to 13, and further preferably conferring enhanced yield-related traits relative to control plants;
(iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
26. Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8 and 25; for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
27. Use of a nucleic acid as defined in item 24 and encoding an epimerase-related like polypeptide for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield in plants relative to control plants.
28. Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8 and 25; as molecular marker.
29. Use of a nucleic acid as defined in item 24 and encoding an epimerase-related like polypeptide as defined in any of items 1 and 4 to 8 and 25 as molecular marker.
30. A method for the production of a product comprising the steps of growing the plants according to item 12, 18 or 20 and producing said product from or by
(i) said plants; or
(ii) parts, including seeds, of said plants. 31. Construct according to item 14 or 15 comprised in a plant cell.
32. Recombinant chromosomal DNA comprising the construct according to item 14 or 15 comprised. Moreover concerning epimerase-related like polypeptides, the invention is in particular characterized by any one or more of the following embodiments:
I. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide by introducing and expressing in a plant said nucleic acid encoding said epimerase-related like polypeptide, wherein said epimerase-related like polypeptide has at least 80 % overall sequence identity to the amino acid represented by SEQ ID NO: 198.
II. Method according to embodiment I, wherein said epimerase-related like polypeptide comprises one or more of the following motifs:
(i) Motif 7: CREEGV[DE][QK]VFVD[AG]AH[AS]IG[QSC]V[PDE][VI][DN][VM][KR]
[ED]IGADFY[TV]SNLHKWFFCPP[SA]VAFL[YH] (SEQ ID NO: 273),
(ii) Motif 8: EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK] [RN]WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
(iii) Motif 9: S[LI]VDNATTAAAIVLQ[HQ][VAI][AG][WR][AS]FAEG[RKN]FA[KR][GN] D[AVT]V[LV]MLH[YC]AY[GQ][AS]VKKSI[EQH]AYV (SEQ ID NO: 275)
III. Method according to embodiment I or I I, wherein said enhanced yield-related traits comprises increased biomass.
IV. Method according to any one of embodiments I to I II, wherein said enhanced yield- related traits comprises increased seed yield relative to control plants.
V. Method according to any of embodiments I to IV, wherein said epimerase-related like polypeptide as used herein comprises at least two conserved domains selected from th e g rou p com pri si n g PyrdxlP-dep_Trfase_major (SSF53383), PTHR1 1601 , Aminotran_5 (PF00266) and PyrdxlP-dep_Trfase_major_sub1 (G3DSA:3.40.640.10), and preferably comprises i) an Aminotran_5 conserved domain and ii) at least one other co n s erved d om a i n se l e cted from th e g ro u p co m p ri si n g PyrdxIP- dep_Trfase_major (SSF53383), PTHR1 1601 , and PyrdxlP-dep_Trfase_major_sub1 (G3DSA:3.40.640.10),
VI. Method according to any of embodiments I to IV, wherein said epimerase-related like polypeptide comprises a conserved domain with at least 50% sequence identity to a conserved domain as represented by any one of:
- amino acid coordinates 32 to 449 in SEQ ID NO:198 (motif 10);
- amino acid coordinates 47 to 276 in SEQ ID NO:198 (motif 1 1 );
- amino acid coordinates 92 to 364 in SEQ ID NO:198 (motif 12); and
- amino acid coordinates 59 to 323 in SEQ ID NO: 198 (motif 13).
VII. Method according to any of embodiments I to VI, wherein said nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa.
VIII . Method according to any one of embodiments I to VI I , wherein said nucleic acid encoding said epimerase-related like polypeptide encodes any one of the polypeptides listed in Table A2 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
IX. Method according to any one of embodiments I to VI II , wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A2.
X. Method according to any one of embodiments I to IX, wherein said nucleic acid is operably linked to a GOS2 promoter, preferably to a GOS2 promoter from rice.
XI. Construct comprising:
(i) nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments I and V to IX;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i), and preferably a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice, and optionally
(iii) a transcription termination sequence.
XII. Plant, plant part or plant cell transformed with a construct according to embodiment XI. XIII. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments I and V to
IX; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
XIV. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from the introduction and expression therein of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodi ments I and V to IX; or a transgenic plant cell derived from said transgenic plant.
XV. Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments I and V to IX; for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
Moreover concerning PLPCase polypeptides, the present invention relates to the following specific embodiments:
1. A method for enhancing yield-related traits in plants relative to control plants, comprising m o d u l a t i n g e x p r e s s i o n i n a plant of a nucleic acid encoding a Phospholipase/carboxylesterase (PLPCase) polypeptide, wherein said PLPCase polypeptide comprises an I nterPro accession IPR003140 corresponding to PFAM accession number PF022030 Phospholipase/carboxylesterase (PLPCase) domain. 2. Method according to embodiment 1 , wherein said modulated expression is effected by introduci ng and expressing in a plant said nucleic acid encodi ng said PLPCase polypeptide.
3. Method according to embodiments 1 or 2, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased root biomass and/or increased seed yield relative to control plants.
4. Method according to any one of embodiments 1 to 3, wherein said enhanced yield- related traits are obtained under non-stress conditions.
5. Method according to any one of embodiments 1 to 3, wherein said enhanced yield- related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
6. Method according to any of embodiments 1 to 5, wherein said PLPCase polypeptide comprises one or more of the following motifs:
(i) Motif 14: E[FY]G[KR]T[HY]WRPKG[KR]HQATIVWLHGLGDNG[LSA]S[SW]SQLL [ED][ST]LPLPNIKWICPTA (SEQ ID NO: 348),
(ii) Motif 15: PDD[WIVL]EGLDASAAH[IV]ANLLS[TS]EP[AS]D[VI]K[VL]G[IV]G (SEQ ID
NO: 349),
(iii) Motif 16: FSMGAA[IT]ALYSA[TA]C[YF]A[MHL] (SEQ ID NO: 350)
7. Method according to any one of embodiments 1 to 6, wherein said nucleic acid encoding a PLPCase is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably from Medicago truncatula.
8. Method according to any one of embodiments 1 to 7, wherein said nucleic acid encoding a PLPCase encodes any one of the polypeptides listed in Table A3 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
9. Method according to any one of embodiments 1 to 8, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A3.
10. Method according to any one of embodiments 1 to 9, wherein said nucleic acid encodes the polypeptide represented by SEQ ID NO: 285.
1 1 . Method according to any one of embodiments 1 to 10, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
12. Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of embodiments 1 to 1 1 , wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10.
13. Construct comprising:
(i) nucleic acid encoding a PLPCase as defined in any of embodiments 1 and 6 to 10;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence.
14. Construct according to embodiment 13, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
15. Use of a construct according to embodiment 13 or 14 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants.
16. Plant, plant part or plant cell transformed with a construct according to embodiment 13 or 14.
17. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
18. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10 or a transgenic plant cell derived from said transgenic plant.
19. Transgenic plant according to embodiment 12, 16 or 18, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal , such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
20. Harvestable parts of a plant according to embodiment 1 8 or 19, wherein said harvestable parts are preferably root biomass and/or seeds.
21 . Products derived from a plant according to embodiment 1 8 or 19 and/or from harvestable parts of a plant according to embodiment 20.
22. Use of a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 1 and 6 to 10 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for root biomass, increased greenness index and/or increased seed yield in plants relative to control plants.
23. A method for the production of a product comprising the steps of growing the plants according to embodiment 16, 18 or 19 and producing said product from or by
(i) said plants; or
(ii) parts, including seeds, of said plants.
24. Construct according to embodiment 13 or 14 comprised in a plant cell.
The present invention also relates to the following embodiments:
1. A method for enhancing yield-related traits in plants relative to control plants, comprising introducing and expressing in a plant of a nucleic acid encoding a DUF642 polypeptide, wherein said DUF642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
2. Method according to embodiment 1 , wherein said nucleic acid encodes the polypeptide represented by S EQ I D NO: 2 or SEQ I D NO: 4 or a nucleic acid encodi ng a polypeptide having at least 90% sequence identity to SEQ ID NO: 2 and/or SEQ I D NO: 4.
3. Method according to any one of embodiments 1 to 9, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
4. Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of embodiments 1 to 3, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 to 3.
5. Construct comprising:
(i) nucleic acid encoding a DUF642 as defined in any of embodiments 1 to 3;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence. 6. Construct according to embodiment 5, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice. 7. Use of a construct according to embodiment 5 or 6 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants.
8. Plant, plant part or plant cell transformed with a construct according to embodiment 5 or 6.
9. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding a
DUF642 polypeptide as defined in any of embodiments 1 to 3; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development. 10. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 to 3 or a transgenic plant cell derived from said transgenic plant.
1 1 . Transgenic plant according to embodiment 4, 8 or 10, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn, teff, milo or oats.
12. Harvestable parts of a plant according to embodiment 1 1 , wherein said harvestable parts are preferably shoot biomass and/or seeds.
13. Products derived from a plant according to embodiment 1 1 and/or from harvestable parts of a plant according to embodiment 12.
14. Use of a n u cl e ic acid encoding a DUF642 polypeptide as defined in any of embodiments 1 to 3 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
15. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an epimerase- related like polypeptide by introducing and expressing in a plant said nucleic acid encoding said epimerase-related like polypeptide, wherein said epimerase-related like polypeptide has at least 80 % overall sequence identity to the amino acid represented by SEQ ID NO: 198. Method according to embodiment 15, wherein said epimerase-related like polypeptide comprises one or more of the following motifs:
(i) Motif 7: CREEGV[DE][QK]VFVD[AG]AH[AS]IG[QSC]V[PDE][VI][DN][VM][KR] [ED]IGADFY[TV]SNLHKWFFCPP[SA]VAFL[YH] (SEQ ID NO: 273),
(ii) Motif 8: EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK] [RN]WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274),
(iii) Motif 9: S[LI]VDNATTAAAIVLQ[HQ][VAI][AG][WR][AS]FAEG[RKN]FA[KR][GN] D[AVT]V[LV]MLH[YC]AY[GQ][AS]VKKSI[EQH]AYV (SEQ ID NO: 275) Method according to embodiment 15 or 16, wherein said enhanced yield-related traits comprises increased biomass. Method according to any one of embodiments 15 to 17, wherein said enhanced yield- related traits comprises increased seed yield relative to control plants. Method according to any of embodiments 15 to 18, wherein said epimerase-related like polypeptide as used herein comprises at least two conserved domains selected from the group comprising PyrdxIP-dep Trfase major (SSF53383), PTHR1 1601 , A m i n o t r a n _ 5 ( PF00266) and PyrdxlP-dep_Trfase_major_sub1 (G3DSA:3.40.640.1 0), and preferably com prises an Am inotra n_5 conserved domain and at least one other conserved domai ns selected from the group comprising PyrdxlP-dep_Trfase_major (SSF53383), PTHR1 1601 , and PyrdxIP- dep_Trfase_major_sub1 (G3DSA:3.40.640.10), Method according to any of embodiments 15 to 18, wherein said epimerase-related like polypeptide comprises a conserved domain with at least 50% sequence identity to a conserved domain as represented by any one of:
- amino acid coordinates 32 to 449 in SEQ ID NO:198 (motif 10);
- amino acid coordinates 47 to 276 in SEQ ID NO: 198 (motif 11 );
- amino acid coordinates 92 to 364 in SEQ ID NO: 198 (motif 12); and
- amino acid coordinates 59 to 323 in SEQ ID NO: 198 (motif 13). Method according to any of embodiments 15 to 20, wherein said nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa. Method according to any one of embodiments 15 to 21 , wherein said nucleic acid encoding said epimerase-related like polypeptide encodes any one of the polypeptides listed in Table A or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid. 23. Method according to any one of embodiments 15 to 22, wherein said nucleic aci sequence encodes an orthologue or paralogue of any of the polypeptides given i Table A2.
Method according to any one of embodiments 15 to 23, wherein said nucleic acid is operably linked to a GOS2 promoter, preferably to a GOS2 promoter from rice.
Construct comprising:
(i) nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 5 and 19 to 23;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i), and preferably a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice, and optionally
(iii) a transcription termination sequence.
Plant, plant part or plant cell transformed with a construct according to embodiment 25.
Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 15 and 19 to 23; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development. 28. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from the introduction and expression therein of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 15 and 19 to 23; or a transgenic plant cell derived from said transgenic plant.
29. Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of embodiments 15 and 19 to 23; for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
30. A method for enhancing yield-related traits in plants relative to control plants, comprising introducing and expressing in a plant of a nucleic acid encoding SEQ I D NO: 285 or homologues having 80% sequence identity to SEQ ID NO: 285.
31 . Method according to embodiment 30, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased root biomass and/or increased seed yield relative to control plants.
32. Method according to any one of embodiments 30 to 31 , wherein said enhanced yield- related traits are obtained under non-stress conditions.
33. Method according to any one of embodiments 30 to 31 , wherein said enhanced yield- related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency. 34. Method according to any one of embodiments 30 to 33, wherein said nucleic acid encoding a PLPCase is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably from Medicago truncatula. 35. Method according to any one of embodiments 30 to 34, wherein said nucleic acid encoding a PLPCase encodes any one of the polypeptides listed in Table A3 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid, provided said nucleic acid has 80% sequence identity to SEQ ID NO: 285.
36. Method according to any one of embodiments 30 to 35, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
37. Plant, plant part thereof, includi ng seeds, or plant cell, obtai nable by a method according to any one of embodiments 30 to 36, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 30 and 35 to 39.
38. Construct comprising:
(i) nucleic acid encoding a PLPCase as defined in any of embodiments 30 and 34 to 36;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence. 39. Construct according to embodiment 38, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
40. Use of a construct according to embodiment 38 or 39 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants.
41 . Plant, plant part or plant cell transformed with a construct according to embodiment 38 or 39.
Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants, comprising:
a. introducing and expressing in a plant cell or plant a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 30 and 34 to 36; and b. cultivating said plant cell or plant under conditions promoting plant growth and development.
Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a PLPCase polypeptide as defined in any of embodiments 30 and 34 to 36 or a transgenic plant cell derived from said transgenic plant.
Transgenic plant according to embodiment 37, 41 or 43, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats. 45. Harvestable parts of a plant according to embodiment 43 or 44, wherein said harvestable parts are preferably root biomass and/or seeds.
46. Prod ucts derived from a plant according to embodiment 43 or 44 and/or from harvestable parts of a plant according to embodiment 45.
47. Use of a n ucleic acid encod i ng a PLPCase polypeptide as defined in any of embodiments 30 and 34 to 36 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for root biomass, increased greenness index and/or increased seed yield in plants relative to control plants. Definitions
The following defin itions will be used throughout the present application . The section captions and headings in this application are for convenience and reference purpose only and should not affect in any way the meaning or interpretation of this application . The technical terms and expressions used within the scope of this application are generally to be given the meaning commonly applied to them in the pertinent art of plant biology, molecular biology, bioinformatics and plant breeding. All of the following term definitions apply to the complete content of this application. The term "essentially", "about", "approximately" and the like in connection with an attribute or a value, particularly also define exactly the attribute or exactly the value, respectively. The term "about" in the context of a given numeric value or range relates in particular to a value or range that is within 20%, within 10%, or within 5% of the value or range given. As used herein, the term "comprising" also encompasses the term "consisting of.
Peptide(s)/Protein(s)
The terms "peptides", "oligopeptides", "polypeptide" and "protein" are used interchangeably herein and refer to amino acids in a polymeric form of any length, linked together by peptide bonds, unless mentioned herein otherwise.
Polynucleotide(s)/Nucleic acid(s)/Nucleic acid sequence(s)/nucleotide sequence(s)
The terms "polynucleotide(s)", "nucleic acid sequence(s)", "nucleotide sequence(s)", "nucleic acid(s)", "nucleic acid molecule" are used i nterchangeably herein and refer to nucleotides, either ribonucleotides or deoxyribonucleotides or a combination of both , in a polymeric unbranched form of any length. Homologue(s)
"Homologues" of a protein encompass peptides, oligopeptides, polypeptides, proteins and enzymes havi ng ami no acid su bstitutions, deletions and/or i nsertions relative to the unmodified protein in question and having similar biological and functional activity as the unmodified protein from which they are derived.
Orthologues and paralogues are two d ifferent forms of homologues and encompass evolutionary concepts used to describe the ancestral relationships of genes. Paralogues are genes within the same species that have originated through duplication of an ancestral gene; orthologues are genes from different organ isms that have origi nated th rough speciation, and are also derived from a common ancestral gene.
A "deletion" refers to removal of one or more amino acids from a protein. An "insertion" refers to one or more amino acid residues being introduced into a predetermined site in a protein. Insertions may comprise N-terminal and/or C-terminal fusions as well as intra-sequence insertions of single or multiple amino acids. Generally, insertions within the amino acid sequence will be smaller than N- or C-terminal fusions, of the order of about 1 to 1 0 residues. Examples of N- or C-terminal fusion proteins or peptides include the binding domain or activation domain of a transcriptional activator as used in the yeast two-hybrid system, phage coat proteins, (histidine)-6-tag, glutathione S- transferase-tag, protein A, maltose-binding protein, dihydrofolate reductase, Tag*100 epitope, c-myc epitope, FLAG®-epitope, lacZ, CMP (calmodulin-binding peptide), HA epitope, protein C epitope and VSV epitope.
A "substitution" refers to replacement of amino acids of the protein with other amino acids having similar properties (such as similar hydrophobicity, hydrophilicity, antigenicity, propensity to form or break a-helical structures or β-sheet structures). Amino acid substitutions are typically of single residues, but may be clustered depending upon functional constraints placed upon the polypeptide and may range from 1 to 10 amino acids. The amino acid substitutions are preferably conservative amino acid substitutions. Conservative substitution tables are well known in the art (see for example Creighton (1984) Proteins. W.H. Freeman and Company (Eds) and Table 1 below).
Table 1 : Examples of conserved amino acid substitutions
Figure imgf000051_0001
Amino acid substitutions, deletions and/or insertions may readily be made using peptide synthetic techniques known in the art, such as solid phase peptide synthesis and the like, or by recombinant DNA manipulation. Methods for the manipulation of DNA sequences to produce substitution, insertion or deletion variants of a protein are well known in the art. For example, techniques for making substitution mutations at predetermined sites in DNA are well known to those skilled in the art and include M 13 mutagenesis, T7-Gen in vitro mutagenesis (USB, Cleveland, OH), QuickChange Site Directed mutagenesis (Stratagene, San Diego, CA), PCR-mediated site-directed mutagenesis or other site-directed mutagenesis protocols (see Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates)).
Derivatives
"Derivatives" include peptides, oligopeptides, polypeptides which may, compared to the amino acid sequence of the naturally-occurring form of the protein, such as the protein of interest, comprise substitutions of amino acids with non-naturally occurring amino acid residues, or additions of non-naturally occurring amino acid residues. "Derivatives" of a protein also encompass peptides, oligopeptides, polypeptides which comprise naturally occurring altered (glycosylated, acylated , prenylated, phosphorylated , myristoylated , sulphated etc.) or non-naturally altered amino acid residues compared to the amino acid sequence of a naturally-occurring form of the polypeptide. A derivative may also comprise on e or more non-amino acid substituents or additions compared to the amino acid sequence from which it is derived, for example a reporter molecule or other ligand, covalently or non-covalently bound to the amino acid sequence, such as a reporter molecule which is bound to facilitate its detection, and non-naturally occurring amino acid residues relative to the amino acid sequence of a naturally-occurring protein. Furthermore, "derivatives" also include fusions of the naturally-occurring form of the protein with tagging peptides such as FLAG, HIS6 or thioredoxin (for a review of tagging peptides, see Terpe, Appl. Microbiol. Biotechnol. 60, 523-533, 2003).
Domain, Motif/Consensus sequence/Signature
The term "domain" refers to a set of amino acids conserved at specific positions along an alignment of sequences of evolutionarily related proteins. While amino acids at other positions can vary between homologues, amino acids that are highly conserved at specific positions indicate amino acids that are likely essential in the structure, stability or function of a protein. Identified by their high degree of conservation in aligned sequences of a family of protein homologues, they can be used as identifiers to determine if any polypeptide in question belongs to a previously identified polypeptide family.
The term "motif or "consensus sequence" or "signature" refers to a short conserved region in the sequence of evolutionarily related proteins. Motifs are frequently highly conserved parts of domains, but may also include only part of the domain, or be located outside of conserved domain (if all of the amino acids of the motif fall outside of a defined domain).
Specialist databases exist for the identification of domains, for example, SMART (Schultz et al. (1998) Proc. Natl. Acad. Sci. USA 95, 5857-5864; Letunic et al. (2002) Nucleic Acids Res 30, 242-244), InterPro (Mulder et al., (2003) Nucl. Acids. Res. 31 , 315-318), Prosite (Bucher and Bairoch (1994), A generalized profile syntax for biomolecular sequences motifs and its function in automatic sequence interpretation . (I n) ISMB-94; Proceedings 2nd International Conference on Intelligent Systems for Molecular Biology. Altman R., Brutlag D. , Karp P. , Lathrop R., Searls D. , Eds., pp53-61 , AAAI Press, Menlo Park; Hulo et al., Nucl. Acids. Res. 32:D134-D137, (2004)), or Pfam (Bateman et al., Nucleic Acids Research 30(1 ): 276-280 (2002)). A set of tools for in silico analysis of protein sequences is available on the ExPASy proteomics server (Swiss Institute of Bioinformatics (Gasteiger et al., ExPASy: the proteomics server for in-depth protein knowledge and analysis, Nucleic Acids Res. 31 :3784-3788(2003)). Domains or motifs may also be identified using routine techniques, such as by sequence alignment.
Methods for the alignment of sequences for comparison are well known in the art, such methods include GAP, BESTFIT, BLAST, FASTA and TFASTA. GAP uses the algorithm of Needleman and Wunsch ((1970) J Mol Biol 48: 443-453) to find the global (i.e. spanning the complete sequences) alignment of two sequences that maximizes the number of matches and minimizes the number of gaps. The BLAST algorithm (Altschul et al. (1990) J Mol Biol 215: 403-10) calculates percent sequence identity and performs a statistical analysis of the similarity between the two sequences. The software for performing BLAST analysis is publicly available through the National Centre for Biotechnology I nformation (NCBI). Homologues may readily be identified using, for example, the ClustalW multiple sequence alignment algorithm (version 1 .83), with the default pairwise alignment parameters, and a scoring method in percentage. Global percentages of similarity and identity may also be determ in ed usin g one of the methods available in the MatGAT software package (Campanella et al. , BMC Bioinformatics. 2003 Jul 10;4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences.). Minor manual editing may be performed to optimise alignment between conserved motifs, as would be apparent to a person skilled in the art. Furthermore, instead of using full-length sequences for the identification of homologues, specific domains may also be used. The sequence identity values may be determined over the entire nucleic acid or amino acid sequence or over selected domains or conserved motif(s), using the programs mentioned above using the default parameters. For local alignments, the Smith-Waterman algorithm is particularly useful (Smith TF, Waterman MS (1981 ) J. Mol. Biol 147(1 );195-7). Reciprocal BLAST
Typically, this involves a first BLAST involving BLASTing a query sequence (for example using any of the sequences listed in Table A of the Examples section) against any sequence database, such as the publicly available NCBI database. BLASTN or TBLASTX (using standard default values) are general ly used when starting from a nucleotide sequence, and BLASTP or TBLASTN (using standard default values) when starting from a protein sequence. The BLAST results may optionally be filtered. The full-length sequences of either the filtered results or non-filtered results are then BLASTed back (second BLAST) against sequences from the organism from which the query sequence is derived. The results of the first and second BLASTs are then compared. A paralogue is identified if a high-ranking hit from the first blast is from the same species as from which the query sequence is derived, a BLAST back then ideally results in the query sequence amongst the highest hits; an orthologue is identified if a high-ranking hit in the first BLAST is not from the same species as from which the query sequence is derived, and preferably results upon BLAST back in the query sequence being among the highest hits.
High-ranking hits are those having a low E-value. The lower the E-value, the more significant the score (or in other words the lower the chance that the hit was found by chance). Computation of the E-value is well known i n the art. In addition to E-values, comparisons are also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In the case of large families, ClustalW may be used, followed by a neighbour joining tree, to help visualize clustering of related genes and to identify orthologues and paralogues.
Hybridisation
The term "hybridisation" as defined herein is a process wherein substantially homologous complementary nucleotide sequences anneal to each other. The hybridisation process can occur entirely in solution, i .e. both complementary nucleic acids are in solution. The hybridisation process can also occur with one of the complementary nucleic acids immobilised to a matrix such as magnetic beads, Sepharose beads or any other resin. The hybridisation process can furthermore occur with one of the complementary nucleic acids immobilised to a solid support such as a nitro-cellulose or nylon membrane or immobilised by e.g. photolithography to, for example, a siliceous glass support (the latter known as nucleic acid arrays or microarrays or as nucleic acid chips). In order to allow hybridisation to occur, the nucleic acid molecules are generally thermally or chemically denatured to melt a double strand into two single strands and/or to remove hairpi ns or other secondary structures from single stranded nucleic acids.
The term "stringency" refers to the conditions under which a hybridisation takes place. The stri ngency of hybridisation is influenced by conditions such as temperature, salt concentration, ionic strength and hybridisation buffer composition. Generally, low stringency conditions are selected to be about 30°C lower than the thermal melting point (Tm) for the specific sequence at a defined ionic strength and pH. Medium stringency conditions are when the temperature is 20°C below Tm, and high stringency conditions are when the temperature is 10°C below Tm. High stringency hybridisation conditions are typically used for isolating hybridising sequences that have high sequence similarity to the target nucleic acid seq uence. However, nucleic acids may deviate in sequence and still encode a substantially identical polypeptide, due to the degeneracy of the genetic code. Therefore medium stringency hybridisation conditions may sometimes be needed to identify such nucleic acid molecules. The Tm is the temperature under defined ionic strength and pH, at which 50% of the target sequence hybridises to a perfectly matched probe. The Tm is dependent upon the solution conditions and the base composition and length of the probe. For example, longer sequences hybridise specifically at higher temperatures. The maximum rate of hybridisation is obtained from about 16°C up to 32°C below Tm. The presence of monovalent cations in the hybridisation solution reduce the electrostatic repulsion between the two nucleic acid strands thereby promoting hybrid formation; this effect is visible for sodium concentrations of up to 0.4M (for higher concentrations, this effect may be ignored). Formamide reduces the melting temperature of DNA-DNA and DNA-RNA duplexes with 0.6 to 0.7°C for each percent formamide, and addition of 50% formamide allows hybridisation to be performed at 30 to 45°C, though the rate of hybridisation will be lowered. Base pair mismatches reduce the hybridisation rate and the thermal stability of the duplexes. On average and for large probes, the Tm decreases about 1 °C per % base mismatch. The Tm may be calculated using the following equations, depending on the types of hybrids:
1 ) DNA-DNA hybrids (Meinkoth and Wahl, Anal. Biochem., 138: 267-284, 1984):
Tm= 81 .5°C + 16.6xlogio[Na+]a + 0.41 x%[G/Cb] - 500x[Lc]-1 - 0.61 x% formamide 2) DNA-RNA or RNA-RNA hybrids:
Tm= 79.8°C+ 18.5 (logio[Na+]a) + 0.58 (%G/Cb) + 1 1 .8 (%G/Cb)2 - 820/Lc
3) oligo-DNA or oligo-RNAd hybrids:
For <20 nucleotides: Tm= 2 (ln)
For 20-35 nucleotides: Tm= 22 + 1 .46 (ln)
a or for other monovalent cation, but only accurate in the 0.01 -0.4 M range.
b only accurate for %GC in the 30% to 75% range.
c L = length of duplex in base pairs.
d oligo, oligonucleotide; ln, = effective length of primer = 2χ(ηο. of G/C)+(no. of A/T). Non-specific binding may be controlled using any one of a number of known techniques such as, for example, blocking the membrane with protein containing solutions, additions of heterologous RNA, DNA, and SDS to the hybridisation buffer, and treatment with Rnase. For non-homologous probes, a series of hybridizations may be performed by varying one of (i) progressively lowering the annealing temperature (for example from 68°C to 42°C) or (ii) progressively lowering the formamide concentration (for example from 50% to 0%) . The skilled artisan is aware of various parameters which may be altered during hybridisation and which will either maintain or change the stringency conditions.
Besides the hybridisation conditions, specificity of hybridisation typically also depends on the fu nction of post-hybridisation washes. To remove background resulting from nonspecific hybridisation, samples are washed with dilute salt solutions. Critical factors of such washes include the ionic strength and temperature of the final wash solution: the lower the salt concentration and the higher the wash temperature, the higher the stringency of the wash . Wash conditions are typical ly performed at or below hybridisation stringency. A positive hybridi sation gives a signal that is at least twice of that of the backgrou nd . Generally, suitable stringent cond itions for nucleic acid hybridisation assays or gene amplification detection procedures are as set forth above. More or less stringent conditions may also be selected. The skilled artisan is aware of various parameters which may be altered during washing and which will either maintain or change the stringency conditions.
For example, typical high stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 65°C in 1x SSC or at 42°C in 1x SSC and 50% formamide, followed by washing at 65°C in 0.3x SSC. Examples of medium stringency hybridisation conditions for DNA hybrids longer than 50 nucleotides encompass hybridisation at 50°C in 4x SSC or at 40°C in 6x SSC and 50% formamide, followed by washing at 50°C in 2x SSC. The length of the hybrid is the anticipated length for the hybridising nucleic acid. When nucleic acids of known sequence are hybridised, the hybrid length may be determined by aligning the sequences and identifying the conserved regions described herein . 1 xSSC is 0.1 5M NaCI and 1 5mM sodium citrate; the hybridisation solution and wash solutions may additionally include 5x Denhardt's reagent, 0.5-1.0% SDS, 100 μg/ml denatured, fragmented salmon sperm DNA, 0.5% sodium pyrophosphate.
For the purposes of defining the level of stringency, reference can be made to Sambrook et al. (2001 ) Molecular Cloning: a laboratory man ual, 3rd Edition, Cold Spring Harbor Laboratory Press, CSH, New York or to Current Protocols in Molecular Biology, John Wiley & Sons, N.Y. (1989 and yearly updates).
Splice variant
The term "splice variant" as used herein encompasses variants of a nucleic acid sequence in which selected introns and/or exons have been excised, replaced, displaced or added, or in which introns have been shortened or lengthened. Such variants will be ones in which the biological activity of the protein is substantially retained; this may be achieved by selectively retaining functional segments of the protein. Such splice variants may be found in nature or may be manmade. Methods for predicting and isolating such splice variants are well known in the art (see for example Foissac and Schiex (2005) BMC Bioinformatics 6: 25). Allelic variant
"Alleles" or "allelic variants" are alternative forms of a given gene, located at the same chromosomal position . Allelic variants encompass Single Nucleotide Polymorphisms (SNPs), as well as Small Insertion/Deletion Polymorphisms (INDELs). The size of INDELs is usually less than 100 bp. SNPs and INDELs form the largest set of sequence variants in naturally occurring polymorphic strains of most organisms.
Endogenous gene
Reference herein to an "endogenous" gene not only refers to the gene in question as found in a plant in its natural form (i.e. , without there being any human intervention), but also refers to that same gene (or a substantially homologous nucleic acid/gene) in an isolated form subsequently (re)introduced into a plant (a transgene). For example, a transgenic plant containing such a transgene may encounter a substantial reduction of the transgene expression and/or substantial reduction of expression of the endogenous gene. The isolated gene may be isolated from an organism or may be manmade, for example by chemical synthesis. Gene shuffling/Directed evolution
"Gene shuffling" or "directed evolution" consists of iterations of DNA shuffling followed by appropriate screening and/or selection to generate variants of nucleic acids or portions thereof encoding proteins having a modified biological activity (Castle et al., (2004) Science 304(5674): 1 151 -4; US patents 5,81 1 ,238 and 6,395,547).
Construct
Artificial DNA (such as but, not limited to plasmids or viral DNA) capable of replication in a host cell and used for introduction of a DNA sequence of interest into a host cell or host organism. Host cells of the invention may be any cell selected from bacterial cells, such as Escherichia coli or Agrobacterium species cells, yeast cells, fungal, algal or cyanobacterial cells or plant cells. The skilled artisan is well aware of the genetic elements that must be present on the genetic construct in order to successfully transform, select and propagate host cells containing the sequence of interest. The sequence of interest is operably linked to one or more control sequences (at least to a promoter) as described herein. Additional regulatory elements may include transcriptional as well as translational enhancers. Those skilled in the art will be aware of terminator and enhancer sequences that may be suitable for use in performing the invention. An intron sequence may also be added to the 5' untranslated region (UTR) or in the coding sequence to increase the amount of the mature message that accumulates in the cytosol, as described in the definitions section. Other control sequences (besides promoter, enhancer, silencer, intron sequences, 3'UTR and/or 5'UTR regions) may be protein and/or RNA stabilizing elements. Such sequences would be known or may readily be obtained by a person skilled in the art.
The genetic constructs of the invention may further include an origin of replication sequence that is required for maintenance and/or replication in a specific cell type. One example is when a genetic construct is required to be maintained in a bacterial cell as an episomal genetic element (e.g. plasmid or cosmid molecule). Preferred origins of replication include, but are not limited to, the f1 -ori and colEl For the detection of the successful transfer of the nucleic acid sequences as used in the methods of the invention and/or selection of transgenic plants comprising these nucleic acids, it is advantageous to use marker genes (or reporter genes). Therefore, the genetic construct may optionally comprise a selectable marker gene. Selectable markers are described in more detail in the "definitions" section herein. The marker genes may be removed or excised from the transgenic cell once they are no longer needed. Techniques for marker removal are known in the art, useful techniques are described above in the definitions section. Regulatory element/Control sequence/Promoter
The terms "regulatory element", "control sequence" and "promoter" are al l used interchangeably herein and are to be taken in a broad context to refer to regulatory nucleic acid sequences capable of effecting expression of the sequences to which they are ligated. The term "promoter" typically refers to a nucleic acid control sequence located upstream from the transcriptional start of a gene and which is involved in recognising and binding of RNA polymerase and other proteins, thereby directing transcription of an operably linked nucleic acid. Encompassed by the aforementioned terms are transcriptional regulatory sequences derived from a classical eukaryotic genomic gene (including the TATA box which is required for accurate transcription initiation , with or without a CCAAT box sequence) and additional regulatory elements (i.e. upstream activating sequences, enhancers and silencers) which alter gene expression in response to developmental and/or external stimuli , or in a tissue-specific manner. Also included within the term is a transcriptional regulatory sequence of a classical prokaryotic gene, in which case it may include a -35 box sequence and/or -10 box transcriptional regulatory sequences. The term "regulatory element" also encompasses a synthetic fusion molecule or derivative that confers, activates or enhances expression of a nucleic acid molecule in a cell, tissue or organ.
A "plant promoter" comprises regulatory elements, which mediate the expression of a coding sequence segment in plant cells. Accordingly, a plant promoter need not be of plant origin, but may originate from viruses or micro-organisms, for example from viruses which attack plant cells. The "plant promoter" can also originate from a plant cell, e.g. from the plant which is transformed with the nucleic acid sequence to be expressed in the inventive process and described herein. This also applies to other "plant" regulatory signals, such as "plant" terminators. The promoters upstream of the nucleotide sequences useful in the methods of the present invention can be modified by one or more nucleotide substitution(s), insertion(s) and/or deletion(s) without interfering with the functionality or activity of either the promoters, the open reading frame (ORF) or the 3'-regulatory region such as terminators or other 3' regulatory regions which are located away from the ORF. It is furthermore possible that the activity of the promoters is increased by modification of their sequence, or that they are replaced completely by more active promoters, even promoters from heterologous organisms. For expression in plants, the nucleic acid molecule must, as described above, be linked operably to or comprise a suitable promoter which expresses the gene at the right point in time and with the required spatial expression pattern.
For the identification of functionally equivalent promoters, the promoter strength and/or expression pattern of a candidate promoter may be analysed for example by operably linking the promoter to a reporter gene and assaying the expression level and pattern of the reporter gene in various tissues of the plant. Suitable well-known reporter genes include for example beta-glucuronidase or beta-galactosidase. The promoter activity is assayed by measuring the enzymatic activity of the beta-glucuronidase or beta-galactosidase. The promoter strength and/or expression pattern may then be compared to that of a reference promoter (such as the one used in the methods of the present invention). Alternatively, promoter strength may be assayed by quantifying mRNA levels or by comparing mRNA levels of the nucleic acid used in the methods of the present invention, with mRNA levels of housekeeping genes such as 18S rRNA, using methods known in the art, such as Northern blotting with densitometric analysis of autoradiograms, quantitative real-time PCR or RT- PCR (Heid et al., 1996 Genome Methods 6: 986-994). Generally by "weak promoter" is intended a promoter that drives expression of a coding sequence at a low level. By "low level" is intended at levels of about 1/10,000 transcripts to about 1/100,000 transcripts, to about 1/500,0000 transcripts per cell. Conversely, a "strong promoter" drives expression of a coding sequence at high level, or at about 1 /10 transcripts to about 1/100 transcripts to about 1/1000 transcripts per cell. Generally, by "medium strength promoter" is intended a promoter that drives expression of a coding sequence at a lower level than a strong promoter, in particular at a level that is in all instances below that obtained when under the control of a 35S CaMV promoter.
Operably linked
The term "operably linked" as used herein refers to a functional linkage between the promoter sequence and the gene of interest, such that the promoter sequence is able to initiate transcription of the gene of interest.
Constitutive promoter
A "constitutive promoter" refers to a promoter that is transcriptionally active during most, but not necessarily all, phases of growth and development and under most environmental cond itions, in at least one cel l , tissue or organ . Table 2a below gives examples of constitutive promoters.
Table 2a: Examples of constitutive promoters
Gene Source Reference
Actin McElroy et al, Plant Cell, 2: 163-171 , 1990
HMGP WO 2004/070039
CAMV 35S Odell et al, Nature, 313: 810-812, 1985
CaMV 19S Nilsson et al., Physiol. Plant. 100:456-462, 1997
GOS2 de Pater et al, Plant J Nov;2(6):837-44, 1992, WO 2004/065596
Ubiquitin Christensen et al, Plant Mol. Biol. 18: 675-689, 1992
Rice cyclophilin Buchholz et al, Plant Mol Biol. 25(5): 837-43, 1994
Maize H3 histone Lepetit et al, Mol. Gen. Genet. 231 :276-285, 1992
Alfalfa H3 histone Wu et al. Plant Mol. Biol. 11 :641 -649, 1988
Actin 2 An et al, Plant J. 10(1 ); 107-121 , 1996
34S FMV Sanger et al., Plant. Mol. Biol., 14, 1990: 433-443
Rubisco small subunit US 4,962,028 ocs Leisner (1988) Proc Natl Acad Sci USA 85(5): 2553
SAD1 Jain et al., Crop Science, 39 (6), 1999: 1696
SAD2 Jain et al., Crop Science, 39 (6), 1999: 1696
nos Shaw et al. (1984) Nucleic Acids Res. 12(20):7831 -7846
V-ATPase WO 01/14572
Super promoter WO 95/14098
G-box proteins WO 94/12015
Ubiquitous promoter
A "ubiquitous promoter" is active in substantially all tissues or cells of an organism. Developmentally-regulated promoter
A "developmentally-regulated promoter" is active during certain developmental stages or in parts of the plant that undergo developmental changes.
Inducible promoter
An "inducible promoter" has induced or increased transcription initiation in response to a chemical (for a review see Gatz 1997, Annu. Rev. Plant Physiol. Plant Mol. Biol., 48:89- 108), environmental or physical stimulus, or may be "stress-inducible", i.e. activated when a plant is exposed to various stress conditions, or a "pathogen-inducible" i.e. activated when a plant is exposed to exposure to various pathogens.
Organ-specific/Tissue-specific promoter
An "organ-specific" or "tissue-specific promoter" is one that is capable of preferentially initiating transcription in certain organs or tissues, such as the leaves, roots, seed tissue etc. For example, a "root-specific promoter" is a promoter that is transcriptionally active predominantly in plant roots, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Promoters able to initiate transcription in certain cells only are referred to herein as "cell-specific".
Examples of root-specific promoters are listed in Table 2b below:
Table 2b: Examples of root-specific promoters
Gene Source Reference
RCc3 Plant Mol Biol. 1995 Jan;27(2):237-48
Arabidopsis PHT1 Koyama et al. J Biosci Bioeng. 2005 Jan;99(1 ):38-42.; Mudge et al. (2002, Plant J. 31 :341 )
Medicago phosphate Xiao et al., 2006, Plant Biol (Stuttg). 2006 Jul;8(4):439-49 transporter
Arabidopsis Pyk10 Nitz et al. (2001) Plant Sci 161 (2): 337-346
root-expressible genes Tingey et al., EMBO J. 6: 1 , 1987.
tobacco auxin-inducible Van der Zaal et al., Plant Mol. Biol. 16, 983, 1991 . gene
β-tubulin Oppenheimer, et al., Gene 63: 87, 1988.
tobacco root-specific Conkling, et al., Plant Physiol. 93: 1203, 1990.
genes
B. napus G1 -3b gene United States Patent No. 5, 401 , 836
SbPRPI Suzuki et al., Plant Mol. Biol. 21 : 109-1 19, 1993.
LRX1 Baumberger et al. 2001 , Genes & Dev. 15:1 128
BTG-26 Brassica napus US 20050044585
LeAMTI (tomato) Lauter et al. (1996, PNAS 3:8139)
The LeNRT1 -1 (tomato) Lauter et al. (1996, PNAS 3:8139)
class I patatin gene Liu et al., Plant Mol. Biol. 17 (6): 1 139-1 154
(potato)
KDC1 (Daucus carota) Downey et al. (2000, J. Biol. Chem. 275:39420)
TobRB7 gene W Song (1997) PhD Thesis, North Carolina State University,
Raleigh, NC USA
OsRAB5a (rice) Wang et al. 2002, Plant Sci. 163:273
ALF5 (Arabidopsis) Diener et al. (2001 , Plant Cell 13:1625)
NRT2;1 Np (N. Quesada et al. (1997, Plant Mol. Biol. 34:265)
plumbaginifolia)
A "seed-specific promoter" is transcriptionally active predominantly in seed tissue, but not necessarily exclusively in seed tissue (in cases of leaky expression). The seed-specific promoter may be active during seed development and/or during germination. The seed specific promoter may be endosperm/aleurone/embryo specific. Examples of seed-specific promoters (endosperm/aleurone/embryo specific) are shown in Table 2c to Table 2f below. Further examples of seed-specific promoters are given in Qing Qu and Takaiwa (Plant Biotechnol. J. 2, 1 13-125, 2004), which disclosure is incorporated by reference herein as if fully set forth.
Table 2c: Examples of seed-specific promoters
Gene source Reference
seed-specific genes Simon et al., Plant Mol. Biol. 5: 191 , 1985;
Scofield et al., J. Biol. Chem. 262: 12202, 1987.;
Baszczynski et al., Plant Mol. Biol. 14: 633, 1990.
Brazil Nut albumin Pearson et al., Plant Mol. Biol. 18: 235-245, 1992.
legumin Ellis et al., Plant Mol. Biol. 10: 203-214, 1988.
glutelin (rice) Takaiwa et al., Mol. Gen. Genet. 208: 15-22, 1986;
Takaiwa et al., FEBS Letts. 221 : 43-47, 1987.
zein Matzke et al Plant Mol Biol, 14(3):323-32 1990
napA Stalberg et al, Planta 199: 515-519, 1996.
wheat LMW and HMW Mol Gen Genet 216:81 -90, 1989; NAR 17:461 -2, 1989 glutenin-1
wheat SPA Albani et al, Plant Cell, 9: 171-184, 1997
wheat α, β, γ-gliadins EMBO J. 3:1409-15, 1984
barley Itr1 promoter Diaz et al. (1995) Mol Gen Genet 248(5):592-8
barley B1 , C, D, hordein Theor Appl Gen 98:1253-62, 1999; Plant J 4:343-55,
1993; Mol Gen Genet 250:750-60, 1996
barley DOF Mena et al, The Plant Journal, 1 16(1 ): 53-62, 1998 blz2 EP99106056.7
synthetic promoter Vicente-Carbajosa et al., Plant J. 13: 629-640, 1998. rice prolamin NRP33 Wu et al, Plant Cell Physiology 39(8) 885-889, 1998 rice a-globulin Glb-1 Wu et al, Plant Cell Physiology 39(8) 885-889, 1998 rice OSH1 Sato et al, Proc. Natl. Acad. Sci. USA, 93: 81 17-8122,
1996
rice a-globulin REB/OHP-1 Nakase et al. Plant Mol. Biol. 33: 513-522, 1997 rice ADP-glucose pyrophos- Trans Res 6:157-68, 1997
phorylase
maize ESR gene family Plant J 12:235-46, 1997
sorghum a-kafirin DeRose et al., Plant Mol. Biol 32:1029-35, 1996
KNOX Postma-Haarsma et al, Plant Mol. Biol. 39:257-71 , 1999 rice oleosin Wu et al, J. Biochem. 123:386, 1998
sunflower oleosin Cummins et al., Plant Mol. Biol. 19: 873-876, 1992
PRO01 17, putative rice 40S WO 2004/070039
ribosomal protein
PRO0136, rice alanine unpublished
aminotransferase
PRO0147, trypsin inhibitor unpublished
ITR1 (barley)
PRO0151 , rice WSI18 WO 2004/070039
PRO0175, rice RAB21 WO 2004/070039
PRO005 WO 2004/070039
PRO0095 WO 2004/070039
a-amylase (Amy32b) Lanahan et al, Plant Cell 4:203-21 1 , 1992; Skriver et al,
Proc Natl Acad Sci USA 88:7266-7270, 1991
cathepsin β-like gene Cejudo et al, Plant Mol Biol 20:849-856, 1992
Barley Ltp2 Kalla et al., Plant J. 6:849-60, 1994
Chi26 Leah et al., Plant J. 4:579-89, 1994
Maize B-Peru Selinger et al., Genetics 149;1125-38,1998 Table 2d: examples of endosperm-specific promoters
Figure imgf000063_0001
Table 2e: Examples of embryo specific promoters:
Figure imgf000063_0002
Table 2f: Examples of aleurone-specific promoters:
Gene source Reference
a-amylase (Amy32b) Lanahan et al, Plant Cell 4:203-21 1 , 1992;
Skriver et al, Proc Natl Acad Sci USA 88:7266-7270, 1991 cathepsin β-like gene Cejudo et al, Plant Mol Biol 20:849-856, 1992
Barley Ltp2 Kalla et al., Plant J. 6:849-60, 1994
Chi26 Leah et al., Plant J. 4:579-89, 1994
Maize B-Peru Selinger et al., Genetics 149;1125-38,1998 A "green tissue-specific promoter" as defined herein is a promoter that is transcriptionally active predominantly in green tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Examples of green tissue-specific promoters which may be used to perform the methods of the invention are shown in Table 2g below.
Table 2g: Examples of green tissue-specific promoters
Figure imgf000064_0001
Another example of a tissue-specific promoter is a meristem-specific promoter, which is transcriptionally active predominantly in meristematic tissue, substantially to the exclusion of any other parts of a plant, whilst still allowing for any leaky expression in these other plant parts. Examples of green meristem-specific promoters which may be used to perform the methods of the invention are shown in Table 2h below.
Table 2h: Examples of meristem-specific promoters
Figure imgf000064_0002
Terminator
The term "terminator" encompasses a control sequence which is a DNA sequence at the end of a transcriptional unit which signals 3' processing and polyadenylation of a primary transcript and termination of transcription. The terminator can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The terminator to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
Selectable marker (gene)/Reporter gene
"Selectable marker", "selectable marker gene" or "reporter gene" includes any gene that confers a phenotype on a cell in which it is expressed to facilitate the identification and/or selection of cells that are transfected or transformed with a nucleic acid construct of the invention. These marker genes enable the identification of a successful transfer of the nucleic acid molecules via a series of different principles. Suitable markers may be selected from markers that confer antibiotic or herbicide resistance, that introduce a new metabolic trait or that allow visual selection. Examples of selectable marker genes include genes conferring resistance to antibiotics (such as nptl l that phosphorylates neomycin and kanamycin, or hpt, phosphorylating hygromycin, or genes conferring resistance to, for example, bleomycin, streptomycin, tetracyclin, chloramphenicol, ampicillin, gentamycin, geneticin (G41 8), spectinomycin or blasticidin), to herbicides (for example bar which provides resistance to Basta®; aroA or gox providing resistance against glyphosate, or the genes conferri ng resistance to, for exampl e, i midazolinone, phosph inoth rici n or sulfonylurea), or genes that provide a metabolic trait (such as manA that allows plants to use mannose as sole carbon source or xylose isomerase for the utilisation of xylose, or antinutritive markers such as the resistance to 2-deoxyglucose). Expression of visual marker genes results in the formation of colour (for example β-glucuronidase, GUS or β- galactosidase with its coloured substrates, for example X-Gal), luminescence (such as the luciferin/luceferase system) or fluorescence (Green Fluorescent Protein , GFP, and derivatives thereof). This list represents only a small number of possible markers. The skilled worker is familiar with such markers. Different markers are preferred, depending on the organism and the selection method.
It is known that upon stable or transient integration of nucleic acids into plant cells, only a minority of the cells takes up the foreign DNA and, if desired, integrates it into its genome, depending on the expression vector used and the transfection technique used. To identify and select these integrants, a gene coding for a selectable marker (such as the ones described above) is usually introduced into the host cells together with the gene of interest. These markers can for example be used in mutants in which these genes are not functional by, for example, deletion by conventional methods. Furthermore, nucleic acid molecules encoding a selectable marker can be introduced into a host cell on the same vector that comprises the sequence encoding the polypeptides of the invention or used in the methods of the invention, or else in a separate vector. Cells which have been stably transfected with the introduced nucleic acid can be identified for example by selection (for example, cells which have integrated the selectable marker survive whereas the other cells die).
Since the marker genes, particularly genes for resistance to antibiotics and herbicides, are no longer required or are undesired in the transgenic host cell once the nucleic acids have been introduced successfully, the process according to the invention for introducing the nucleic acids advantageously employs techniques which enable the removal or excision of these marker genes. One such a method is what is known as co-transformation. The co- transformation method employs two vectors simultaneously for the transformation, one vector bearing the nucleic acid according to the invention and a second bearing the marker gene(s). A large proportion of transformants receives or, in the case of plants, comprises (up to 40% or more of the transformants), both vectors. In case of transformation with Agrobacteria, the transformants usually receive only a part of the vector, i.e. the sequence flanked by the T-DNA, which usually represents the expression cassette. The marker genes can subsequently be removed from the transformed plant by performing crosses. In another method, marker genes integrated into a transposon are used for the transformation together with desired nucleic acid (known as the Ac/Ds technology). The transformants can be crossed with a transposase source or the transformants are transformed with a nucleic acid construct conferring expression of a transposase, transiently or stable. In some cases (approx. 10%), the transposon jumps out of the genome of the host cell once transformation has taken place successfully and is lost. In a further number of cases, the transposon jumps to a different location. In these cases the marker gene must be eliminated by performing crosses. In microbiology, techniques were developed which make possible, or facilitate, the detection of such events. A further advantageous method relies on what is known as recombination systems; whose advantage is that elimination by crossing can be dispensed with. The best-known system of this type is what is known as the Cre/lox system. Cre1 is a recombinase that removes the sequences located between the loxP sequences. If the marker gene is integrated between the loxP sequences, it is removed once transformation has taken place successfully, by expression of the recombinase. Further recombination systems are the HIN/HIX, FLP/FRT and REP/STB system (Tribble et al. , J. Biol. Chem., 275, 2000: 22255-22267; Velmurugan et al., J. Cell Biol. , 149, 2000: 553-566). A site- specific integration into the plant genome of the nucleic acid sequences according to the invention is possible. Naturally, these methods can also be applied to microorganisms such as yeast, fungi or bacteria.
Transgenic/Transgene/Recombinant
For the purposes of the invention, "transgenic", "transgene" or "recombinant" means with regard to, for example, a nucleic acid sequence, an expression cassette, gene construct or a vector comprising the nucleic acid sequence or an organism transformed with the nucleic acid sequences, expression cassettes or vectors according to the invention, all those constructions brought about by recombinant methods in which either
(a) the nucleic acid sequences encoding proteins useful in the methods of the invention, or
(b) genetic control sequence(s) which is operably linked with the nucleic acid sequence according to the invention, for example a promoter, or
(c) a) and b)
are not located in their natural genetic environment or have been modified by recombinant methods, it being possible for the modification to take the form of, for example, a substitution, addition, deletion, inversion or insertion of one or more nucleotide residues. The natural genetic environment is understood as meaning the natural genomic or chromosomal locus in the original plant or the presence in a genomic library. In the case of a genomic library, the natural genetic environment of the nucleic acid sequence is preferably retained, at least in part. The environment flanks the nucleic acid sequence at least on one side and has a sequence length of at least 50 bp, preferably at least 500 bp, especially preferably at least 1000 bp, most preferably at least 5000 bp. A naturally occurring expression cassette - for example the naturally occurring combination of the natural promoter of the nucleic acid sequences with the corresponding nucleic acid sequence encoding a polypeptide useful in the methods of the present invention, as defined above - becomes a transgenic expression cassette when this expression cassette is modified by non-natural, synthetic ("artificial") methods such as, for example, mutagenic treatment. Suitable methods are described, for example, in US 5,565,350 or WO 00/15815.
A transgenic plant for the purposes of the invention is thus understood as meaning, as above, that the nucleic acids used in the method of the invention are not present in, or originating from, the genome of said plant, or are present in the genome of said plant but not at their natural locus in the genome of said plant, it being possible for the nucleic acids to be expressed homologously or heterologously. However, as mentioned, transgenic also means that, while the nucleic acids according to the invention or used in the inventive method are at their natural position in the genome of a plant, the sequence has been modified with regard to the natural sequence, and/or that the regulatory sequences of the natural sequences have been modified. Transgenic is preferably understood as meaning the expression of the nucleic acids according to the invention at an unnatural locus in the genome, i.e. homologous or, preferably, heterologous expression of the nucleic acids takes place. Preferred transgenic plants are mentioned herein.
It shall further be noted that in the context of the present invention, the term "isolated nucleic acid" or "isolated polypeptide" may in some instances be considered as a synonym for a "recombinant nucleic acid" or a "recombinant polypeptide", respectively and refers to a nucleic acid or polypeptide that is not located in its natural genetic environment and/or that has been modified by recombinant methods. Modulation
The term "modulation" means in relation to expression or gene expression, a process in which the expression level is changed by said gene expression in comparison to the control plant, the expression level may be increased or decreased. The original, unmodulated expression may be of any kind of expression of a structural RNA (rRNA, tRNA) or mRNA with subsequent translation. For the purposes of this invention, the original unmodulated expression may also be absence of any expression. The term "modulating the activity" shall mean any change of the expression of the inventive nucleic acid sequences or encoded proteins, which leads to increased yield and/or increased growth of the plants. The expression can increase from zero (absence of, or immeasurable expression) to a certain amount, or can decrease from a certain amount to immeasurable small amounts or zero. Expression
The term "expression" or "gene expression" means the transcription of a specific gene or specific genes or specific genetic construct. The term "expression" or "gene expression" in particular means the transcription of a gene or genes or genetic construct into structural RNA (rRNA, tRNA) or imRNA with or without subsequent translation of the latter into a protein. The process includes transcription of DNA and processing of the resulting mRNA product.
Increased expression/overexpression
The term "increased expression" or "overexpression" as used herein means any form of expression that is additional to the original wild-type expression level. For the purposes of this invention, the original wild-type expression level might also be zero, i.e. absence of expression or immeasurable expression.
Methods for increasing expression of genes or gene products are well documented in the art and include, for example, overexpression driven by appropriate promoters, the use of transcription enhancers or translation enhancers. Isolated nucleic acids which serve as promoter or enhancer elements may be introduced in an appropriate position (typically upstream) of a non-heterologous form of a polynucleotide so as to upregulate expression of a nucleic acid encoding the polypeptide of interest. For example, endogenous promoters may be altered in vivo by mutation, deletion, and/or substitution (see, Kmiec, US 5,565,350; Zarling et al., W09322443), or isolated promoters may be introduced into a plant cell in the proper orientation and distance from a gene of the present invention so as to control the expression of the gene. If polypeptide expression is desired, it is generally desirable to include a polyadenylation region at the 3'-end of a polynucleotide coding region. The polyadenylation region can be derived from the natural gene, from a variety of other plant genes, or from T-DNA. The 3' end sequence to be added may be derived from, for example, the nopaline synthase or octopine synthase genes, or alternatively from another plant gene, or less preferably from any other eukaryotic gene.
An intron sequence may also be added to the 5' untranslated region (UTR) or the coding sequence of the partial coding sequence to increase the amount of the mature message that accumulates in the cytosol. Inclusion of a spliceable intron in the transcription unit in both plant and animal expression constructs has been shown to increase gene expression at both the mRNA and protein levels up to 1000-fold (Buchman and Berg (1988) Mol. Cell biol. 8: 4395-4405; Callis et al. (1987) Genes Dev 1 :1 183-1200). Such intron enhancement of gene expression is typically greatest when placed near the 5' end of the transcription unit. Use of the maize introns Adh1 -S intron 1 , 2, and 6, the Bronze-1 intron are known in the art. For general information see: The Maize Handbook, Chapter 1 16, Freeling and Walbot, Eds., Springer, N.Y. (1994).
Decreased expression
Reference herein to "decreased expression" or "reduction or substantial elimination" of expression is taken to mean a decrease in endogenous gene expression and/or polypeptide levels and/or polypeptide activity relative to control plants. The reduction or substantial elimination is in increasing order of preference at least 10%, 20%, 30%, 40% or 50%, 60%, 70%, 80%, 85%, 90%, or 95%, 96%, 97%, 98%, 99% or more reduced compared to that of control plants.
For the reduction or substantial elimination of expression an endogenous gene in a plant, a sufficient length of substantially contiguous nucleotides of a nucleic acid sequence is required. In order to perform gene silencing, this may be as little as 20, 19, 18, 17, 16, 15, 14, 13, 12, 1 1 , 10 or fewer nucleotides, alternatively this may be as much as the entire gene (including the 5' and/or 3' UTR, either in part or in whole). The stretch of substantially contiguous nucleotides may be derived from the nucleic acid encoding the protein of interest (target gene), or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest. Preferably, the stretch of substantially contiguous nucleotides is capable of forming hydrogen bonds with the target gene (either sense or antisense strand), more preferably, the stretch of substantially contiguous nucleotides has, in increasing order of preference, 50%, 60%, 70%, 80%, 85%, 90%, 95%, 96%, 97% , 98% , 99% , 100% seq uence identity to the target gene (either sense or antisense strand). A nucleic acid sequence encoding a (functional) polypeptide is not a requirement for the various methods discussed herein for the reduction or substantial elimination of expression of an endogenous gene. This reduction or substantial elimination of expression may be achieved using routine tools and techn iques. A preferred method for the reduction or substantial elimination of endogenous gene expression is by introducing and expressing in a plant a genetic construct into which the nucleic acid (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of any one of the protein of interest) is cloned as an inverted repeat (in part or completely), separated by a spacer (non-coding DNA).
In such a preferred method, expression of the endogenous gene is reduced or substantially eliminated through RNA-mediated silencing using an inverted repeat of a nucleic acid or a part thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), preferably capable of forming a hairpin structure. The inverted repeat is cloned in an expression vector comprising control sequences. A non- coding DNA nucleic acid sequence (a spacer, for example a matrix attachment region fragment (MAR), an intron, a polylinker, etc.) is located between the two inverted nucleic acids forming the inverted repeat. After transcription of the inverted repeat, a chimeric RNA with a self-complementary structure is formed (partial or complete). This double-stranded RNA structure is referred to as the hairpin RNA (hpRNA). The hpRNA is processed by the plant into siRNAs that are incorporated into an RNA-induced silencing complex (RISC). The RISC further cleaves the mRNA transcripts, thereby substantially reducing the number of imRNA transcripts to be translated into polypeptides. For further general details see for example, Grierson et al. (1998) WO 98/53083; Waterhouse et al. (1999) WO 99/53050).
Performance of the methods of the invention does not rely on introducing and expressing in a plant a genetic construct into which the nucleic acid is cloned as an inverted repeat, but any one or more of several well-known "gene silencing" methods may be used to achieve the same effects.
One such method for the reduction of endogenous gene expression is RNA-mediated silencing of gene expression (downregulation). Silencing in this case is triggered in a plant by a double stranded RNA sequence (dsRNA) that is substantially similar to the target endogenous gene. This dsRNA is further processed by the plant into about 20 to about 26 nucleotides called short interfering RNAs (siRNAs). The siRNAs are incorporated into an RNA-i nd uced silencing complex (RI SC) that cleaves the m RNA transcript of the endogenous target gene, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. Preferably, the double stranded RNA sequence corresponds to a target gene.
Another example of an RNA silencing method involves the introduction of nucleic acid sequences or parts thereof (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest) in a sense orientation into a plant. "Sense orientation" refers to a DNA sequence that is homologous to an mRNA transcript thereof. Introduced into a plant would therefore be at least one copy of the nucleic acid sequence. The additional nucleic acid sequence wi ll reduce expression of the endogenous gene, giving rise to a phenomenon known as co-suppression. The reduction of gene expression will be more pronounced if several additional copies of a nucleic acid sequence are introduced into the plant, as there is a positive correlation between high transcript levels and the triggering of co-suppression.
Another example of an RNA silencing method involves the use of antisense nucleic acid sequences. An "antisense" nucleic acid sequence comprises a nucleotide sequence that is complementary to a "sense" nucleic acid sequence encoding a protein, i.e. complementary to the coding strand of a double-stranded cDNA molecule or complementary to an mRNA transcript sequence. The antisense nucleic acid sequence is preferably complementary to the endogenous gene to be silenced. The complementarity may be located in the "coding region" and/or in the "non-coding region" of a gene. The term "coding region" refers to a region of the nucleotide sequence comprising codons that are translated into amino acid residues. The term "non-coding region" refers to 5' and 3' sequences that flank the coding region that are transcribed but not translated into amino acids (also referred to as 5' and 3' untranslated regions).
Antisense nucleic acid sequences can be designed according to the rules of Watson and Crick base pairing. The antisense nucleic acid sequence may be complementary to the entire nucleic acid sequence (in this case a stretch of substantially contiguous nucleotides derived from the gene of interest, or from any nucleic acid capable of encoding an orthologue, paralogue or homologue of the protein of interest), but may also be an oligonucleotide that is antisense to only a part of the nucleic acid sequence (including the mRNA 5' and 3' UTR). For example, the antisense oligonucleotide sequence may be complementary to the region surrounding the translation start site of an mRNA transcript encoding a polypeptide. The length of a suitable antisense oligonucleotide sequence is known in the art and may start from about 50, 45, 40, 35, 30, 25, 20, 15 or 10 nucleotides in length or less. An antisense nucleic acid sequence according to the invention may be constructed using chemical synthesis and enzymatic ligation reactions using methods known in the art. For example, an antisense nucleic acid sequence (e.g., an antisense oligonucleotide sequence) may be chemically synthesized usi ng naturally occurring nucleotides or variously modified nucleotides designed to increase the biological stability of the molecules or to increase the physical stability of the duplex formed between the antisense and sense nucleic acid sequences, e.g. , phosphorothioate derivatives and acridine substituted nucleotides may be used. Examples of modified nucleotides that may be used to generate the antisense nucleic acid sequences are well known in the art. Known nucleotide modifications include methylation, cyclization and 'caps' and substitution of one or more of the naturally occurring nucleotides with an analogue such as inosine. Other modifications of nucleotides are well known in the art.
The antisense nucleic acid sequence can be produced biologically using an expression vector into which a nucleic acid sequence has been subcloned in an antisense orientation (i.e., RNA transcribed from the inserted nucleic acid will be of an antisense orientation to a target nucleic acid of interest). Preferably, production of antisense nucleic acid sequences in plants occurs by means of a stably integrated nucleic acid construct comprising a promoter, an operably linked antisense oligonucleotide, and a terminator.
The nucleic acid molecules used for silencing in the methods of the invention (whether introduced into a plant or generated in situ) hybridize with or bind to mRNA transcripts and/or genomic DNA encoding a polypeptide to thereby inhibit expression of the protein, e.g., by inhibiting transcription and/or translation. The hybridization can be by conventional nucleotide complementarity to form a stable duplex, or, for example, in the case of an antisense nucleic acid sequence which binds to DNA duplexes, through specific interactions in the major groove of the double helix. Antisense nucleic acid sequences may be introduced into a plant by transformation or direct injection at a specific tissue site. Alternatively, antisense nucleic acid sequences can be modified to target selected cells and then administered systemically. For example, for systemic administration, antisense nucleic acid sequences can be modified such that they specifically bind to receptors or antigens expressed on a selected cell surface, e.g., by linking the antisense nucleic acid sequence to peptides or antibodies which bind to cell surface receptors or antigens. The antisense nucleic acid sequences can also be delivered to cells using the vectors described herein.
According to a further aspect, the antisense nucleic acid sequence is an a-anomeric nucleic acid seq uence. An a-anomeric nucleic acid sequence forms specific double-stranded hybrids with complementary RNA in which, contrary to the usual b-units, the strands run parallel to each other (Gaultier et al. (1987) Nucl Ac Res 15: 6625-6641 ). The antisense nucleic acid sequence may also comprise a 2'-o-methylribonucleotide (Inoue et al. (1987) Nucl Ac Res 15, 6131 -6148) or a chimeric RNA-DNA analogue (Inoue et al. (1987) FEBS Lett. 215, 327-330). The reduction or substantial elimination of endogenous gene expression may also be performed using ribozymes. Ribozymes are catalytic RNA molecules with ribonuclease activity that are capable of cleaving a single-stranded nucleic acid sequence, such as an mRNA, to which they have a complementary region. Thus, ribozymes (e.g., hammerhead ribozymes (described in Haselhoff and Gerlach (1988) Nature 334, 585-591) can be used to catalytically cleave mRNA transcripts encoding a polypeptide, thereby substantially reducing the number of mRNA transcripts to be translated into a polypeptide. A ribozyme having specificity for a nucleic acid sequence can be designed (see for example: Cech et al. U.S. Patent No. 4,987,071 ; and Cech et al. U.S. Patent No. 5, 1 16,742). Alternatively, mRNA transcripts corresponding to a nucleic acid sequence can be used to select a catalytic RNA having a specific ribonuclease activity from a pool of RNA molecules (Bartel and Szostak (1993) Science 261 , 141 1 -1418). The use of ribozymes for gene silencing in plants is known in the art (e.g., Atkins et al. (1994) WO 94/00012; Lenne et al. (1995) WO 95/03404; Lutziger et al. (2000) WO 00/00619; Prinsen et al. (1997) WO 97/13865 and Scott et al. (1997) WO 97/381 16).
Gene silencing may also be achieved by insertion mutagenesis (for example, T-DNA insertion or transposon insertion) or by strategies as described by, among others, Angell and Bau lcombe ((1999) Plant J 20(3): 357-62), (Amplicon VIGS WO 98/36083), or Baulcombe (WO 99/15682).
Gene silencing may also occur if there is a mutation on an endogenous gene and/or a mutation on an isolated gene/nucleic acid subsequently introduced into a plant. The reduction or substantial elimination may be caused by a non-functional polypeptide. For example, the polypeptide may bind to various interacting proteins; one or more mutation(s) and/or truncation(s) may therefore provide for a polypeptide that is still able to bind interacting proteins (such as receptor proteins) but that cannot exhibit its normal function (such as signalling ligand).
A further approach to gene silencing is by targeting nucleic acid sequences complementary to the regulatory region of the gene (e.g., the promoter and/or enhancers) to form triple helical structures that prevent transcription of the gene in target cells. See Helene, C , Anticancer Drug Res. 6, 569-84, 1991 ; Helene et al., Ann. N.Y. Acad. Sci. 660, 27-36 1992; and Maher, LJ. Bioassays 14, 807-15, 1992.
Other methods, such as the use of antibodies directed to an endogenous polypeptide for inhibiting its function in planta, or interference in the signalling pathway in which a polypeptide is involved, will be well known to the skilled man. In particular, it can be envisaged that manmade molecules may be useful for inhibiting the biological function of a target polypeptide, or for i nterfering with the signalling pathway in which the target polypeptide is involved. Alternatively, a screening program may be set up to identify in a plant population natural variants of a gene, which variants encode polypeptides with reduced activity. Such natural variants may also be used for example, to perform homologous recombination.
Artificial and/or natural microRNAs (miRNAs) may be used to knock out gene expression and/or imRNA translation. Endogenous miRNAs are single stranded small RNAs of typically 19-24 nucleotides long. They function primarily to regulate gene expression and/ or mRNA translation. Most plant microRNAs (miRNAs) have perfect or near-perfect complementarity with their target sequences. However, there are natural targets with up to five mismatches. They are processed from longer non-coding RNAs with characteristic fold-back structures by double-strand specific RNases of the Dicer family. Upon processing, they are incorporated i n th e RNA-induced silencing complex (RISC) by binding to its main component, an Argonaute protein. MiRNAs serve as the specificity components of RISC, since they base-pair to target nucleic acids, mostly mRNAs, in the cytoplasm. Subsequent regulatory events include target mRNA cleavage and destruction and/or translational inhibition. Effects of miRNA overexpression are thus often reflected in decreased mRNA levels of target genes.
Artificial microRNAs (ami RNAs), which are typically 21 nucleotides in length , can be genetically engineered specifically to negatively regulate gene expression of single or multiple genes of interest. Determinants of plant microRNA target selection are well known in the art. Empirical parameters for target recognition have been defined and can be used to aid in the design of specific amiRNAs, (Schwab et al., Dev. Cell 8, 517-527, 2005). Convenient tools for design and generation of amiRNAs and their precursors are also available to the public (Schwab et al., Plant Cell 18, 1 121 -1 133, 2006).
For optimal performance, the gene silencing techniques used for reducing expression in a plant of an endogenous gene requires the use of nucleic acid sequences from monocotyledonous plants for transformation of monocotyledonous plants, and from dicotyledonous plants for transformation of dicotyledonous plants. Preferably, a nucleic acid sequence from any given plant species is introduced into that same species. For example, a nucleic acid sequence from rice is transformed into a rice plant. However, it is not an absolute requirement that the nucleic acid sequence to be introduced originates from the same plant species as the plant in which it will be introduced. It is sufficient that there is substantial homology between the endogenous target gene and the nucleic acid to be introduced. Described above are examples of various methods for the reduction or substantial elimination of expression in a plant of an endogenous gene. A person skilled in the art would readily be able to adapt the aforementioned methods for silencing so as to achieve reduction of expression of an endogenous gene in a whole plant or in parts thereof through the use of an appropriate promoter, for example.
Transformation
The term "introduction" or "transformation" as referred to herein encompasses the transfer of an exogenous polynucleotide into a host cell, irrespective of the method used for transfer. Plant tissue capable of subsequent clonal propagation, whether by organogenesis or embryogenesis, may be transformed with a genetic construct of the present invention and a whole plant regenerated there from. The particular tissue chosen will vary depending on the clonal propagation systems available for, and best suited to, the particular species being transformed. Exemplary tissue targets include leaf disks, pollen, embryos, cotyledons, hypocotyls, megagametophytes, callus tissue, existing meristematic tissue (e.g., apical meristem, axillary buds, and root meristems), and induced meristem tissue (e.g., cotyledon meristem and hypocotyl meristem). The polynucleotide may be transiently or stably introduced into a host cell and may be maintained non-integrated, for example, as a plasmid. Alternatively, it may be integrated into the host genome. The resulting transformed plant cell may then be used to regenerate a transformed plant in a manner known to persons skilled in the art. Alternatively, a plant cell that cannot be regenerated into a plant may be chosen as host cell, i.e. the resulting transformed plant cell does not have the capacity to regenerate into a (whole) plant.
The transfer of foreign genes i nto the genome of a plant is cal led transformation . Transformation of plant species is now a fairly routine technique. Advantageously, any of several transformation methods may be used to introd uce the gene of interest into a suitable ancestor cell. The methods described for the transformation and regeneration of plants from plant tissues or plant cells may be utilized for transient or for stable transformation. Transformation methods include the use of liposomes, electroporation, chemicals that increase free DNA uptake, injection of the DNA directly into the plant, particle gun bombardment, transformation using viruses or pollen and microprojection. Methods may be selected from the calcium/polyethylene glycol method for protoplasts (Krens, F.A. et al., (1982) Nature 296, 72-74; Negrutiu I et al. (1987) Plant Mol Biol 8: 363- 373); electroporation of protoplasts (Shillito R.D. et al. (1985) Bio/Technol 3, 1099-1 102); microinjection into plant material (Crossway A et al., (1986) Mol. Gen Genet 202: 179-185); DNA or RNA-coated particle bombardment (Klein TM et al., (1987) Nature 327: 70) infection with (non-integrative) viruses and the like. Transgenic plants, including transgenic crop pla nts , a re prefera bly prod uced vi a
Figure imgf000075_0001
transformation. An advantageous transformation method is the transformation in planta. To this end , it is possible, for example, to allow the agrobacteria to act on plant seeds or to inoculate the plant meristem with agrobacteria. It has proved particularly expedient in accordance with the invention to allow a suspension of transformed agrobacteria to act on the intact plant or at least on the flower primordia. The plant is subsequently grown on until the seeds of the treated plant are obtained (Clough and Bent, Plant J. (1998) 16, 735-743). Methods for Agrobacterium-medlated transformation of rice include well known methods for rice transformation, such as those described in any of the following: European patent application EP 1 198985 A1 , Aldemita and Hodges (Planta 199: 612-617, 1996); Chan et al. (Plant Mol Biol 22 (3): 491 -506, 1993), Hiei et al. (Plant J 6 (2): 271 -282, 1994), which disclosures are incorporated by reference herein as if fully set forth. In the case of corn transformation, the preferred method is as described in either Ishida et al. (Nat. Biotechnol 14(6): 745-50, 1996) or Frame et al. (Plant Physiol 129(1 ): 13-22, 2002), which disclosures are incorporated by reference herein as if fully set forth. Said methods are further described by way of example in B. Jenes et al., Techniques for Gene Transfer, in: Transgenic Plants, Vol. 1 , Engineering and Utilization, eds. S.D. Kung and R. Wu, Academic Press (1993) 128-143 and in Potrykus Annu. Rev. Plant Physiol. Plant Molec. Biol. 42 (1991 ) 205-225). The nucleic acids or the construct to be expressed is preferably cloned into a vector, wh ich is suitable for transforming Agrobacterium tumefaciens, for example pBin 19 (Bevan et al., Nucl. Acids Res. 12 (1984) 871 1 ). Agrobacteria transformed by such a vector can then be used in known manner for the transformation of plants, such as plants used as a model , like Arabidopsis (Arabidopsis thaliana is with in th e scope of the present i nvention not considered as a crop plant), or crop plants such as, by way of example, tobacco plants, for example by immersing bruised leaves or chopped leaves in an agrobacterial solution and then cu ltu ri ng them in suitable med ia . The transformation of plants by means of Agrobacterium tumefaciens is described, for example, by Hofgen and Willmitzer in Nucl. Acid Res. (1988) 16, 9877 or is known inter alia from F.F. White, Vectors for Gene Transfer in Higher Plants; in Transgenic Plants, Vol. 1 , Engineering and Utilization, eds. S.D. Kung and R. Wu, Academic Press, 1993, pp. 15-38.
In addition to the transformation of somatic cells, which then have to be regenerated into intact plants, it is also possible to transform the cells of plant meristems and in particular those cells which develop into gametes. In this case, the transformed gametes follow the natural plant development, giving rise to transgenic plants. Thus, for example, seeds of Arabidopsis are treated with agrobacteria and seeds are obtained from the developing plants of which a certain proportion is transformed and thus transgenic [Feldman, KA and Marks MD (1987). Mol Gen Genet 208:1 -9; Feldmann K (1992). In: C Koncz, N-H Chua and J Shell, eds, Methods in Arabidopsis Research. Word Scientific, Singapore, pp. 274-289]. Alternative methods are based on the repeated removal of the inflorescences and incubation of the excision site in the center of the rosette with transformed agrobacteria, whereby transformed seeds can likewise be obtained at a later point in time (Chang (1994). Plant J. 5: 551 -558; Katavic (1994). Mol Gen Genet, 245: 363-370). However, an especially effective method is the vacuum infiltration method with its modifications such as the "floral dip" method. In the case of vacuum infiltration of Arabidopsis, intact plants under reduced pressure are treated with an agrobacterial suspension [Bechthold, N (1993). C R Acad Sci Paris Life Sci, 316: 1 194-1 199], while in the case of the "floral dip" method the developing floral tissue is incubated briefly with a surfactant-treated agrobacterial suspension [Clough, SJ and Bent AF (1998) The Plant J. 16, 735-743]. A certain proportion of transgenic seeds are harvested in both cases, and these seeds can be distinguished from non-transgenic seeds by growing under the above-described selective conditions. In addition the stable transformation of plastids is of advantages because plastids are inherited maternally is most crops reducing or eliminating the risk of transgene flow through pollen. The transformation of the chloroplast genome is generally achieved by a process which has been schematically displayed i n Klaus et al . , 2004 [Nature Biotechnology 22 (2), 225-229]. Briefly the sequences to be transformed are cloned together with a selectable marker gene between flanking sequences homologous to the chloroplast genome. These homologous flanking sequences direct site specific integration into the plastome. Plastidal transformation has been described for many different plant species and an overview is given in Bock (2001 ) Transgenic plastids in basic research and plant biotechnology. J Mol Biol. 2001 Sep 21 ; 312 (3):425-38 o r M a l iga , P (2003) Progress towa rd s com merci al izatio n of pl asti d transformation technology. Trends Biotechnol. 21 , 20-28. Further biotechnological progress has recently been reported in form of marker free plastid transformants, which can be produced by a transient co-integrated maker gene (Klaus et al., 2004, Nature Biotechnology 22(2), 225-229).
The genetically modified plant cells can be regenerated via all methods with which the skilled worker is fami liar. Suitable methods can be fou nd in the abovementioned publications by S.D. Kung and R. Wu, Potrykus or Hofgen and Willmitzer. Alternatively, the genetically modified plant cells are non-regenerable into a whole plant.
Generally after transformation, plant cells or cell groupings are selected for the presence of one or more markers which are encoded by plant-expressible genes co-transferred with the gene of interest, following which the transformed material is regenerated into a whole plant. To select transformed plants, the plant material obtained in the transformation is, as a rule, subjected to selective conditions so that transformed plants can be distinguished from untransformed plants. For example, the seeds obtained in the above-described manner can be planted and, after an initial growing period, subjected to a suitable selection by spraying. A further possibility consists in growing the seeds, if appropriate after sterilization, on agar plates using a suitable selection agent so that only the transformed seeds can grow into plants. Alternatively, the transformed plants are screened for the presence of a selectable marker such as the ones described above.
Following DNA transfer and regeneration, putatively transformed plants may also be evaluated, for instance using Southern analysis, for the presence of the gene of interest, copy number and/or genomic organisation. Alternatively or additionally, expression levels of the newly introduced DNA may be monitored using Northern and/or Western analysis, both techniques being well known to persons having ordinary skill in the art. The generated transformed plants may be propagated by a variety of means, such as by clonal propagation or classical breeding techniques. For example, a first generation (or T1 ) transformed plant may be selfed and homozygous second-generation (or T2) transformants selected, and the T2 plants may then further be propagated through classical breeding techniques. The generated transformed organisms may take a variety of forms. For example, they may be chimeras of transformed cells and non-transformed cells; clonal transformants (e.g. , all cells transformed to contain the expression cassette); grafts of transformed and untransformed tissues (e.g., in plants, a transformed rootstock grafted to an untransformed scion). T-DNA activation tagging
"T-DNA activation" tagging (Hayashi et al. Science (1992) 1350-1353), involves insertion of T-DNA, usually containing a promoter (may also be a translation enhancer or an intron), in the genomic region of the gene of interest or 10 kb up- or downstream of the coding region of a gene in a configuration such that the promoter directs expression of the targeted gene. Typically, regulation of expression of the targeted gene by its natural promoter is disrupted and the gene falls under the control of the newly introduced promoter. The promoter is typically embedded in a T-DNA. This T-DNA is randomly inserted into the plant genome, for example, through Agrobacterium infection and leads to modified expression of genes near the inserted T-DNA. The resulting transgenic plants show dominant phenotypes due to modified expression of genes close to the introduced promoter.
TILLING
The term "TILLING" is an abbreviation of "Targeted Induced Local Lesions In Genomes" and refers to a mutagenesis technology useful to generate and/or identify nucleic acids encoding proteins with modified expression and/or activity. TILLING also allows selection of plants carrying such mutant variants. These mutant variants may exhibit modified expression, either in strength or in location or in timing (if the mutations affect the promoter for example). These mutant variants may exhibit higher activity than that exhibited by the gene in its natural form. TILLING combines high-density mutagenesis with high-throughput screening methods. The steps typically followed in TILLING are: (a) EMS mutagenesis (Redei GP and Koncz C (1992) In Methods in Arabidopsis Research, Koncz C, Chua NH, Schell J, eds. Singapore, World Scientific Publishing Co, pp. 16-82; Feldmann et al., (1994) In Meyerowitz EM, Somerville CR, eds, Arabidopsis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY, pp 137-172; Lightner J and Caspar T (1998) In J Martinez-Zapater, J Salinas, eds, Methods on Molecular Biology, Vol. 82. Humana Press, Totowa, NJ, pp 91 - 104); (b) DNA preparation and pooling of individuals; (c) PCR amplification of a region of interest; (d) denaturation and annealing to allow formation of heteroduplexes; (e) DHPLC, where the presence of a heterodu plex in a pool is detected as an extra peak in the chromatogram; (f) identification of the mutant individual; and (g) sequencing of the mutant PCR product. Methods for TILLING are well known in the art (McCallum et al., (2000) Nat Biotechnol 18: 455-457; reviewed by Stemple (2004) Nat Rev Genet 5(2): 145-50).
Homologous recombination
"Homologous recombination" allows introduction in a genome of a selected nucleic acid at a defined selected position. Homologous recombination is a standard technology used routi nely in biologi ca l sci en ces for lower organ isms such as yeast or the moss Physcomitrella. Methods for performing homologous recombination in plants have been described not only for model plants (Offringa et al. (1990) EMBO J 9(10): 3077-84) but also for crop plants, for example rice (Terada et al. (2002) Nat Biotech 20(10): 1030-4; lida and Terada (2004) Curr Opin Biotech 15(2): 132-8), and approaches exist that are generally applicable regardless of the target organism (Miller et al, Nature Biotechnol. 25, 778-785, 2007).
Yield related Trait(s)
A "Yield related trait" is a trait or feature which is related to plant yield. Yield-related traits may comprise one or more of the following non-limitative list of features: early flowering time, yield, biomass, seed yield, early vigour, greenness index, growth rate, agronomic traits, such as e.g. tolerance to submergence (which leads to yield in rice), Water Use Efficiency (WUE), Nitrogen Use Efficiency (NUE), etc.
Reference herein to enhanced yield-related traits, relative to of control plants is taken to mean one or more of an increase in early vigour and/or in biomass (weight) of one or more parts of a plant, which may include (i) aboveground parts and preferably aboveground harvestable parts and/or (ii) parts below ground and preferably harvestable below ground. In particular, such harvestable parts are seeds. Yield
The term "yield" in general means a measurable produce of economic value, typically related to a specified crop, to an area, and to a period of time. Individual plant parts directly contribute to yield based on their number, size and/or weight, or the actual yield is the yield per square meter for a crop and year, which is determined by dividing total production (includes both harvested and appraised production) by planted square meters. The terms "yield" of a plant and "plant yield" are used interchangeably herein and are meant to refer to vegetative biomass such as root and/or shoot biomass, to reproductive organs, and/or to propagules such as seeds of that plant.
Flowers in maize are unisexual; male inflorescences (tassels) originate from the apical stem and female inflorescences (ears) arise from axillary bud apices. The female inflorescence produces pairs of spikelets on the surface of a central axis (cob). Each of the female spikelets encloses two fertile florets, one of them will usually mature into a maize kernel once fertilized. Hence a yield increase in maize may be manifested as one or more of the following: increase in the number of plants established per square meter, an increase in the number of ears per plant, an increase in the number of rows, number of kernels per row, kernel weight, thousand kernel weight, ear length/diameter, increase in the seed filling rate, which is the number of filled florets (i.e. florets containing seed) divided by the total number of florets and multiplied by 100), among others. Inflorescences in rice plants are named panicles. The panicle bears spikelets, which are the basic units of the panicles, and which consist of a pedicel and a floret. The floret is borne on the pedicel and includes a flower that is covered by two protective glumes: a larger glume (the lemma) and a shorter glume (the palea). Hence, taking rice as an example, a yield increase may manifest itself as an increase in one or more of the following: number of plants per square meter, number of panicles per plant, panicle length, number of spikelets per panicle, number of flowers (or florets) per panicle; an increase in the seed filling rate which is the number of filled florets (i .e. florets containing seeds) divided by the total number of florets and multiplied by 100; an increase in thousand kernel weight, among others.
Early flowering time
Plants having an "early flowering time" as used herein are plants which start to flower earlier than control plants. Hence this term refers to plants that show an earlier start of flowering. Flowering time of plants can be assessed by counting the number of days ("time to flower") between sowing and the emergence of a first inflorescence. The "flowering time" of a plant can for instance be determined using the method as described in WO 2007/093444.
Early vigour
"Early vigour" refers to active healthy well-balanced growth especially during early stages of plant growth, and may result from increased plant fitness due to, for example, the plants being better adapted to their environment (i.e. optimizing the use of energy resources and partitioning between shoot and root). Plants having early vigour also show increased seedling survival and a better establishment of the crop, which often results in highly uniform fields (with the crop growing in uniform manner, i.e. with the majority of plants reaching the various stages of development at substantially the same time), and often better and higher yield. Therefore, early vigour may be determined by measuring various factors, such as thousand kernel weight, percentage germination, percentage emergence, seedling growth, seedling height, root length, root and shoot biomass and many more.
Increased growth rate
The increased growth rate may be specific to one or more parts of a plant (including seeds), or may be throughout substantially the whole plant. Plants having an increased growth rate may have a shorter life cycle. The life cycle of a plant may be taken to mean the time needed to grow from a mature seed up to the stage where the plant has produced mature seeds, similar to the starting material. This life cycle may be influenced by factors such as speed of germination, early vigour, growth rate, greenness index, flowering time and speed of seed maturation. The increase in growth rate may take place at one or more stages in the life cycle of a plant or during substantially the whole plant life cycle. Increased growth rate during the early stages in the life cycle of a plant may reflect enhanced vigour. The increase in growth rate may alter the harvest cycle of a plant allowing plants to be sown later and/or harvested sooner than would otherwise be possible (a similar effect may be obtained with earlier flowering time). If the growth rate is sufficiently increased, it may allow for the further sowing of seeds of the same plant species (for example sowing and harvesting of rice plants followed by sowing and harvesting of further rice plants all within one conventional growing period). Similarly, if the growth rate is sufficiently increased, it may allow for the further sowing of seeds of different plants species (for example the sowing and harvesting of corn plants followed by, for example, the sowing and optional harvesting of soybean, potato or any other suitable plant). Harvesting additional times from the same rootstock in the case of some crop plants may also be possible. Altering the harvest cycle of a plant may lead to an increase in annual biomass production per square meter (due to an increase in the number of times (say in a year) that any particular plant may be grown and harvested). An increase in growth rate may also allow for the cultivation of transgenic plants in a wider geographical area than their wild-type counterparts, since the territorial limitations for growing a crop are often determined by adverse environmental conditions either at the time of planting (early season) or at the time of harvesting (late season). Such adverse conditions may be avoided if the harvest cycle is shortened. The growth rate may be determined by deriving various parameters from growth curves, such parameters may be: T-Mid (the time taken for plants to reach 50% of their maximal size) and T-90 (time taken for plants to reach 90% of their maximal size), amongst others.
Stress resistance
An increase in yield and/or growth rate occurs whether the plant is under non-stress conditions or whether the plant is exposed to various stresses compared to control plants. Plants typically respond to exposure to stress by growing more slowly. In conditions of severe stress, the plant may even stop growing altogether. Mild stress on the other hand is defined herein as being any stress to which a plant is exposed which does not result in the plant ceasing to grow altogether without the capacity to resume growth. Mild stress in the sense of the invention leads to a reduction in the growth of the stressed plants of less than 40%, 35% , 30% or 25%, more preferably less than 20% or 15% in comparison to the control plant under non-stress conditions. Due to advances in agricultural practices (irrigation, fertilization, pesticide treatments) severe stresses are not often encountered in cultivated crop plants. As a consequence, the compromised growth induced by mild stress is often an undesirable feature for agriculture. Abiotic stresses may be due to drought or excess water, anaerobic stress, salt stress, chemical toxicity, oxidative stress and hot, cold or freezing temperatures.
"Biotic stresses" are typically those stresses caused by pathogens, such as bacteria, viruses, fungi, nematodes and insects.
The "abiotic stress" may be an osmotic stress caused by a water stress, e.g. due to drought, salt stress, or freezing stress. Abiotic stress may also be an oxidative stress or a cold stress. "Freezing stress" is intended to refer to stress due to freezing temperatures, i.e. temperatures at which available water molecules freeze and turn into ice. "Cold stress", also called "chilling stress", is intended to refer to cold temperatures, e.g. temperatures below 10°, or preferably below 5°C, but at which water molecules do not freeze. As reported in Wang et al. (Planta (2003) 218: 1 -14), abiotic stress leads to a series of morphological, physiological, biochemical and molecular changes that adversely affect plant growth and productivity. Drought, salinity, extreme temperatures and oxidative stress are known to be interconnected and may induce growth and cellular damage through similar mechanisms. Rabbani et al. (Plant Physiol (2003) 133: 1755-1767) describes a particularly high degree of "cross talk" between drought stress and high-salinity stress. For example, drought and/or salinisation are manifested primarily as osmotic stress, resulting in the disruption of homeostasis and ion distribution in the cell. Oxidative stress, which frequently accompanies high or low temperature, salinity or drought stress, may cause denaturing of functional and structural proteins. As a consequence, these diverse environmental stresses often activate similar cell signalling pathways and cellular responses, such as the production of stress proteins, up-regulation of anti-oxidants, accumulation of compatible solutes and growth arrest. The term "non-stress" conditions as used herein are those environmental conditions that allow optimal growth of plants. Persons skilled in the art are aware of normal soil cond itions and climatic conditions for a given location. Plants with optimal growth conditions, (grown under non-stress conditions) typically yield in increasing order of preference at least 97%, 95%, 92%, 90%, 87%, 85%, 83%, 80%, 77% or 75% of the average production of such plant in a given environment. Average production may be calculated on harvest and/or season basis. Persons skilled in the art are aware of average yield productions of a crop. In particular, the methods of the present invention may be performed under non-stress conditions. In an example, the methods of the present invention may be performed under non-stress conditions such as mild drought to give plants having increased yield relative to control plants.
In another embodiment, the methods of the present invention may be performed under stress conditions.
In an example, the methods of the present invention may be performed under stress conditions such as drought to give plants having increased yield relative to control plants. In another example, the methods of the present invention may be performed under stress conditions such as nutrient deficiency to give plants having increased yield relative to control plants.
Nutrient deficiency may result from a lack of nutrients such as nitrogen, phosphates and other phosphorous-containing compounds, potassium, calcium, magnesium, manganese, iron and boron, amongst others.
In yet another example, the methods of the present invention may be performed under stress conditions such as salt stress to give plants having increased yield relative to control plants. The term salt stress is not restricted to common salt (NaCI), but may be any one or more of: NaCI, KCI, LiCI, MgCI2, CaCI2, amongst others.
In yet another example, the methods of the present invention may be performed under stress conditions such as cold stress or freezing stress to give plants having increased yield relative to control plants.
Increase/Improve/Enhance
The terms "increase", "improve" or "enhance" are interchangeable and shall mean in the sense of the application at least a 3%, 4%, 5%, 6%, 7%, 8%, 9% or 10%, preferably at least 15% or 20%, more preferably 25% , 30% , 35% or 40% more yield and/or growth i n comparison to control plants as defined herein. Seed yield
Increased seed yield may manifest itself as one or more of the following:
a) an increase in seed biomass (total seed weight) which may be on an individual seed basis and/or per plant and/or per square meter;
b) increased number of flowers per plant;
c) increased number of seeds;
d) increased seed filling rate (which is expressed as the ratio between the number of filled florets divided by the total number of florets);
e) increased harvest index, which is expressed as a ratio of the yield of harvestable parts, such as seeds, divided by the biomass of aboveground plant parts; and f) increased thousand kernel weight (TKW), which is extrapolated from the number of seeds counted and their total weight. An increased TKW may result from an increased seed size and/or seed weight, and may also result from an increase in embryo and/or endosperm size.
The terms "filled florets" and "filled seeds" may be considered synonyms.
An increase in seed yield may also be manifested as an increase in seed size and/or seed volume. Furthermore, an increase in seed yield may also manifest itself as an increase in seed area and/or seed length and/or seed width and/or seed perimeter.
Greenness Index
The "greenness index" as used herein is calculated from digital images of plants. For each pixel belonging to the plant object on the image, the ratio of the green value versus the red value (i n the RGB model for encoding color) is calculated. The green ness index is expressed as the percentage of pixels for which the green-to-red ratio exceeds a given threshold. Under normal growth conditions, under salt stress growth conditions, and under reduced nutrient availability growth conditions, the greenness index of plants is measured in the last imaging before flowering. In contrast, under drought stress growth conditions, the greenness index of plants is measured in the first imaging after drought.
Biomass
The term "biomass" as used herein is intended to refer to the total weight of a plant. Within the definition of biomass, a distinction may be made between the biomass of one or more parts of a plant, which may include any one or more of the following:
aboveground parts such as but not limited to shoot biomass, seed biomass, leaf biomass, etc.;
- aboveground harvestable parts such as but not limited to shoot biomass, seed biomass, leaf biomass, etc.;
parts below ground, such as but not limited to root biomass, tubers, bulbs, etc.;
harvestable parts below ground, such as but not limited to root biomass, tubers, bulbs, etc.;
harvestable parts partially below ground such as but not limited to beets and other hypocotyl areas of a plant, rhizomes, stolons or creeping rootstalks;
- vegetative biomass such as root biomass, shoot biomass, etc.;
- reproductive organs; and
- propagules such as seed. Marker assisted breeding
Such breeding programmes sometimes require introduction of allelic variation by mutagenic treatment of the plants, using for example EMS mutagenesis; alternatively, the programme may start with a col lection of a llelic variants of so called "natural" origi n caused unintentionally. Identification of allelic variants then takes place, for example, by PCR. This is followed by a step for selection of superior allelic variants of the sequence in question and which give increased yield. Selection is typically carried out by monitoring growth performance of plants containing different allelic variants of the sequence in question. Growth performance may be monitored in a greenhouse or in the field. Further optional steps include crossing plants in which the superior allelic variant was identified with another plant. This could be used, for example, to make a combination of interesting phenotypic features.
Use as probes in (gene mapping)
Use of nucleic acids encoding the protein of interest for genetically and physically mapping the genes requires only a nucleic acid sequence of at least 15 nucleotides in length. These nucleic acids may be used as restriction fragment length polymorphism (RFLP) markers. Southern blots (Sambrook J, Fritsch EF and Maniatis T (1989) Molecular Cloning, A Laboratory Manual) of restriction-digested plant genomic DNA may be probed with the nucleic acids encoding the protein of interest. The resulting banding patterns may then be subjected to genetic analyses using computer programs such as MapMaker (Lander et al. (1987) Genomics 1 : 174-181 ) in order to construct a genetic map. In addition, the nucleic acids may be used to probe Southern blots containing restriction endonuclease-treated genomic DNAs of a set of individuals representing parent and progeny of a defined genetic cross. Segregation of the DNA polymorphisms is noted and used to calculate the position of the nucleic acid encoding the protein of interest in the genetic map previously obtained using this population (Botstein et al. (1980) Am. J. Hum. Genet. 32:314-331 ).
The prod uction and use of plant gene-derived probes for use in genetic mapping is described in Bernatzky and Tanksley (1986) Plant Mol. Biol. Reporter 4: 37-41 . Numerous publications describe genetic mapping of specific cDNA clones using the methodology outlined above or variations thereof. For example, F2 intercross populations, backcross populations, randomly mated populations, near isogenic lines, and other sets of individuals may be used for mapping. Such methodologies are well known to those skilled in the art.
The nucleic acid probes may also be used for physical mapping (i .e. , placement of sequences on physical maps; see Hoheisel et al. In: Non-mammalian Genomic Analysis: A Practical Guide, Academic press 1996, pp. 319-346, and references cited therein).
In another embodiment, the nucleic acid probes may be used in direct fluorescence in situ hybridisation (FISH) mapping (Trask (1991 ) Trends Genet. 7: 149-154). Although current methods of FISH mapping favour use of large clones (several kb to several hundred kb; see Laa n et al . (1 995) Genome Res. 5: 1 3-20) , improvements i n sensitivity may allow performance of FISH mapping using shorter probes.
A variety of nucleic acid amplification-based methods for genetic and physical mapping may be carried out using the nucleic acids. Examples include allele-specific amplification (Kazazian (1989) J. Lab. Clin. Med 1 1 :95-96), polymorphism of PCR-amplified fragments (CAPS; Sheffield et al. (1993) Genomics 16:325-332), allele-specific ligation (Landegren et al. (1988) Science 241 : 1077-1080), nucleotide extension reactions (Sokolov (1990) Nucleic Acid Res. 18:3671 ), Radiation Hybrid Mapping (Walter et al. (1997) Nat. Genet. 7:22-28) and Happy Mapping (Dear and Cook (1989) Nucleic Acid Res. 17:6795-6807). For these methods, the sequence of a nucleic acid is used to design and produce primer pairs for use in the amplification reaction or in primer extension reactions. The design of such primers is well known to those skilled in the art. In methods employing PCR-based genetic mapping, it may be necessary to identify DNA sequence differences between the parents of the mapping cross in the region corresponding to the instant nucleic acid sequence. This, however, is generally not necessary for mapping methods. Plant
The term "plant" as used herein encompasses whole plants, ancestors and progeny of the plants and plant parts, including seeds, shoots, stems, leaves, roots (including tubers), flowers, and tissues and organs, wherein each of the aforementioned comprise the gene/nucleic acid of interest. The term "plant" also encompasses plant cells, suspension cultures, callus tissue, embryos, meristematic regions, gametophytes, sporophytes, pollen and microspores, again wherein each of the aforementioned comprises the gene/nucleic acid of interest.
Plants that are particularly useful in the methods of the invention include all plants which belong to the superfamily Viridiplantae, in particular monocotyledonous and dicotyledonous plants including fodder or forage legumes, ornamental plants, food crops, trees or shrubs selected from the list comprising Acer spp., Actinidia spp., Abelmoschus spp., Agave sisalana, Agropyron spp., Agrostis stolonifera, Allium spp., Amaranthus spp., Ammophila arenaria, Ananas comosus, Annona spp., Apium graveolens, Arachis spp, Artocarpus spp., Asparagus officinalis, Avena spp. (e.g. Avena sativa, Avena fatua, Avena byzantina, Avena fatua var. sativa, Avena hybrida), Averrhoa carambola, Bambusa sp., Benincasa hispida, Bertholletia excelsea, Beta vulgaris, Brassica spp. (e.g. Brassica napus, Brassica rapa ssp. [canola, oilseed rape, turnip rape]), Cadaba farinosa, Camellia sinensis, Canna indica, Cannabis sativa, Capsicum spp., Carex elata, Carica papaya, Carissa macrocarpa, Carya spp., Carthamus tinctorius, Castanea spp., Ceiba pentandra, Cichorium endivia, Cinnamomum spp., Citrullus lanatus, Citrus spp., Cocos spp., Coffea spp., Colocasia esculenta, Cola spp., Corchorus sp., Coriandrum sativum, Corylus spp., Crataegus spp., Crocus sativus, Cucurbita spp., Cucumis spp., Cynara spp., Daucus carota, Desmodium spp., Dimocarpus longan, Dioscorea spp., Diospyros spp., Echinochloa spp., Elaeis (e.g. Elaeis guineensis, Elaeis oleifera), Eleusine coracana, Eragrostis tef, Erianthus sp., Eriobotrya japonica, Eucalyptus sp., Eugenia uni flora, Fagopyrum spp., Fagus spp., Festuca arundinacea, Ficus carica, Fortunella spp., Fragaria spp., Ginkgo biloba, Glycine spp. (e.g. Glycine max, Soja hispida or Soja max), Gossypium hirsutum, Helianthus spp. (e.g. Helianthus annuus), Hemerocallis fulva, Hibiscus spp., Hordeum spp. (e.g. Hordeum vulgare), Ipomoea batatas, Juglans spp., Lactuca sativa, Lathyrus spp., Lens culinaris, Linum usitatissimum, Litchi chinensis, Lotus spp., Luffa acutangula, Lupinus spp., Luzula sylvatica, Lycopersicon spp. (e.g. Lycopersicon esculentum, Lycopersicon lycopersicum, Lycopersicon pyriforme), Macrotyloma spp., Malus spp., Malpighia emarginata, Mammea americana, Mangifera indica, Manihot spp., Manilkara zapota, Medicago sativa, Melilotus spp., Mentha spp., Miscanthus sinensis, Momordica spp., Morus nigra, Musa spp., Nicotiana spp., Olea spp., Opuntia spp., Ornithopus spp., O/yza spp. ('e.g. Oryza sativa, Oryza latifolia), Panicum miliaceum, Panicum virgatum, Passiflora edulis, Pastinaca sativa, Pennisetum sp., Persea spp., Petroselinum crispum, Phalaris arundinacea, Phaseolus spp., Phleum pratense, Phoenix spp., Phragmites australis, Physalis spp., Pinus spp., Pistacia vera, Pisum spp., Poa spp., Populus spp., Prosopis spp., Prunus spp., Psidium spp., Punica granatum, Pyrus communis, Quercus spp., Raphanus sativus, Rheum rhabarbarum, R/bes spp., Ricinus communis, Rubus spp., Saccharum spp., Sa//x sp., Sambucus spp., Secale cereaie, Sesamum spp., Sinapis sp., Solanum spp. ('e.g. Solanum tuberosum, Solanum integrifolium or Solanum lycopersicum), Sorghum bicolor, Spinacia spp., Syzygium spp., Tagetes spp., Tamarindus indica, Theobroma cacao, Trifolium spp., Tripsacum dactyloides, Triticosecale rimpaui, Triticum spp. ('e.g. Triticum aestivum, Triticum durum, Triticum turgidum, Triticum hybernum, Triticum macha, Triticum sativum, Triticum monococcum or Triticum vulgare), Tropaeolum minus, Tropaeolum majus, Vaccinium spp., V/'c/'a spp., V/'gna spp., V/'o/a odorata, Vitis spp., Zea mays, Zizania palustris, Ziziphus spp., amongst others. Control plant(s)
The choice of suitable control plants is a routine part of an experimental setup and may include corresponding wild type plants or corresponding plants without the gene of interest. The control plant is typically of the same plant species or even of the same variety as the plant to be assessed. The control plant may also be a nullizygote of the plant to be assessed. Nullizygotes (or null control plants) are individuals missing the transgene by segregation. Further, control plants are grown under equal growing conditions to the growing conditions of the plants of the invention, i.e. in the vicinity of, and simultaneously with, the plants of the invention. A "control plant" as used herein refers not only to whole plants, but also to plant parts, including seeds and seed parts.
Description of figures
The present invention will now be described with reference to the following figures in which: Figure 1 represents the domain structure of SEQ ID NO: 2 with conserved motifs.
Figure 2 represents the domain structure of SEQ ID NO: 4 with conserved motifs.
Figure 3 represents a multiple alignment of various DU F642 polypeptides. These alignments can be used for defining further motifs or signature sequences, when using conserved amino acids. The corresponding SEQ ID NO's for the aligned polypeptide sequences shown in Figure 3 are:
Annotation SEQ ID NO:
A.lyrata_340195 58
A.thaliana_AT1 G80240.1 68 B.napus_TC65362 72
B.napus_TC77368 74
O.sativa_LOC_Os01g42520.1 6
P.virgatum_TC46275 18
S.bicolor_Sb03g027650.1 20
Z.mays_TC458850 36
Zea_mays_GRMZM2G034985_T02 42
T.aestivum_c60008104@1 1410 34
O.sativa_LOC_Os04g41710.1 8
O.sati va_LOC_Os04g41740.1 10
Os_DUF642.3 2
O.sativa LOC Os04g41750.1 12
S.bicolor_Sb06g021280.1 24
Z.mays_ZM07MC22756_BFb0088A01 @22693 40
Zea_mays_GRMZM2G051898_T01 44
S.bicolor_Sb06g021290.1 26
O.sati va_LOC_Os04g41759.1 14
S.bicolor_Sb06g021320.1 32
S.bicolor_Sb06g021300.1 28
Z.mays_TC468877 38
S.bicolor_Sb06g021310.1 30
O.sativa_LOC_Os04g41770.1 16
S.bicolor_Sb06g021270.1 22
Zea_mays_GRMZM2G051912_T01 46
Zea_mays_GRMZM2G405071_T01 48
O.sativa_LOC_Os02g1 1040.1 50
Os_DUF642.2 4
P.virgatum_TC392 52
S.bicolor_Sb04g007160.1 54
Z.mays_TC467870 56
P.sitchensis_TA14284_3332 122
P.taeda_TA10429_3352 124
A.lyrata_912808 62
A.thaliana_AT G29980.1 66
A.lyrata_934049 64 C.annuum_TC19321 78
S.tuberosum_TC189725 150
J.hindsii_x_regia_TA1 156_432290 102
G.hirsutum_TC135941 84
G.raimondii TC1 124 96
G.max_GM06MC25068_saa05g06@24507 92
G.max_TC286277 94
L.japonicus_TC41787 104
M.domestica_TC32901 108
P.trifoliata_TA6477_37690 134
P. trichocarpa_DUF 158
P. trichocarpa MUB2 160
T.officinale_TA3338_50225 156
H.vulgare_TC163732 98
T.aestivum_TC292522 152
O.sativa_LOC_Os01g55190.1 1 16
P.virgatum_TC7090 136
S.bicolor_Sb03g034960.1 142 officinarum_TC76182 148
Z.mays_c62082358gm030403@7546 172
Z.mays_ZM07MC26525_BFb021 1 C02@26447 176
Zea_mays_GRMZM2G324705_T01 180
Z.officinale_TA720_94328 178
P.sitchensis_TA10533_3332 120
P.taeda_TA4773_3352 126
O.sativa_LOC_Os03g59300.1 1 18
S.bicolor_Sb01 g004270.1 140
Z.mays_c57213778gm030403@389 170
Z.mays_TC506958 174
P.trichocarpa_735032 130
V.vinifera_GSVIVT00025589001 166
S.lycopersicum_TC198542 144
Triphysaria_sp_TC1 1756 162
G.max_Glyma09g36220.1 88
M.truncatula_AC174305_19.4 1 10 G.max_Glyma15g43180.1 90
P.vulgaris_TC10932 138
A.lyrata_478145 60
A.thaliana_AT3G08030.1 70
B.napus TC89135 76
G.hirsutum_TC161608 86
T.cacao_TC4474 154
L.serriola_TC5542 106
C.sinensis_TC3550 80
P.trichocarpa_549292 128
P.trichocarpa_833200 132
V.vinifera GSVIVT00028751001 168
F.vesca_TA10399_57918 82
N.benthamiana_TC1 1 106 1 12
N.tabacum_TC43533 1 14
S.lycopersicum_TC199778 146
Triphysaria_sp_TC1599 164
l.nil_TC4208 100
Figure 4 represents a multiple alignment of a selection (clade A) of DUF642 polypeptides from Figure 3. The corresponding SEQ ID NO's for the aligned polypeptide sequences shown in Figure 4 are:
Annotation SEQ ID NO:
O.sativa_LOC_Os01g42520.1 6
P.virgatum TC46275 18
S.bicolor_Sb03g027650.1 20
Z.mays_TC458850 36
Zea_mays_GRMZM2G034985_T02 42
T.aestivum_c60008104@1 1410 34
O.sativa_LOC_Os04g41710.1 8
O.sati va_LOC_Os04g41740.1 10
Os DUF642.3 2
O.sativa_LOC_Os04g41750.1 12
SEQ ID NO: 24 for S.bicolor_Sb06g021280.1 24
Z.mays_ZM07MC22756_BFb0088A01 @22693 40
Zea_mays_GRMZM2G051898_T01 44 S.bicolor_Sb06g021290.1 26
O.sati va_LOC_Os04g41759.1 14
S.bicolor_Sb06g021320.1 32
S.bicolor_Sb06g021300.1 28
Z.mays TC468877 38
S.bicolor_Sb06g021310.1 30
O.sativa_LOC_Os04g41770.1 16
S.bicolor_Sb06g021270.1 22
Zea_mays_GRMZM2G051912_T01 46
Zea_mays_GRMZM2G405071_T01 48
O.sativa_LOC_Os02g1 1040.1 50
Os DUF642.2 4
P.virgatum_TC392 52
S.bicolor_Sb04g007160.1 54
Z.mays_TC467870 56
Figure 5 shows a phylogenetic tree of DUF642 polypeptides, as described in Example 2. Clade A is encircled, the remainder of the branches of the tree are grouped in clade B. Figure 6 shows the MATGAT table of Example 3.
Figure 7 represents the binary vector used for increased expression in Oryza sativa of a DUF642-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2).
Figure 8 represents the domain structure of SEQ ID NO: 198 with conserved motifs.
Figure 9 represents a multiple alignment of the epimerase-related like polypeptides as listed in table A. These alignments can be used for defining further motifs or signature sequences, when using conserved amino acids.
Figure 10 shows phylogenetic tree of epimerase-related like polypeptides. To obtain the tree, protein sequences were aligned with MAFFT, a bootstrapped Neighbour Joining (NJ) tree was calculated with QuickTree (100 repeats, uncorrected), which was visualized with Dendroscope (for further details on the used techniques see example 2)
Figure 1 1 shows the MATGAT table of Example 3.
Figure 12 represents the binary vector used for increased expression in Oryza sativa of a nucleic acid encoding an epimerase-related like polypeptide under the control of a rice GOS2 promoter (pGOS2).
Figure 13 represents the domain structure of SEQ ID NO: 285 with conserved motifs.
Figure 14 shows phylogenetic tree of PLPCase polypeptides, showing three clusters.
Figure 15 shows the MatGAT table of Example 3.
Figure 16 represents the binary vector used for increased expression in Oryza sativa of a PLPCase-encoding nucleic acid under the control of a rice GOS2 promoter (pGOS2). Examples
The present invention will now be described with reference to the following examples, which are by way of illustration only. The following examples are not intended to limit the scope of the invention. Unless otherwise indicated, the present invention employs conventional techniques and methods of plant biology, molecular biology, bioinformatics and plant breedings.
DNA manipulation: unless otherwise stated, recombinant DNA techniques are performed according to standard protocols described in (Sambrook (2001 ) Molecular Cloning: a laboratory manual, 3rd Edition Cold Spring Harbor Laboratory Press, CSH, New York) or in Volumes 1 and 2 of Ausubel et al. (1994), Current Protocols in Molecular Biology, Current Protocols. Standard materials and methods for plant molecular work are described in Plant Molecular Biology Labfax (1993) by R.D.D. Croy, published by BIOS Scientific Publications Ltd (UK) and Blackwell Scientific Publications (UK).
Example 1 : Identification of sequences related to the nucleic acid sequence used in the methods of intervention
1. DUF642 polypeptides
Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 1 and SEQ ID NO: 2; and SEQ ID NO: 3 and SEQ ID NO: 4 were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid of SEQ ID NO: 1 was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E-value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
Table A1 provides a list of nucleic acid and protein sequences related to SEQ ID NO: 1 , SEQ ID NO: 2, SEQ ID NO: 3 and SEQ ID NO: 4. Table A1 : Examples of DUF642 nucleic acids and polypeptides:
Plant Source_name Nucleic acid Protein
SEQ ID NO: SEQ ID NO:
0. sativa _DUF642.3 1 2
0. sativa_DUF642.2 3 4
O.sativa_LOC_Os01 g42520.1 5 6
O.sativa_LOC_Os04g41710.1 7 8
O.sativa_LOC_Os04g41740.1 9 10
O.sativa_LOC_Os04g41750.1 1 1 12
O.sativa_LOC_Os04g41759.1 13 14
O.sativa_LOC_Os04g41770.1 15 16
P.virgatum_TC46275 17 18
S.bicolor_Sb03g027650.1 19 20
S.bicolor_Sb06g021270.1 21 22
S.bicolor_Sb06g021280.1 23 24
S.bicolor_Sb06g021290.1 25 26
S.bicolor_Sb06g021300.1 27 28
S.bicolor_Sb06g021310.1 29 30
S.bicolor_Sb06g021320.1 31 32
T.aestivum_c60008104@11410 33 34
Z.mays_TC458850 35 36
Z.mays_TC468877 37 38
Z.mays_ZM07MC22756_BFb0088A01 @22693 39 40
Z. mays_GRMZM2G034985_T02 41 42
Z. mays_GRMZM2G051898_T01 43 44
Z. mays_GRMZM2G051912_T01 45 46
Z. mays_GRMZM2G405071_T01 47 48
O.sativa_LOC_Os02g1 1040.1 49 50
P.virgatum_TC392 51 52
S.bicolor_Sb04g007160.1 53 54
Z.mays_TC467870 55 56
A.lyrata_340195 57 58
A.lyrata_478145 59 60
A.lyrata_912808 61 62
A.lyrata_934049 63 64
A.thaliana_AT1 G29980.1 65 66
A.thaliana_AT1 G80240.1 67 68
A.thaliana_AT3G08030.1 69 70
B.napus_TC65362 71 72
B.napus_TC77368 73 74
B.napus_TC89135 75 76 C.annuum_TC19321 77 78
C.sinensis_TC3550 79 80
F.vesca_TA10399_57918 81 82
G.hirsutum_TC135941 83 84
G.hirsutum_TC161608 85 86
G.max_Glyma09g36220.1 87 88
G.max_Glyma15g43180.1 89 90
G.max_GM06MC25068_saa05g06@24507 91 92
G.max_TC286277 93 94
G.raimondii_TC1 124 95 96
H.vulgare_TC163732 97 98 l.nil_TC4208 99 100
J.hindsii_x_regia_TA1 156_432290 101 102
L.japonicus_TC41787 103 104
L.serriola_TC5542 105 106
M.domestica_TC32901 107 108
M.truncatula_AC174305_19.4 109 1 10
N.benthamiana_TC1 1 106 1 1 1 1 12
N.tabacum_TC43533 1 13 1 14
O.sativa_LOC_Os01 g55190.1 1 15 1 16
O.sativa_LOC_Os03g59300.1 1 17 1 18
P.sitchensis_TA10533_3332 1 19 120
P.sitchensis_TA14284_3332 121 122
P.taeda_TA10429_3352 123 124
P.taeda_TA4773_3352 125 126
P.trichocarpa_549292 127 128
P.trichocarpa_735032 129 130
P.trichocarpa_833200 131 132
P.trifoliata_TA6477_37690 133 134
P.virgatum_TC7090 135 136
P.vulgaris_TC10932 137 138
S.bicolor_Sb01 g004270.1 139 140
S.bicolor_Sb03g034960.1 141 142
S.lycopersicum_TC198542 143 144
S.lycopersicum_TC199778 145 146
S.officinarum_TC76182 147 148
S.tuberosum_TC189725 149 150
T.aestivum_TC292522 151 152
T.cacao TC4474 153 154
T.officinale_TA3338_50225 155 156
P.trichocarpa_DUF 157 158 P. trichocarpa PP_MUB2 159 160
Triphysaria_sp_TC1 1756 161 162
Triphysaria_sp_TC1599 163 164
V.vinifera_GSVIVT00025589001 165 166
V.vinifera_GSVIVT00028751001 167 168
Z.mays_c57213778gm030403@389 169 170
Z.mays_c62082358gm030403@7546 171 172
Z.mays_TC506958 173 174
Z.mays_ZM07MC26525_BFb021 1C02@26447 175 176
Z.officinale_TA720_94328 177 178
Z. mays_GRMZM2G324705_T01 179 180
2. epimerase-related like polypeptides
Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 197 and SEQ ID NO: 198 were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calculating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid of SEQ I D NO: 197 was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E- value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
Table A2 provides SEQ ID NO: 197 and SEQ I D NO: 198. and a list of nucleic acid and protein sequences related to SEQ ID NO: 197 and SEQ ID NO: 198. Table A2: Examples of an epimerase-related like nucleic acids and polypeptides:
Plant Source SEQ ID NO: SEQ ID NO:
protein nucleic acid
Poptr_epimerase-related 198 197
Z.mays_ZM07MC24472_BFb0052A17@24402 200 199
A.lyrata_486720 202 201 A.lyrata_489502 204 203
A.thaliana_AT3G62130.1 206 205
A.thaliana_AT5G26600.1 208 207
Aquilegia_sp_TC26581 210 209
B.napus_TC63646 212 21 1
C.clementina_TC23968 214 213
C.sinensis TC2568 216 215
G.hirsutum_TC132670 218 217
G.max_Glyma02g01070.1 220 219
G.max_Glyma03g38740.1 222 221
G.max_Glyma19g41330.1 224 223
G.max_Glyma20g22430.1 226 225
H.vulgare_TC158694 228 227
M.truncatula_AC151948_16.5 230 229
M.truncatula_AC166315_9.4 232 231
O.sativa_LOC_Os01 g18640.1 234 233
O.sativa_LOC_Os01 g18660.1 236 235
P.patens_175806 238 237
P.patens_TC39863 240 239
P.persica_TC12771 242 241
P.trichocarpa_570656 244 243
P.trichocarpa_572528 246 245
S.bicolor_Sb03g01 1840.1 248 247
S.bicolor_Sb03g01 1840.2 250 249
S.bicolor_Sb03g01 1840.3 252 251
S.bicolor_Sb03g01 1850.1 254 253
S.lycopersicum_TC191918 256 255
S.moellendorffii_232064 258 257
S.moellendorffii_413706 260 259
S.tuberosum_TC167698 262 261
T.aestivum_TC278728 264 263
V.vinifera_GSVIVT00028240001 266 265
Z.mays_TC513613 268 267
Zea_mays_GRMZM2G077212_T01 270 269
Zea_mays_GRMZM2G322186_T01 272 271 3. PLPCase polypeptides
Sequences (full length cDNA, ESTs or genomic) related to SEQ ID NO: 284 and SEQ ID NO: 285 were identified amongst those maintained in the Entrez Nucleotides database at the National Center for Biotechnology Information (NCBI) using database sequence search tools, such as the Basic Local Alignment Tool (BLAST) (Altschul et al. (1990) J. Mol. Biol. 215:403-410; and Altschul et al. (1997) Nucleic Acids Res. 25:3389-3402). The program is used to find regions of local similarity between sequences by comparing nucleic acid or polypeptide sequences to sequence databases and by calcu lating the statistical significance of matches. For example, the polypeptide encoded by the nucleic acid of SEQ I D NO: 284 was used for the TBLASTN algorithm, with default settings and the filter to ignore low complexity sequences set off. The output of the analysis was viewed by pairwise comparison, and ranked according to the probability score (E-value), where the score reflect the probability that a particular alignment occurs by chance (the lower the E- value, the more significant the hit). In addition to E-values, comparisons were also scored by percentage identity. Percentage identity refers to the number of identical nucleotides (or amino acids) between the two compared nucleic acid (or polypeptide) sequences over a particular length. In some instances, the default parameters may be adjusted to modify the stringency of the search. For example the E-value may be increased to show less stringent matches. This way, short nearly exact matches may be identified.
Table A3 provides a list of nucleic acid and protein sequences related to SEQ ID NO: 284 and SEQ ID NO: 285.
Table A3: Examples of PLPCase nucleic acids and polypeptides:
Plant Source Nucleic acid Protein
SEQ ID NO: SEQ ID NO:
M.truncatula_PLPCase 284 285
A.thaliana_AT3G15650.1 #1 286 287
A.thaliana_AT1 G52470.1 #1 288 289
G.max_Glyma13g43990.1#1 290 291
G.max_Glyma08g22420.1#1 292 293
G.max_Glyma07g03670.1#1 294 295
A.thaliana_AT1 G52700.1 #1 296 297
G.max_GM06MC00001_45093526@1#1 298 299
P.trichocarpa_TC89207#1 300 301
T.aestivum_c55164328@10990#1 302 303
Z.mays_c58236581 gm030403@14151#1 304 305
H.vulgare_BI948365#1 306 307
H.annuus_TC40709#1 308 309
B.napus_TC92944#1 310 31 1
B.napus_BN06MC12702_43481925@12666#1 312 313
A.thaliana_AT5G20060.1 #1 314 315 B.napus_BN06MC00524_46010623@523#1 316 317
H.annuus_TC45565#1 318 319
M.truncatula_AC148176_15.5#1 320 321
O.sativa_LOC_Os01 g07960.1 #1 322 323
Z.mays_TC480822#1 324 325
P . tri ch oca rpa_scaff_VI .1824# 1 326 327
P.trichocarpa_809106#1 328 329
G.max_TC317555#1 330 331
G.max_Glyma04g07280.1#1 332 333
Z.mays_TC563901#1 334 335
Z.mays_ZM07MC31087_BFb0267E17@30994#1 336 337
T.aestivum_TC296583#1 338 339
Zea_mays_GRMZM2G481362_T01 #1 340 341
O.sativa_LOC_Os01 g42690.1 #1 342 343
O.sativa_LOC_Os05g51050.1 #1 344 345
Z.mays_ZM07MC23122_BFb0221 H24@23057#1 346 347
Sequences have been tentatively assembled and publicly disclosed by research institutions, such as The Institute for Genomic Research (TIGR; beginning with TA). For instance, the Eukaryotic Gene Orthologs (EGO) database may be used to identify such related sequences, either by keyword search or by using the BLAST algorithm with the nucleic acid sequence or polypeptide sequence of interest. Special nucleic acid sequence databases have been created for particular organisms, e.g. for certain prokaryotic organisms, such as by the Joint Genome Institute. Furthermore, access to proprietary databases, has allowed the identification of novel nucleic acid and polypeptide sequences.
Example 2: Alignment of sequences to the polypeptide sequences used in the methods of the invention
1. DUF642 polypeptides
Alignment of polypeptide sequences was performed using the AlignX alignment of Vector NTI, Invitrogen, 10.3 (2006) with gap opening penalty of 10.0, gap extension penalty of 0.05 and gap separation penalty range 8. The DUF642 polypeptides are aligned in Figure 2, showing DUF642 polypeptides of clades A and B. Figure 3 shows an alignment of the DUF642 polypeptides of clade A (as shown in Figure 5). A phylogenetic tree of DUF642 polypeptides (Figure 5) was constructed by aligning DUF642 sequences using MAFFT (Katoh and Toh (2008) - Briefings in Bioinformatics 9:286-298). A neighbour-joining tree was calculated using Quick-Tree (Howe et al. (2002), Bioinformatics 18(1 1 ): 1546-7), 100 bootstrap repetitions. The dendrogram was drawn using Dendroscope (Huson et al. (2007), BMC Bioinformatics 8(1 ):460). Confidence levels for 100 bootstrap repetitions are indicated for major branchings. 2. epimerase-related like polypeptides
Alignment of polypeptide sequences was performed using MAFFT (version 6.624, L-INS-I method - Katoh and Toh (2008) - Briefings in Bioinformatics 9:286-298). Minor manual editing was done to further optimize the alignment. A representative number of epimerase- related like polypeptides are aligned in Figure 9.
A phylogenetic tree of epimerase-related like polypeptides (Figure 10) was constructed by aligning epimerase-related like sequences using MAFFT (Katoh and Toh (2008) - Briefings in Bioinformatics 9:286-298). A neighbour-joining tree was calculated using Quick-Tree (Howe et al . (2002), Bioi nformatics 18(1 1 ): 1 546-7), 100 bootstrap repetitions. The dendrogram was drawn using Dendroscope (Huson et al. (2007), BMC Bioinformatics 8(1 ):460). Confidence levels for 100 bootstrap repetitions are indicated for major branchings. 3. PLPCase polypeptides
Alignment of polypeptide sequences is performed using the ClustalW 2.0 algorithm of progressive alignment (Thompson et al. (1997) Nucleic Acids Res 25:4876-4882; Chenna et al. (2003). Nucleic Acids Res 31 :3497-3500) with standard setting (slow alignment, similarity matrix: Gonnet, gap opening penalty 10, gap extension penalty: 0.2). Minor manual editing was done to further optimise the alignment.
A phylogenetic tree of PLPCase polypeptides (Figure 14) was constructed by aligning PLPCase sequences using MAFFT (Katoh and Toh (2008) - Briefings in Bioinformatics 9:286-298). A neighbour-joining tree was calculated using Quick-Tree (Howe et al. (2002), Bioinformatics 18(1 1 ): 1546-7), 100 bootstrap repetitions. A circular dendrogram was drawn using Dendroscope 2.0.1 (Huson et al. (2007), BMC Bioinformatics 8(1 ):460). Confidence levels for 100 bootstrap repetitions are indicated for major branchings.
Example 3: Calculation of global percentage identity between polypeptide sequences
Global percentages of similarity and identity between full length polypeptide sequences useful in performing the methods of the invention were determined using MatGAT (Matrix Global Alignment Tool) software (BMC Bioinformatics. 2003 4:29. MatGAT: an application that generates similarity/identity matrices using protein or DNA sequences. Campanella JJ, Biti ncka L, S mal ley J ; software h osted by Led ion Biti ncka) . MatGAT generates similarity/identity matrices for DNA or protein sequences without needing pre-alignment of the data. The program performs a series of pair-wise alignments using the Myers and Miller global alignment algorithm, calculates similarity and identity, and then places the results in a distance matrix. 1. DUF642 polypeptides
Results of an analysis for clade A are shown in Figure 6 for the global similarity and identity over the full length of the polypeptide sequences. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line. Parameters used in the comparison were: Scoring matrix: Blosum62, First Gap: 12, Extending Gap: 2. The sequence identity (in %) between the DUF642 polypeptide sequences of clade A+B useful in performing the methods of the invention can be as low as 29,7 % (is generally higher than 29,7%) compared to SEQ ID NO: 2 or 4. The sequence identity (in %) between the DUF642 polypeptide sequences of clade A useful in performing the methods of the invention can be as low as 38,4 % (is generally higher than 38,4%) compared to SEQ ID NO: 2 or 4. Table B1 : Description of proteins in figure 6:
1. Os_DUF642.3
2. Os_DUF642.2
3. O.sativa_LOC_Os01 g42520.1
4. O.sativa_LOC_Os04g41710.1
5. O.sativa_LOC_Os04g41740.1
6. O.sativa_LOC_Os04g41750.1
7. O.sativa_LOC_Os04g41759.1
8. O.sativa_LOC_Os04g41770.1
9. P.virgatum_TC46275
~ 10. S.bicolor_Sb03g027650.1
1 1. S.bicolor_Sb06g021270.1
12. S.bicolor_Sb06g021280.1
~ 13. S.bicolor_Sb06g021290.1
~14. S.bicolor_Sb06g021300.1
~ 15. S.bicolor_Sb06g021310.1
~ 16. S.bicolor_Sb06g021320.1
17. T.aestivum_c60008104@11410
18. Z.mays_TC458850
19. Z.mays_TC468877
20. Z.mays_ZM07MC22756_BFb0088A01 @22693
21. Zea_mays_GRMZM2G034985_T02
22. Zea_mays_GRMZM2G051898_T01
23. Zea mays GRMZM2G051912 T01
24. Zea_mays_GRMZM2G405071_T01
25. O.sativa_LOC_Os02g1 1040.1
26. P.virgatum TC392
27. S.bicolor_Sb04g007160.1
28. Z.mays_TC467870 2. epimerase-related like polypeptides
Results of the analysis are shown in Figure 1 1 for the global similarity and identity over the full length of the polypeptide sequences. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line. Parameters used in the comparison were: Scoring matrix: Blosum62, First Gap: 12, Extendi ng Gap: 2. The sequence identity (in %) between the epimerase-related like polypeptide sequences useful in performing the methods of the invention is generally higher than 40% compared to SEQ ID NO: 198. A MATGAT table for local alignment of a specific domain, or data on % identity/similarity between specific domains can also be made.
3. PLPCase polypeptides
Results of the analysis are shown in Figure 15 for the global similarity and identity over the full length of the polypeptide sequences. Sequence similarity is shown in the bottom half of the dividing line and sequence identity is shown in the top half of the diagonal dividing line. Parameters used in the comparison were: Scoring matrix: Blosum62, First Gap: 12, Extending Gap: 2. The sequence identity (in %) between the PLPCase polypeptide sequences useful in performing the methods of the invention can be as low as 24%, but is generally higher than 24%, compared to SEQ ID NO: 285.
Table B2: Description of proteins in figure 15:
1 . M.truncatula_PLPCase
2. A.thaliana_AT3G15650.1#1
3. A.thaliana_AT1 G52470.1#1
4. G.max_Glyma13g43990.1#1
5. G.max_Glyma08g22420.1#1
6. G.max_Glyma07g03670.1#1
7. A.thaliana_AT1 G52700.1#1
8. G.max_GM06MC00001_45093526@1 #1
9. P.trichocarpa_TC89207#1
10. T.aestivum_c55164328@10990#1
1 1. Z.mays_c58236581 gm030403@14151 #1
12. H.vulgare_BI948365#1
13. H.annuus_TC40709#1
14. B.napus_TC92944#1
15. B.napus_BN06MC12702_43481925@12666#1
16. A.thaliana_AT5G20060.1 #1
17. B.napus_BN06MC00524_46010623@523#1
18. H.annuus_TC45565#1
19. M.truncatula_AC148176_15.5#1
20. O.sativa_LOC_Os01g07960.1#1 21. Z.mays_TC480822#1
22. P.trichocarpa_scaff_VI.1824#1
23. P.trichocarpa_809106#1
24. G.max_TC317555#1
25. G.max_Glyma04g07280.1#1
26. Z.mays_TC563901#1
27. Z.mays_ZM07MC31087_BFb0267E17@30994#1
28. T.aestivum_TC296583#1
29. Zea_mays_GRMZM2G481362_T01#1
30. O.sativa_LOC_Os01g42690.1#1
31. O.sativa_LOC_Os05g51050.1 #1
32. Z.mays_ZM07MC23122_BFb0221 H24@23057#1
As can be seen from the MatGAT table in figure 15, PLPCase can be separated into three clusters: Cluster A: containing PLPCase of dicot origin, Cluster B: containing PLPCase of dicot and monocot origin and Cluster C: containing PLPCase of monocot origin.
Example 4: Identification of domains comprised in polypeptide sequences useful in performing the methods of the invention
The Integrated Resource of Protein Families, Domains and Sites (InterPro) database is an integrated interface for the commonly used signature databases for text- and sequence- based searches. The InterPro database combines these databases, which use different methodologies and varying degrees of biological information about well-characterized proteins to derive protein signatures. Collaborating databases include SWISS-PROT, PROSITE, TrEMBL, PRINTS, ProDom and Pfam, Smart and TIGRFAMs. Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains and families. Pfam is hosted at the Sanger Institute server in the United Kingdom. Interpro is hosted at the European Bioinformatics Institute in the United Kingdom.
1. DUF642 polypeptides
The results of the InterPro scan (InterPro database, release 4.7) of the polypeptide sequence as represented by SEQ ID NO: 2 and 4, respectively, are presented in Table C1.
Table C1 : InterPro scan results (major accession numbers) of the polypeptide sequence as represented by SEQ ID NO: 2 and 4.
Figure imgf000101_0001
In an embodiment a DUF642 polypeptide comprises a conserved domain (or motif) with at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to a conserved domain from amino acid 51 to 371 in SEQ ID NO:2 or from amino acid 28 to 194 of SEQ ID NO: 4.
2. epimerase-related like polypeptides
The results of the InterPro scan (InterPro database, release 30.0) of the polypeptide sequence as represented by SEQ ID NO: 198 are presented in Table C2.
Table C2: InterPro scan results (major accession numbers) of the polypeptide sequence as represented by SEQ ID NO: 198.
Figure imgf000103_0001
An epimerase-related like polypeptide according to the invention comprises a conserved domain (or motif) with at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% sequence identity to or consists of a conserved domain selected from any one of:
- amino acid coordinates 32 to 449 in SEQ ID NO: 198;
- amino acid coordinates 47 to 276 in SEQ ID NO: 198;
- amino acid coordinates 92 to 364 in SEQ ID NO: 198; and
- amino acid coordinates 59 to 323 in SEQ I D NO: 198.
3. PLPCase polypeptides
The results of the InterPro scan (InterPro database, version 4.6) of the polypeptide sequence as represented by SEQ ID NO: 285 are presented in Table C3.
Table C3: InterPro scan results (major accession numbers) of the polypeptide sequence as represented by SEQ ID NO: 285.
Figure imgf000104_0001
In an embodiment a PLPCase polypeptide comprises a conserved domain or motif with at least 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87% , 88%, 89% , 90% , 91 %, 92%, 93%, 94% , 95% , 96%, 97% , 98%, or 99% sequence identity to a conserved domain from amino acid 24 to 248 in SEQ ID NO: 285.
Example 5: Topology prediction of the polypeptide sequences useful in performing the methods of invention
TargetP 1.1 predicts the subcellular location of eukaryotic proteins. The location assignment is based on the predicted presence of any of the N-terminal pre-sequences: chloroplast transit peptide (cTP), mitochondrial targeting peptide (mTP) or secretory pathway signal peptide (SP). Scores on which the final prediction is based are not really probabilities, and they do not necessarily add to one. However, the location with the highest score is the most likely according to TargetP, and the relationship between the scores (the reliability class) may be an indication of how certain the prediction is. The reliability class (RC) ranges from 1 to 5, where 1 indicates the strongest prediction. For the sequences predicted to contain an N-terminal presequence a potential cleavage site can also be predicted. TargetP is maintained at the server of the Technical University of Denmark.
A number of parameters must be selected before analysing a sequence, such as organism group (non-plant or plant), cutoff sets (none, predefined set of cutoffs, or user-specified set of cutoffs), and the calculation of prediction of cleavage sites (yes or no).
Many other algorithms can be used to perform such analyses, including:
ChloroP 1.1 hosted on the server of the Technical University of Denmark;
• Protein Prowler Subcellular Localisation Predictor version 1 .2 hosted on the server of the Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia; · PENCE Proteome Analyst PA-GOSUB 2.5 hosted on the server of the University of Alberta, Edmonton, Alberta, Canada;
TMHMM, hosted on the server of the Technical University of Denmark
PSORT (URL: psort.org)
PLOC (Park and Kanehisa, Bioinformatics, 19, 1656-1663, 2003).
Example 6: Cloning of the nucleic acid sequence used in methods of the invention
1. DUF642 polypeptides
The nucleic acid sequence was amplified by PCR using as template a custom-made Oryza sativa seedlings cDNA library. PCR was performed using a commercially available proofreading Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μΙ PCR mix.
In a first experiment A, the primers used were prm16414 (SEQ ID NO: 190; sense): 5'- ggggacaagtttgtacaaaaaagcaggcttaaacaatgagaagaaaaacagagatg-3' and prm16415 (SEQ ID NO: 191 ; reverse, complementary): 5'-ggggaccactttgtacaagaaagctgggtataatattacagaaggaaccg -3', which include the AttB sites for Gateway recombination.
In a second experiment B, the primers used were prm16412 (SEQ ID NO: 192; sense): 5'- ggggacaagtttgtacaaaaaagcaggcttaaacaatggtgctggtggtccc-3' and prm16413 (SEQ ID NO: 193; reverse, complementary): 5'-ggggaccactttgtacaagaaagctgggttagtacgacatcgcggca-3', wh ich include the AttB sites for Gateway recombination.
The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed , during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an "entry clone", pDUF642. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology. In the first experiment A, the entry clone comprising SEQ ID NO: 1 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 189) for constitutive expression was located upstream of this Gateway cassette.
In the second experiment B, the entry clone comprising SEQ ID NO: 3 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ ID NO: 189) for constitutive expression was located upstream of this Gateway cassette.
In a further experiment, all steps as described above were executed for the cloning of SEQ ID NO: 159. Prime rs u se d we re prm 1 31 82 ( S E Q I D N O : 1 95 ; se n se) : 5 '- ggggacaagtttgtacaaaaaagcaggcttaaacaatgtttcaaagct caacaaga-3' and prm13183 (SEQ ID NO: 196; reverse, complementary): 5'-ggggaccactttgta caagaaagctgggtctctttctccccattcaaac 3', which include the AttB sites for Gateway recombination.
The entry clone comprising SEQ I D NO: 159 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (S EQ I D NO: 189) for constitutive expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vectors pGOS2::DUF642 (Figure 7) were transformed into Agrobacterium strain LBA4044 according to methods well known in the art. 2. epimerase-related like polypeptides
The nucleic acid sequence was amplified by PCR using as template a custom-made Populus trichocarpa seedlings cDNA library. PCR was performed using a commercially available proofreading Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μΙ PCR mix. The primers used were prm18733 (SEQ ID NO: 276; sense, start codon in bold): 5' ggggacaagtttgtacaaaaaagcaggcttaaacaatgcaagaaaactccaaagat 3' and prm18734 (SEQ ID NO: 277; reverse, complementary): 5' ggggaccactttgtacaagaaagctg ggtgcataccttctcactctggat 3', which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed, during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an "entry clone", pERL ("ERL" stands for "epimerase-related like"). Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ I D NO: 197 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ I D NO: 278) for constitutive expression was located upstream of this Gateway cassette. After the LR recombination step, the resulting expression vector pGOS2::ERL (Figure 12) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
3. PLPCase polypeptides
The nucleic acid sequence was amplified by PCR using as template a custom-made Medicago truncatula seedlings cDNA library. PCR was performed using a commercially available proofreading Taq DNA polymerase in standard conditions, using 200 ng of template in a 50 μΙ PCR mix. The primers used were prm15409 (SEQ ID NO: 362; sense, start codon in bold): 5'-ggggacaagtttgtacaaaaaagcaggcttaaacaatgagtcacgcgcattctc-3' and prm 1 541 0 (S EQ I D NO: 363; reverse, complementary) : 5'-ggggaccactttgtacaagaaa gctgggtaa aatagttttgtcatttacgacg-3', which include the AttB sites for Gateway recombination. The amplified PCR fragment was purified also using standard methods. The first step of the Gateway procedure, the BP reaction, was then performed , during which the PCR fragment recombined in vivo with the pDONR201 plasmid to produce, according to the Gateway terminology, an "entry clone", pPLPCase. Plasmid pDONR201 was purchased from Invitrogen, as part of the Gateway® technology.
The entry clone comprising SEQ I D NO: 284 was then used in an LR reaction with a destination vector used for Oryza sativa transformation. This vector contained as functional elements within the T-DNA borders: a plant selectable marker; a screenable marker expression cassette; and a Gateway cassette intended for LR in vivo recombination with the nucleic acid sequence of interest already cloned in the entry clone. A rice GOS2 promoter (SEQ I D NO: 361 ) for constitutive expression was located upstream of this Gateway cassette.
After the LR recombination step, the resulting expression vector pGOS2:: PLPCase (Figure 16) was transformed into Agrobacterium strain LBA4044 according to methods well known in the art.
In the same way an expression vector comprising SEQ ID NO: 286 was prepared using primers prm1541 1 (SEQ ID NO: 364, sense): 5'- ggggacaagtttgtacaaaaaagcaggcttaaacaa tgagctattctcgtcaaagc-3' and prm15412 (SEQ ID NO: 365; reverse, complementary): 5'- ggggaccactttgtacaagaaagctgggttgctgagaagatgcttgtaaa-3'.
Example 7: Plant transformation
Rice transformation
The Agrobacterium containing the expression vector was used to transform Oryza sativa plants. Matu re dry seeds of the rice japon ica cu ltivar Nipponbare were dehusked . Sterilization was carried out by incubating for one minute in 70% ethanol, followed by 30 to 60 minutes, preferably 30 minutes in sodium hypochlorite solution (depending on the grade of contamination), followed by a 3 to 6 times, preferably 4 time wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in light for 6 days scutellum-derived calli is transformed with Agrobacterium as described herein below. Alternatively, the incubation step in ethanol was followed by a 30 minutes incubation in 0.2% HgC , followed by a 6 times 15 minutes wash with sterile distilled water. The sterile seeds were then germinated on a medium containing 2,4-D (callus induction medium). After incubation in the dark for four weeks, embryogenic, scutellum-derived calli were excised and propagated on the same medium. After two weeks, the calli were multiplied or propagated by subculture on the same medium for another 2 weeks. Embryogenic callus pieces were sub-cultured on fresh medium 3 days before co-cultivation (to boost cell division activity).
Agrobacterium strain LBA4404 containing the expression vector was used for co-cultivation. Agrobacterium was inoculated on AB medium with the appropriate antibiotics and cultured for 3 days at 28°C. The bacteria were then collected and suspended in liquid co-cultivation medium to a density (Οϋβοο) of about . The calli were immersed in the suspension for 1 to 15 minutes. The callus tissues were then blotted dry on a filter paper and transferred to solidified, co-cultivation medium and incubated for 3 days in the dark at 25°C. After washing away the Agrobacterium, the calli were grown on 2,4-D-containing medium for 10 to 14 days (growth time for indica: 3 weeks) under light at 28°C - 32°C in the presence of a selection agent. Alternatively co-cultivated calli were grown on 2,4-D-containing medium for 4 weeks in the dark at 28°C in the presence of a selection agent. During this period, rapidly growing resistant callus developed. After transfer of this material to regeneration media, the embryogenic potential was released and shoots developed in the next four to six weeks. Shoots were excised from the calli and incubated for 2 to 3 weeks on an auxin-containing medium from which they were transferred to soil. Hardened shoots were grown under high humidity and short days in a greenhouse.
Transformation of rice cultivar indica can also be done in a similar way as give above according to techniques well known to a skilled person.
Approximately 35 to 90 independent TO rice transformants were generated for one construct. The primary transformants were transferred from a tissue culture chamber to a greenhouse. After a quantitative PCR analysis to verify copy number of the T-DNA insert, only single copy transgenic plants that exhibit tolerance to the selection agent were kept for harvest of T1 seed. Seeds were then harvested three to five months after transplanting. The method yielded single locus transformants at a rate of over 50 % (Aldemita and Hodges1996, Chan et al. 1993, Hiei et al. 1994).
Example 8: Transformation of other crops
Corn transformation
Transformation of maize (Zea mays) is performed with a modification of the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. Transformation is genotype- dependent in corn and only specific genotypes are amenable to transformation and regeneration. The inbred line A188 (University of Minnesota) or hybrids with A188 as a parent are good sources of donor material for transformation, but other genotypes can be used successfully as well. Ears are harvested from corn plant approximately 1 1 days after pollination (DAP) when the length of the immature embryo is about 1 to 1 .2 mm. Immature embryos are cocultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. Excised embryos are grown on callus induction medium, then maize regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25 °C for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to maize rooting medium and incubated at 25 °C for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert. Wheat transformation
Transformation of wheat is performed with the method described by Ishida et al. (1996) Nature Biotech 14(6): 745-50. The cultivar Bobwhite (available from CIMMYT, Mexico) is commonly used in transformation. Immature embryos are co-cultivated with Agrobacterium tumefaciens containing the expression vector, and transgenic plants are recovered through organogenesis. After incubation with Agrobacterium, the embryos are grown in vitro on callus induction medium, then regeneration medium, containing the selection agent (for example imidazolinone but various selection markers can be used). The Petri plates are incubated in the light at 25 °C for 2-3 weeks, or until shoots develop. The green shoots are transferred from each embryo to rooting medium and incubated at 25 °C for 2-3 weeks, until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert. Soybean transformation
Soybean is transformed according to a modification of the method described in the Texas A&M patent US 5,164,310. Several commercial soybean varieties are amenable to transformation by this method. The cultivar Jack (available from the Illinois Seed foundation) is commonly used for transformation. Soybean seeds are sterilised for in vitro sowing. The hypocotyl , the radicle and one cotyledon are excised from seven-day old young seedlings. The epicotyl and the remaining cotyledon are further grown to develop axillary nodes. These axillary nodes are excised and incubated with Agrobacterium tumefaciens containing the expression vector. After the cocultivation treatment, the explants are washed and transferred to selection media. Regenerated shoots are excised and placed on a shoot elongation medium. Shoots no longer than 1 cm are placed on rooting medium until roots develop. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Rapeseed/canola transformation
Cotyledonary petioles and hypocotyls of 5-6 day old young seedling are used as explants for tissue culture and transformed according to Babic et al. (1998, Plant Cell Rep 17: 183- 188). The commercial cultivar Westar (Agriculture Canada) is the standard variety used for transformation, but other varieties can also be used. Canola seeds are surface-sterilized for in vitro sowing. The cotyledon petiole explants with the cotyledon attached are excised from the in vitro seedlings, and inoculated with Agrobacterium (containing the expression vector) by dipping the cut end of the petiole explant into the bacterial suspension. The explants are then cultured for 2 days on MSBAP-3 medium containing 3 mg/l BAP, 3 % sucrose, 0.7 % Phytagar at 23 °C, 16 hr light. After two days of co-cultivation with Agrobacterium, the petiole explants are transferred to MSBAP-3 medium containing 3 mg/l BAP, cefotaxime, carbenicillin, or timentin (300 mg/l) for 7 days, and then cultured on MSBAP-3 medium with cefotaxime, carbenicillin, or timentin and selection agent until shoot regeneration. When the shoots are 5 - 10 mm in length, they are cut and transferred to shoot elongation medium (MSBAP-0.5, containing 0.5 mg/l BAP). Shoots of about 2 cm in length are transferred to the rooting medium (MS0) for root induction. The rooted shoots are transplanted to soil in the greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Alfalfa transformation
A regenerating clone of alfalfa {Medicago sativa) is transformed using the method of (McKersie et al., 1999 Plant Physiol 119: 839-847). Regeneration and transformation of alfalfa is genotype dependent and therefore a regenerating plant is required. Methods to obtain regenerating plants have been described. For example, these can be selected from the cultivar Rangelander (Agriculture Canada) or any other commercial alfalfa variety as described by Brown DCW and A Atanassov (1985. Plant Cell Tissue Organ Culture 4: 1 1 1 - 1 12). Alternatively, the RA3 variety (University of Wisconsin) has been selected for use in tissue culture (Walker et al., 1978 Am J Bot 65:654-659). Petiole explants are cocultivated with an overnight culture of Agrobacterium tumefaciens C58C1 pMP90 (McKersie et al., 1999 Plant Physiol 1 19: 839-847) or LBA4404 containing the expression vector. The explants are cocultivated for 3 d in the dark on SH induction medium containing 288 mg/ L Pro, 53 mg/ L thioproline, 4.35 g/ L K2S04, and 100 μιη acetosyringinone. The explants are washed in half-strength Murashige-Skoog medium (Murashige and Skoog, 1962) and plated on the same SH induction medium without acetosyringinone but with a suitable selection agent and suitable antibiotic to inhibit Agrobacterium growth. After several weeks, somatic embryos are transferred to BOi2Y development medium containing no growth regulators, no anti biotics, and 50 g/ L sucrose. Somatic embryos are subsequently germinated on half-strength Murashige-Skoog medium. Rooted seedlings were transplanted into pots and grown in a greenhouse. T1 seeds are produced from plants that exhibit tolerance to the selection agent and that contain a single copy of the T-DNA insert.
Cotton transformation
Cotton is transformed using Agrobacterium tumefaciens according to the method described in US 5,159,135. Cotton seeds are surface sterilised in 3% sodium hypochlorite solution during 20 minutes and washed in distilled water with 500 pg/ml cefotaxime. The seeds are then transferred to SH-medium with 50pg/ml benomyl for germination. Hypocotyls of 4 to 6 days old seedlings are removed, cut into 0.5 cm pieces and are placed on 0.8% agar. An Agrobacterium suspension (approx. 108 cells per ml, diluted from an overnight culture transformed with the gene of interest and suitable selection markers) is used for inoculation of the hypocotyl explants. After 3 days at room temperature and lighting, the tissues are transferred to a solid medium (1 .6 g/l Gelrite) with Murashige and Skoog salts with B5 vitamins (Gamborg et al., Exp. Cell Res. 50:151 -158 (1968)), 0.1 mg/l 2,4-D, 0.1 mg/l 6- furfurylaminopurine and 750 pg/ml MgCL2, and with 50 to 100 pg/ml cefotaxime and 400- 500 μg/ml carbenicillin to kill residual bacteria. Individual cell lines are isolated after two to three months (with subcultures every four to six weeks) and are further cultivated on selective medium for tissue amplification (30°C, 16 hr photoperiod). Transformed tissues are subsequently further cultivated on non-selective medium during 2 to 3 months to give rise to somatic embryos. Healthy looking embryos of at least 4 mm length are transferred to tubes with SH medium in fine vermiculite, supplemented with 0.1 mg/l indole acetic acid, 6 furfurylaminopurine and gibberellic acid. The embryos are cultivated at 30°C with a photoperiod of 16 hrs, and plantlets at the 2 to 3 leaf stage are transferred to pots with vermiculite and nutrients. The plants are hardened and subsequently moved to the greenhouse for further cultivation.
Sugarbeet transformation
Seeds of sugarbeet (Beta vulgaris L.) are sterilized in 70% ethanol for one minute followed by 20 min. shaking in 20% Hypochlorite bleach e.g. Clorox® regular bleach (commercially available from Clorox, 1221 Broadway, Oakland, CA 94612, USA). Seeds are rinsed with sterile water and air dried followed by plating onto germinating medium (Murashige and Skoog (MS) based medium (Murashige, T., and Skoog, ., 1962. Physiol. Plant, vol. 15, 473- 497) including B5 vitamins (Gamborg et al.; Exp. Cell Res., vol. 50, 151 -8.) supplemented with 10 g/l sucrose and 0,8% agar). Hypocotyl tissue is used essentially for the initiation of shoot cultures according to Hussey and Hepher (Hussey, G., and Hepher, A., 1978. Annals of Botany, 42, 477-9) and are maintained on MS based medium supplemented with 30g/l sucrose plus 0,25mg/l benzylamino purine and 0,75% agar, pH 5,8 at 23-25°C with a 16- hour photoperiod. Agrobacterium tumefaciens strain carrying a binary plasmid harbouring a selectable marker gene, for example nptll, is used in transformation experiments. One day before transformation, a liquid LB culture including antibiotics is grown on a shaker (28°C, 150rpm) until an optical density (O.D.) at 600 nm of ~ 1 is reached. Overnight-grown bacterial cu ltu res are centrifuged and resuspended in inoculation medium (O.D. ~1 ) including Acetosyringone, pH 5,5. Shoot base tissue is cut into slices (1 .0 cm x 1 .0 cm x 2.0 mm approximately). Tissue is immersed for 30s in liquid bacterial inoculation medium. Excess liquid is removed by filter paper blotting. Co-cultivation occurred for 24-72 hours on MS based medium incl. 30g/l sucrose followed by a non-selective period including MS based medium, 30g/l sucrose with 1 mg/l BAP to induce shoot development and cefotaxim for eliminating the Agrobacterium. After 3-10 days explants are transferred to similar selective medium harbouring for example kanamycin or G418 (50-100 mg/l genotype dependent). Tissues are transferred to fresh medium every 2-3 weeks to maintain selection pressure. The very rapid initiation of shoots (after 3-4 days) indicates regeneration of existing meristems rather than organogenesis of newly developed transgenic meristems. Small shoots are transferred after several rounds of subculture to root induction medium containing 5 mg/l NAA and kanamycin or G418. Additional steps are taken to reduce the potential of generating transformed plants that are chimeric (partially transgenic). Tissue samples from regenerated shoots are used for DNA analysis. Other transformation methods for sugarbeet are known in the art, for example those by Linsey & Gallois (Linsey, K., and Gallois, P., 1990. Journal of Experimental Botany; vol. 41 , No. 226; 529-36) or the methods published in the international application published as W09623891A.
Sugarcane transformation
Spindles are isolated from 6-month-old field grown sugarcane plants (Arencibia et al., 1998. Transgenic Research, vol. 7, 213-22; Enriquez-Obregon et al., 1998. Planta, vol. 206, 20- 27). Material is sterilized by immersion in a 20% Hypochlorite bleach e.g. Clorox® regular bleach (commercially available from Clorox, 1221 Broadway, Oakland, CA 94612, USA) for 20 minutes. Transverse sections around 0,5cm are placed on the medium in the top-up direction. Plant material is cultivated for 4 weeks on MS (Murashige, T., and Skoog, ., 1962. Physiol. Plant, vol. 15, 473-497) based medium incl. B5 vitamins (Gamborg, O., et al., 968. Exp. Cell Res . , vol . 50 , 1 51 -8) supplemented with 20g/l sucrose, 500 mg/l casein hydrolysate, 0,8% agar and 5mg/l 2,4-D at 23°C in the dark. Cultures are transferred after 4 weeks onto identical fresh medium. Agrobacterium tumefaciens strain carrying a binary plasmid harbouring a selectable marker gene, for example hpt, is used in transformation experiments. One day before transformation, a liquid LB culture including antibiotics is grown on a shaker (28°C, 150rpm) until an optical density (O.D.) at 600 nm of ~0,6 is reached. Overnight-grown bacterial cultures are centrifuged and resuspended in MS based inoculation medium (O.D. ~0,4) including acetosyringone, pH 5,5. Sugarcane embryogenic callus pieces (2-4 mm) are isolated based on morphological characteristics as compact structure and yellow colour and dried for 20 min. in the flow hood followed by immersion in a liquid bacterial inoculation medium for 10-20 minutes. Excess liquid is removed by filter paper blotting. Co-cultivation occurred for 3-5 days in the dark on filter paper which is placed on top of MS based medium incl. B5 vitamins containing 1 mg/l 2,4-D. After co- cultivation calli are washed with sterile water followed by a non-selective cultivation period on similar medium containing 500 mg/l cefotaxime for eliminating remaining Agrobacterium cells. After 3-10 days explants are transferred to MS based selective medium incl. B5 vitamins containing 1 mg/l 2,4-D for another 3 weeks harbouring 25 mg/l of hygromycin (genotype dependent). All treatments are made at 23°C under dark conditions. Resistant calli are further cultivated on medium lacking 2,4-D includi ng 1 mg/l BA and 25 mg/l hygromycin under 16 h light photoperiod resulting in the development of shoot structures. Shoots are isolated and cultivated on selective rooting medium (MS based including, 20g/l sucrose, 20 mg/l hygromycin and 500 mg/l cefotaxime). Tissue samples from regenerated shoots are used for DNA analysis. Other transformation methods for sugarcane are known in the art, for example from the in-ternational application published as WO2010/151634A and the granted European patent EP1831378.
Example 9: Phenotypic evaluation procedure
9.1 Evaluation setup
35 to 90 independent TO rice transformants were generated. The primary transformants were transferred from a tissue culture chamber to a greenhouse for growing and harvest of T1 seed. Six events, of which the T1 progeny segregated 3:1 for presence/absence of the transgene, were retained. For each of these events, approximately 10 T1 seedlings containing the transgene (hetero- and homo-zygotes) and approximately 10 T1 seedlings lacking the transgene (nullizygotes) were selected by monitoring visual marker expression. The transgenic plants and the corresponding nullizygotes were grown side-by-side at random positions. Greenhouse conditions were of shorts days (12 hours light), 28°C in the light and 22°C in the dark, and a relative humidity of 70%. Plants grown under non-stress conditions were watered at regular intervals to ensure that water and nutrients were not limiting and to satisfy plant needs to complete growth and development, unless they were used in a stress screen.
From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048x1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles. T1 events can be further evaluated in the T2 generation following the same evaluation procedure as for the T1 generation, e.g. with less events and/or with more individuals per event. Drought screen
T1 or T2 plants were grown in potting soil under normal conditions until they approached the heading stage. They were then transferred to a "dry" section where irrigation was withheld. Soil moisture probes were inserted in randomly chosen pots to monitor the soil water content (SWC). When SWC went below certain thresholds, the plants were automatically re-watered continuously until a normal level was reached again. The plants were then re-transferred again to normal conditions. The rest of the cultivation (plant maturation, seed harvest) was the same as for plants not grown under abiotic stress conditions. Growth and yield parameters were recorded as detailed for growth under normal conditions.
Nitrogen use efficiency screen
T1 or T2 plants were grown in potting soil under normal conditions except for the nutrient solution. The pots were watered from transplantation to maturation with a specific nutrient solution containing reduced N nitrogen (N) content, usually between 7 to 8 times less. The rest of the cultivation (plant maturation, seed harvest) was the same as for plants not grown under abiotic stress. Growth and yield parameters were recorded as detailed for growth under normal conditions.
Salt stress screen
T1 or T2 plants are grown on a substrate made of coco fibers and particles of baked clay (Argex) (3 to 1 ratio). A normal nutrient solution is used during the first two weeks after transplanting the plantlets in the greenhouse. After the first two weeks, 25 mM of salt (NaCI) is added to the nutrient sol ution , u nti l the plants are harvested. Growth and yield parameters are recorded as detailed for growth under normal conditions.
9.2 Statistical analysis: F test
A two factor ANOVA (analysis of variants) was used as a statistical model for the overall evaluation of plant phenotypic characteristics. An F test was carried out on all the parameters measured of all the plants of all the events transformed with the gene of the present invention. The F test was carried out to check for an effect of the gene over all the transformation events and to verify for an overall effect of the gene, also known as a global gene effect. The threshold for significance for a true global gene effect was set at a 5% probability level for the F test. A significant F test value points to a gene effect, meaning that it is not only the mere presence or position of the gene that is causing the differences in phenotype.
When two experiments with overlapping events are carried out, a combined analysis is performed. This is useful to check consistency of the effects over the two experiments, and if this is the case, to accumulate evidence from both experiments in order to increase confidence in the conclusion. The method used is a mixed-model approach that takes into account the multilevel structure of the data (i.e. experiment - event - segregants). P values are obtained by comparing likelihood ratio test to chi square distributions.
9.3 Parameters measured
From the stage of sowing until the stage of maturity the plants were passed several times through a digital imaging cabinet. At each time point digital images (2048x1536 pixels, 16 million colours) were taken of each plant from at least 6 different angles as described in WO2010/031780. These measurements were used to determine different parameters.
Biomass-related parameter measurement
The plant aboveground area (or leafy biomass) ("AreaMax") was determined by counting the total number of pixels on the digital images from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from the different angles and was converted to a physical surface value expressed in square mm by calibration. Experiments show that the aboveground plant area measured this way correlates with the biomass of plant parts above ground. The above ground area is the area measured at the time point at which the plant had reached its maximal leafy biomass.
Increase in root biomass is expressed as an increase in total root biomass ("rootMax") (measured as maximum biomass of roots observed during the lifespan of a plant); or as an increase in the root/shoot index ("RootShlnd"), measured as the ratio between root mass and shoot mass in the period of active growth of root and shoot. In other words, the root/shoot index is defined as the ratio of the rapidity of root growth to the rapidity of shoot growth in the period of active growth of root and shoot. Root biomass can be determined using a method as described in WO 2006/029987.
Parameters related to development time
The early vigour is the plant aboveground area three weeks post-germination. Early vigour was determined by counting the total number of pixels from aboveground plant parts discriminated from the background. This value was averaged for the pictures taken on the same time point from different angles and was converted to a physical surface value expressed in square mm by calibration.
AreaEmer is an indication of quick early development when this value is decreased compared to control plants. It is the ratio (expressed in %) between the time a plant needs to make 30 % of the final biomass and the time needs to make 90 % of its final biomass.
The "time to flower" or "flowering time" ("TimetoFlower") of the plant can be determined using the method as described in WO 2007/093444. Seed-related parameter measurements
The mature primary panicles were harvested, counted, bagged, barcode-labelled and then dried for three days in an oven at 37°C. The panicles were then threshed and all the seeds were collected and counted. The seeds are usually covered by a dry outer covering, the husk. The filled husks (herein also named filled florets) were separated from the empty ones using an air-blowing device. The empty husks were discarded and the remaining fraction was counted again. The filled husks were weighed on an analytical balance.
The total number of seeds was determined by counting the number of filled husks that remained after the separation step. The total seed weight was measured by weighing all filled husks harvested from a plant.
The total seed weight ("totalwgseeds") was measured by weighing all filled husks harvested from a plant.
The total number of seeds (or florets = "nrtotalseeds") per plant was determined by counting the number of husks (whether filled or not) harvested from a plant.
Thousand Kernel Weight (TKW) is extrapolated from the number of seeds counted and their total weight ("totalwgseeds/nrfilledseeds * 1000").
The Harvest Index (HI) in the present invention is defined as the ratio between the total seed weight and the above ground area (mm2) (- 'totalwgseeds/AreaMax), multiplied by a factor 106.
The number of flowers per panicle ("flowerperpan") as defined in the present invention is the ratio between the total number of seeds over the number of mature primary panicles (- 'nrtotalseeds/firstpan" and "firstpan" = number of panicles in the first flush).
The "seed fill rate" or "seed filling rate" as defined in the present invention is the proportion (expressed as a %) of the number of filled seeds (i.e. florets containing seeds = "nrfilledseeds") over the total number of seeds (i.e. total number of florets = "nrtotalseed"). In other words, the seed filling rate is the percentage of florets that are filled with seed. Example 10: Results of the phenotypic evaluation of the transgenic plants
1. DUF642 polypeptides
The results of the evaluation of transgenic rice plants expressing a DUF642 nucleic acid under non-stress conditions are presented below. In the first experiment A using SEQ ID NO: 1 , an increase of at least 5 % was observed for total seed yield (Totalwgseeds), number of seeds (nrfilledseed), seed fill rate (fillrate) and harvest index.
The results of the evaluation of transgenic rice plants in the T1 generation and expressing a nucleic acid encoding the DUF642 polypeptide of SEQ ID NO: 2 under non-stress conditions are presented below in Table D1 . When grown under non-stress conditions, an increase of at least 5 % was observed for total seed yield (Totalwgseeds), number of seeds (nrfilledseed), seed fill rate (fillrate) and harvest index. Moreover, two lines showed an increase in aboveground biomass (AreaMax), and one line showed an increase of Maximum height of the gravity center of the leafy biomass (GravityYMax).
Table D1 : Data summary for transgenic rice plants; for each parameter, the overall percent increase is shown for the T1 generation), for each parameter the p-value is O.05.
Figure imgf000117_0001
In the second experiment B using SEQ ID NO: 3, an increase of at least 5 % was observed for total seed yield (Totalwgseeds), seed fill rate (fillrate) and greenness before flowering.
The results of the evaluation of transgenic rice plants in the T1 generation and expressing a nucleic acid encoding the DUF642 polypeptide of SEQ ID NO: 4 under non-stress conditions are presented below in Table D2. When grown under non-stress conditions, an increase of at least 5 % was observed for total seed yield (Totalwgseeds), seed fill rate (fill- rate) and greenness before flowering. Moreover, two lines showed an increase in above- ground biomass (AreaMax), Height of the highest tip of the plant (HeightMax) and Maximum height of the gravity center of the leafy biomass (GravityYMax).
Table D2: Data summary for transgenic rice plants; for each parameter, the overall percent increase is shown for the T1 generation, for each parameter the p-value is <0.05.
Figure imgf000117_0002
In a further experiment, SEQ ID NO: 159 (in clade B) was used instead of SEQ ID NO: 1 in a drought screen as described above. The results of the evaluation of transgenic rice plants in the T1 generation and expressing a nucleic acid encoding the DUF642 polypeptide of SEQ I D NO: 160 under drought conditions showed an increase of at least 5 % total number of seeds (nrtotalseed) and for aboveground biomass (AreaMax).
In yet another experiment, rice plants transformed with SEQ ID NO: 173 under control of the rice GOS2 promoter were used in a nitrogen use efficiency screen described above. The transgenic rice plants showed an increased fillrate compared to the control plants (overall increase for the 6 tested T1 lines was 10%, p<0.05). 2. epimerase-related like polypeptides
The results of the evaluation of transgenic rice plants of the T1 generation expressing the nucleic acid encoding an epimerase-related like polypeptide of SEQ ID NO: 198 under non- stress conditions are presented below in Table D3.
When grown under non-stress conditions, an increase of at least 5 % was observed for parameters such as seed yield, including total weight of seeds (totalwgseeds), harvest index, and fill rate.
Table D3: Data summary for transgenic rice plants; for each parameter, the overall percent increase is shown for the plants of the T1 generation as compared to control plants, for each parameter the p-value is <0.05.
Figure imgf000118_0001
In addition, it could be noted that transgenic rice plants of at least one event showed an increase of at least 3% for the parameter thousand kernel weight (TKW) as compared to control plants.
Transgenic rice plants of at least two events showed an increase of at least 5% (and in particular on average 8 and 1 1 % increase, respectively) in biomass, particularly above ground biomass( AreaMax), as compared to control plants.
Furthermore, there was a clear tendency for transgenic plants of at least four events to have an increase of at least 5% in number of filled seeds (nrfilledseed) as compared to control plants. 3. PLPCase polypeptides
The results of the evaluation of transgenic rice plants in the T1 generation and expressing a nucleic acid comprising the longest Open Reading Frame in SEQ I D NO: 284 under nitrogen deficiency-stress conditions are presented below. See previous Examples for details on the generations of the transgenic plants.
The results of the evaluation of transgenic rice plants in the T1 generation and expressing a nucleic acid encoding the PLPCase polypeptide of SEQ ID NO: 285 under stress conditions are presented below in Table D4. When grown under nitrogen deficiency-stress conditions, an increase of at least 5 % was observed for root biomass (RootMax, which is the maximal rootmass measured during the life of the plant and RootThickMax, which is the maximal mass of thick roots measured during the life of the plant). Table D4: Data summary for transgenic rice plants; for each parameter, the overall percent increase is shown for the T1 generation, for each parameter the p-value is <0.05.
Figure imgf000119_0001
In addition, plants expressing the above PLPCase showed two lines which were clearly positive for greenness index; three lines were clearly positive for roothinmax, which is the maximal mass of thin roots measured during the life of the plant; and one line was clearly positive for number of filled seeds.
The evaluation of transgenic rice plants expressing a nucleic acid encoding the PLPCase polypeptide of SEQ ID NO: 287 under non-stress conditions are presented below in Table D5. When grown under non-stress conditions, an increase of at least 5 % was observed for root biomass (Root/Shoot Index), and for seed yield (fill rate). In addition, two plant lines expressing the FeS nucleic acid of SEQ ID NO: 286 showed increased total root biomass (resp increase of 14% and 1 1 % , p<0.1 ) and a third line showed increased amount of biomass of roots below a certain thickness threshold (RootThin, +7%, p<0.1 ).
Table D5: Data summary for transgenic rice plants; for each parameter, the overall percent increase is shown, for each parameter the p-value is <0.05.
Parameter Overall increase
Root/Shoot Index 1 1.9
fill rate 8.5

Claims

Claims
1. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding a DUF642 polypeptide, wherein said DUF642 polypeptide comprises an InterPro accession IPR006946 DUF642 domain , preferably said DU F642 polypeptide comprises the signature sequence FSAARTCAQ (SEQ ID NO: 194).
2. Method according to claim 1 , wherei n said modulated expression is effected by introducing and expressing i n a plant said nucleic acid encodi ng said DUF642 polypeptide.
3. Method according to claim 1 or 2, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased biomass and/or increased seed yield relative to control plants.
4. Method according to any one of claims 1 to 3, wherein said enhanced yield-related traits are obtained under non-stress conditions or under abiotic stress conditions.
5. Method according to any of claims 1 to 4, wherein said DUF642 polypeptide comprises one or more of the following motifs:
(i) Motif 1 : N[LAM][VL]KNG[DG]FEEGP[WYH][MI][FLI]P[NG][TS][STR][WL]GVL[LVI] P[PTS][NKM][LQDV][EDV][DE][ED][THY]S[PS]L[PS][GP]W[IMT][IV] (SEQ ID NO:
181 ),
(ii) Motif 2: [VLA][EKAT][KPR]G[SAM][LRH]Y[SA][LIV][TI]F[SG]A[AS]RTCAQ[DLAS] E[SVRL]L[NR][VI] (SEQ ID NO: 182),
(iii) Motif 3: D[PE][AT]CGP[LI][IL]D[AS][VIF]AI[KR] (SEQ ID NO: 183)
6. Method according to any one of claims 1 to 5, wherein said nucleic acid encoding a DUF642 is of plant origin, preferably from a monocotyledonous plant, further preferably from the family Poaceae, more preferably from the genus Oryza, most preferably from Oryza sativa.
7. Method according to any one of claims 1 to 6, wherein said nucleic acid encoding a DUF642 encodes any one of the polypeptides listed in Table A1 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
8. Method according to any one of claims 1 to 7, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A1.
9. Method according to any one of claims 1 to 8, wherein said nucleic acid encodes the polypeptide represented by SEQ ID NO: 2 or SEQ ID NO: 4 or a nucleic acid encoding a polypeptide having at least 90% sequence identity to SEQ ID NO: 2 and/or SEQ ID NO: 4.
10. Method according to any one of claims 1 to 9 wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
1 1 . Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of claims 1 to 10, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a DUF642 polypeptide as defined in any of claims 1 and 5 to 9.
12. Construct comprising:
(i) nucleic acid encoding a DUF642 as defined in any of claims 1 and 5 to 9;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence.
13. Construct according to claim 12, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
14. Use of a construct according to claim 12 or 13 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants.
15. Plant, plant part or plant cell transformed with a construct according to claim 12 or 13.
16. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding a DUF642 polypeptide as defined in any of claims 1 and 5 to 9; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
17. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide as defined in any of claims 1 and 5 to 9 or a transgenic plant cell derived from said transgenic plant.
18. Transgenic plant according to claim 1 1 , 15 or 17, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, einkorn, teff, milo or oats.
19. Harvestable parts of a plant according to claim 18, wherein said harvestable parts are preferably shoot biomass and/or seeds.
20. Products derived from a plant according to claim 18 and/or from harvestable parts of a plant according to claim 19.
2 . Use of a nucleic acid encoding a DUF642 polypeptide as defined in any of claims 1 and 5 to 9 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
22. Plant having increased yield, particularly increased biomass and/or increased seed yield, relative to control plants, resulting from modulated expression of a nucleic acid encoding a DUF642 polypeptide, or a transgenic plant cell originating from or being part of said transgenic plant.
23. A method for the production of a product comprising the steps of growing the plants of the invention and producing said product from or by
a. the plants of the invention; or
b. parts, including seeds, of these plants.
24. Plant according to claim 1 1 , 15, or 21 , or a transgenic plant cell originating thereof, or a method according to claim 22, wherein said plant is a crop plant, preferably a dicot such as sugar beet, alfalfa, trefoil, chicory, carrot, cassava, cotton, soybean, canola or a monocot, such as sugarcane, or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum emmer, spelt, secale, einkorn, teff, milo and oats.
25. Construct according to claim 12 or 13 comprised in a plant cell.
26. Recombinant chromosomal DNA comprising the construct according to claim 12 or 13.
27. A method for enhancing yield-related traits in plants relative to control plants, comprising modulating expression in a plant of a nucleic acid encoding an epimerase-related like polypeptide, wherein said epimerase-related like polypeptide comprises one or more of the following motifs:
(i) Motif 7: CREEGV[DE][QK]VFVD[AG]AH[AS]IG[QSC]V[PDE][VI][DN][VM][KR]
[ED]IGADFY[TV]SNLHKWFFCPP[SA]VAFL[YH] (SEQ ID NO: 273),
(ii) Motif 8: EF[SA]HH[DN]P[GAN]VAR[IV]NNGSFG[CS]CP[AG]S[VI][LI]AAQ[ARK]
[RN] WQ[LR][LRQ]FL[RQA]QPD[AD]FYF[ND]xL[QRK][PK]G (SEQ ID NO: 274), (Ni) Motif 9: S[LI]VDNATTAAAIVLQ[HQ][VAI][AG][WR][AS]FAEG[RKN]FA[KR][GN] D[AVT]V[LV]MLH[YC]AY[GQ][AS]VKKSI[EQH]AYV (SEQ ID NO: 275)
28. Method according to claim 27, wherein said modulated expression is effected by introducing and expressing in a plant said nucleic acid encoding said epimerase-related like polypeptide.
29. Method according to claim 27 or 28, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased biomass and/or increased seed yield relative to control plants.
30. Method according to any of claims 27 to 29, wherein said epimerase-related like polypeptide as used herein comprises a conserved domain with at least 50% sequence identity to a conserved domain as represented by any one of:
- amino acid coordinates 32 to 449 in SEQ ID NO:198 (motif 10);
- amino acid coordinates 47 to 276 in SEQ ID NO:198 (motif 1 1 );
- amino acid coordinates 92 to 364 in SEQ ID NO:198 (motif 12); and
amino acid coordinates 59 to 323 in SEQ ID NO: 198 (motif 13).
31 . Method according to any of claims 27 or 30, wherein said nucleic acid encodes a polypeptide havi ng at least 40 % overall sequence identity to the amin o acid represented by SEQ ID NO: 198.
32. Method according to any of claims 27 to 31 , wherein said nucleic acid encoding said epimerase-related like polypeptide is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Salicaceae, more preferably from the genus Populus, most preferably from Populus trichocarpa.
33. Method according to any one of claims 27 to 32, wherein said nucleic acid encoding said epimerase-related like polypeptide encodes any one of the polypeptides listed in Table A2 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
34. Method according to any one of claims 27 to 33, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A2.
35. Method according to any one of claims 27 to 34, wherein said enhanced yield-related traits are obtained under non-stress conditions.
36. Method according to any one of claims 27 to 34, wherein said enhanced yield-related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
37. Method according to any one of claims 27 to 36, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
38. Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of claims 27 to 37, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding an epimerase-related like polypeptide as defined in any of claims 27 and 30 to 34.
39. Construct comprising:
(i) nucleic acid encoding an epimerase-related like polypeptide as defined in any of claims 27 and 30 to 34;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence.
40. Construct according to claim 39, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
41 . Use of a construct according to claim 39 or 40 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants.
42. Plant, plant part or plant cell transformed with a construct according to claim 39 or 40.
43. Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass relative to control plants, comprising: (i) introducing and expressing in a plant cell or plant a nucleic acid encoding an epimerase-related like polypeptide as defined in any of claims 27 and 30 to 34; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
44. Transgenic plant havi ng enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of claims 27 and 30 to 34; or a transgenic plant cell derived from said transgenic plant.
45. Transgenic plant according to claim 38, 42 or 44, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
46. Harvestable parts of a plant according to any of claims 38, 42, 44 or 45, wherein said harvestable parts are preferably shoot biomass and/or seeds.
47. Products derived from a plant according to any of claims 38, 42, 44 or 45 and/or from harvestable parts of a plant according to claim 46.
48. Isolated nucleic acid molecule selected from:
(i) a nucleic acid represented by SEQ ID NO: 199 ;
(ii) the complement of a nucleic acid represented by SEQ ID NO: 199;
(iii) a nucleic acid encoding epimerase-related like polypeptide having in increasing order of preference at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%, 79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%,
87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96% , 97%, 98% , or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs 7 to 13, and further preferably conferring enhanced yield- related traits relative to control plants.
(iv) a nucleic acid molecule which hybridizes with a nucleic acid molecule of (i) to (iii) under high stringency hybridization conditions and preferably confers enhanced yield-related traits relative to control plants.
49. Isolated polypeptide selected from:
(i) an amino acid sequence represented by SEQ ID NO: 200;
(ii) an amino acid sequence having, in increasing order of preference, at least 50%, 51 %, 52%, 53%, 54%, 55%, 56%, 57%, 58%, 59%, 60%, 61 %, 62%, 63%, 64%, 65%, 66%, 67%, 68%, 69%, 70%, 71 %, 72%, 73%, 74%, 75%, 76%, 77%, 78%,
79%, 80%, 81 %, 82%, 83%, 84%, 85%, 86%, 87%, 88%, 89%, 90%, 91 %, 92%, 93%, 94%, 95%, 96%, 97%, 98%, or 99% sequence identity to the amino acid sequence represented by SEQ ID NO: 200, and additionally or alternatively comprising one or more motifs having in increasing order of preference at least 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% or more sequence identity to any one or more of the motifs 7 to 13, and further preferably conferring enhanced yield-related traits relative to control plants;
(iii) derivatives of any of the amino acid sequences given in (i) or (ii) above.
50. Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of claims 27 and 30 to 34 and 49, or a nucleic acid as defined in claim 48 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield, and more preferably for increasing seed yield and/or for increasing biomass in plants relative to control plants.
51 . Use of a nucleic acid encoding an epimerase-related like polypeptide as defined in any of claims 27 and 30 to 34 and 49 or a nucleic acid as defined in claim 48 as molecular marker.
52. A method for the production of a product comprising the steps of growing the plants according to claim 38, 42 or 44 and producing said product from or by
(i) said plants; or
(ii) parts, including seeds, of said plants.
53. Construct according to claim 39 or 40 comprised in a plant cell.
54. Recombinant chromosomal DNA comprising the construct according to claim 39 or 40 comprised.
55. A method for enhancing yield-related traits in plants relative to control plants, co m pri si n g m od u lati n g expressi on i n a pl a nt of a n ucle i c aci d en cod i n g a Phospholipase/carboxylesterase (PLPCase) polypeptide, wherein said PLPCase polypeptide comprises an InterPro accession IPR003140 corresponding to PFAM accession number PF022030 Phospholipase/carboxylesterase (PLPCase) domain.
56. Method according to claim 55, wherein said modulated expression is effected by introduci ng and expressing in a plant said nucleic acid encodi ng said PLPCase polypeptide.
57. Method according to claims 55 or 56, wherein said enhanced yield-related traits comprise increased yield relative to control plants, and preferably comprise increased root biomass and/or increased seed yield relative to control plants.
58. Method according to any one of claims 55 to 57, wherein said enhanced yield-related traits are obtained under non-stress conditions.
59. Method according to any one of claims 55 to 57, wherein said enhanced yield-related traits are obtained under conditions of drought stress, salt stress or nitrogen deficiency.
60. Method according to any of claims 55 to 59, wherein said PLPCase polypeptide comprises one or more of the following motifs:
(i) Motif 14: E[FY]G[KR]T[HY]WRPKG[KR]HQATIVWLHGLGDNG[LSA]S[SW]SQLL [ED][ST]LPLPNIKWICPTA (SEQ ID NO: 348),
(ii) Motif 15: PDD[WIVL]EGLDASAAH[IV]ANLLS[TS]EP[AS]D[VI]K[VL]G[IV]G (SEQ ID NO: 349), (iii) Motif 16: FSMGAA[IT]ALYSA[TA]C[YF]A[MHL] (SEQ ID NO: 350)
61 . Method according to any one of claims 55 to 60, wherein said nucleic acid encoding a PLPCase is of plant origin, preferably from a dicotyledonous plant, further preferably from the family Fabaceae, more preferably from the genus Medicago, most preferably from Medicago truncatula.
62. Method according to any one of claims 55 to 61 , wherein said nucleic acid encoding a PLPCase encodes any one of the polypeptides listed in Table A3 or is a portion of such a nucleic acid, or a nucleic acid capable of hybridising with such a nucleic acid.
63. Method according to any one of claims 55 to 62, wherein said nucleic acid sequence encodes an orthologue or paralogue of any of the polypeptides given in Table A3.
64. Method according to any one of claims 55 to 63, wherein said nucleic acid encodes the polypeptide represented by SEQ ID NO: 285.
65. Method according to any one of claims 55 to 64, wherein said nucleic acid is operably linked to a constitutive promoter, preferably to a medium strength constitutive promoter, preferably to a plant promoter, more preferably to a GOS2 promoter, most preferably to a GOS2 promoter from rice.
66. Plant, plant part thereof, including seeds, or plant cell, obtainable by a method according to any one of claims 55 to 65, wherein said plant, plant part or plant cell comprises a recombinant nucleic acid encoding a PLPCase polypeptide as defined in any of claims 55 and 60 to 64.
67. Construct comprising:
(i) nucleic acid encoding a PLPCase as defined in any of claims 55 and 60 to 64;
(ii) one or more control sequences capable of driving expression of the nucleic acid sequence of (i); and optionally
(iii) a transcription termination sequence.
68. Construct accord ing to clai m 67, wherein one of said control sequences is a constitutive promoter, preferably a medium strength constitutive promoter, preferably to a plant promoter, more preferably a GOS2 promoter, most preferably a GOS2 promoter from rice.
69. Use of a construct according to claim 67 or 68 in a method for making plants having enhanced yield-related traits, preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants.
70. Plant, plant part or plant cell transformed with a construct according to claim 67 or 68.
71 . Method for the production of a transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased root biomass, increased greenness index and/or increased seed yield relative to control plants, comprising:
(i) introducing and expressing in a plant cell or plant a nucleic acid encoding a PLPCase polypeptide as defined in any of claims 55 and 60 to 64; and
(ii) cultivating said plant cell or plant under conditions promoting plant growth and development.
72. Transgenic plant having enhanced yield-related traits relative to control plants, preferably increased yield relative to control plants, and more preferably increased seed yield and/or increased biomass, resulting from modulated expression of a nucleic acid encoding a PLPCase polypeptide as defined in any of claims 55 and 60 to 64 or a transgenic plant cell derived from said transgenic plant.
73. Transgenic plant according to claim 66, 70 or 72, or a transgenic plant cell derived therefrom, wherein said plant is a crop plant, such as beet, sugarbeet or alfalfa; or a monocotyledonous plant such as sugarcane; or a cereal, such as rice, maize, wheat, barley, millet, rye, triticale, sorghum, emmer, spelt, secale, einkorn, teff, milo or oats.
74. Harvestable parts of a plant according to claim 72 or 73, wherein said harvestable parts are preferably root biomass and/or seeds.
75. Products derived from a plant according to claim 72 or 73 and/or from harvestable parts of a plant according to claim 74.
76. Use of a nucleic acid encoding a PLPCase polypeptide as defined in any of claims 55 and 60 to 64 for enhancing yield-related traits in plants relative to control plants, preferably for increasing yield , and more preferably for root biomass, increased greenness index and/or increased seed yield in plants relative to control plants.
77. A method for the production of a product comprising the steps of growing the plants according to claim 70, 72 or 73 and producing said product from or by
(i) said plants; or
(ii) parts, including seeds, of said plants.
78. Construct according to claim 67 or 68 comprised in a plant cell.
PCT/IB2012/050878 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof WO2012117324A1 (en)

Priority Applications (11)

Application Number Priority Date Filing Date Title
DE112012001017T DE112012001017T5 (en) 2011-02-28 2012-02-27 Plants with enhanced yield-related traits and methods for their production
EA201391243A EA201391243A1 (en) 2011-02-28 2012-02-27 PLANTS OWNED WITH INCREASED PROFITABILITY-ASSOCIATED PROPERTIES AND METHOD OF THEIR RECEIVING
MX2013009749A MX2013009749A (en) 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof.
BR112013021836A BR112013021836A2 (en) 2011-02-28 2012-02-27 plants that have improved yield characteristics and production methods
EP12751992.4A EP2681323A4 (en) 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof
US14/001,804 US20130340120A1 (en) 2011-02-28 2012-02-27 Plants Having Enhanced Yield-Related Traits and Producing Methods Thereof
AU2012222993A AU2012222993A1 (en) 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof
CN201280020339.7A CN103492573A (en) 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof
CA2826591A CA2826591A1 (en) 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof
ZA2013/07172A ZA201307172B (en) 2011-02-28 2013-09-25 Plants having enhanced yield-related traits and producing methods thereof
US15/877,863 US20180291393A1 (en) 2011-02-28 2018-01-23 Plants having enhanced yield-related traits and producing methods thereof

Applications Claiming Priority (12)

Application Number Priority Date Filing Date Title
US201161447119P 2011-02-28 2011-02-28
US201161447127P 2011-02-28 2011-02-28
US61/447,127 2011-02-28
EP11156244.3 2011-02-28
EP11156187 2011-02-28
EP11156187.4 2011-02-28
EP11156244 2011-02-28
US61/447,119 2011-02-28
US201161478068P 2011-04-22 2011-04-22
US61/478,068 2011-04-22
EP11163577.7 2011-04-22
EP11163577 2011-04-22

Related Child Applications (2)

Application Number Title Priority Date Filing Date
US14/001,804 A-371-Of-International US20130340120A1 (en) 2011-02-28 2012-02-27 Plants Having Enhanced Yield-Related Traits and Producing Methods Thereof
US15/877,863 Continuation US20180291393A1 (en) 2011-02-28 2018-01-23 Plants having enhanced yield-related traits and producing methods thereof

Publications (1)

Publication Number Publication Date
WO2012117324A1 true WO2012117324A1 (en) 2012-09-07

Family

ID=46757397

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/IB2012/050878 WO2012117324A1 (en) 2011-02-28 2012-02-27 Plants having enhanced yield-related traits and producing methods thereof

Country Status (12)

Country Link
US (2) US20130340120A1 (en)
EP (2) EP2681323A4 (en)
CN (1) CN103492573A (en)
AR (1) AR085505A1 (en)
AU (1) AU2012222993A1 (en)
BR (1) BR112013021836A2 (en)
CA (1) CA2826591A1 (en)
DE (1) DE112012001017T5 (en)
EA (1) EA201391243A1 (en)
MX (1) MX2013009749A (en)
WO (1) WO2012117324A1 (en)
ZA (1) ZA201307172B (en)

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023154887A1 (en) * 2022-02-11 2023-08-17 Northeast Agricultural University Methods and compositions for increasing protein and/or oil content and modifying oil profile in a plant
WO2023151007A1 (en) * 2022-02-11 2023-08-17 Northeast Agriculture University Methods and compositions for increasing protein and/or oil content and modifying oil profile in a plant

Families Citing this family (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
CN107254478B (en) * 2017-06-23 2020-07-10 山西大学 Tomato S LL CD gene and application thereof
CN108003227B (en) * 2018-01-16 2021-03-19 四川农业大学 Rice early flowering time related protein and coding gene thereof
CN111100196B (en) * 2019-11-08 2021-07-13 上海交通大学 Bioactive polypeptide QILSVPGWTYSR, and preparation method and application thereof
CN110713529B (en) * 2019-11-14 2022-04-01 中国农业科学院郑州果树研究所 Application of VvDUF642 gene in causing abortion of plant seeds
CN110819639B (en) * 2019-12-19 2022-06-21 中国烟草总公司郑州烟草研究院 Tobacco low-temperature early-flowering related gene NtDUF599 and application thereof
CN113024668B (en) * 2021-03-02 2022-07-22 中国农业科学院郑州果树研究所 DUF642 protein monoclonal antibody and application thereof
CN116376964B (en) * 2023-04-27 2023-12-05 广东省农业科学院水稻研究所 Gene for regulating low-temperature germination of rice and application thereof

Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2009141824A2 (en) * 2008-05-22 2009-11-26 Evogene Ltd. Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficieny
WO2010086221A1 (en) * 2009-01-28 2010-08-05 Basf Plant Science Company Gmbh Plants having enhanced yield-related traits and a method for making the same

Family Cites Families (41)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US4962028A (en) 1986-07-09 1990-10-09 Dna Plant Technology Corporation Plant promotors
US5004863B2 (en) 1986-12-03 2000-10-17 Agracetus Genetic engineering of cotton plants and lines
US5116742A (en) 1986-12-03 1992-05-26 University Patents, Inc. RNA ribozyme restriction endoribonucleases and methods
US4987071A (en) 1986-12-03 1991-01-22 University Patents, Inc. RNA ribozyme polymerases, dephosphorylases, restriction endoribonucleases and methods
AU3756889A (en) 1988-06-01 1990-01-05 The Texas A & M University System Method for transforming plants via the shoot apex
AU4115693A (en) 1992-04-24 1993-11-29 Sri International In vivo homologous sequence targeting in eukaryotic cells
HUT71929A (en) 1992-06-29 1996-02-28 Gene Shears Pty Ltd Nucleic acids and methods of use thereof for controlling viral pathogens
US5401836A (en) 1992-07-16 1995-03-28 Pioneer Hi-Bre International, Inc. Brassica regulatory sequence for root-specific or root-abundant gene expression
WO1994012015A1 (en) 1992-11-30 1994-06-09 Chua Nam Hai Expression motifs that confer tissue- and developmental-specific expression in plants
JPH09505461A (en) 1993-07-22 1997-06-03 ジーン シェアーズ プロプライアタリー リミティド DNA virus ribozyme
AU687961B2 (en) 1993-11-19 1998-03-05 Biotechnology Research And Development Corporation Chimeric regulatory regions and gene cassettes for expression of genes in plants
EP0733059B1 (en) 1993-12-09 2000-09-13 Thomas Jefferson University Compounds and methods for site-directed mutations in eukaryotic cells
US5605793A (en) 1994-02-17 1997-02-25 Affymax Technologies N.V. Methods for in vitro recombination
US6395547B1 (en) 1994-02-17 2002-05-28 Maxygen, Inc. Methods for generating polynucleotides having desired characteristics by iterative selection and recombination
DE19503359C1 (en) 1995-02-02 1996-02-22 Kws Kleinwanzlebener Saatzucht Plants with increased tolerance towards stress
HUP9802535A3 (en) 1995-10-06 2001-04-28 Plant Genetic Systems Nv Seed shattering
US7390937B2 (en) 1996-02-14 2008-06-24 The Governors Of The University Of Alberta Plants with enhanced levels of nitrogen utilization proteins in their root epidermis and uses thereof
GB9607517D0 (en) 1996-04-11 1996-06-12 Gene Shears Pty Ltd The use of DNA Sequences
GB9703146D0 (en) 1997-02-14 1997-04-02 Innes John Centre Innov Ltd Methods and means for gene silencing in transgenic plants
GB9710475D0 (en) 1997-05-21 1997-07-16 Zeneca Ltd Gene silencing
GB9720148D0 (en) 1997-09-22 1997-11-26 Innes John Centre Innov Ltd Gene silencing materials and methods
PT1068311E (en) 1998-04-08 2011-07-20 Commw Scient Ind Res Org Methods and means for obtaining modified phenotypes
TR200100705T2 (en) 1998-06-26 2001-10-22 Iowa State University Research Foundation, Inc. Methods for replacing enzyme and acetyl in plants.
US6555732B1 (en) 1998-09-14 2003-04-29 Pioneer Hi-Bred International, Inc. Rac-like genes and methods of use
US20100293669A2 (en) * 1999-05-06 2010-11-18 Jingdong Liu Nucleic Acid Molecules and Other Molecules Associated with Plants and Uses Thereof for Plant Improvement
US20070011783A1 (en) * 1999-05-06 2007-01-11 Jingdong Liu Nucleic acid molecules and other molecules associated with plants and uses thereof for plant improvement
CA2366104C (en) 1999-07-22 2010-07-06 Japan As Represented By Director General Of National Institute Of Agrobiological Resources, Ministry Of Agriculture, Forestry And Fisheries Ultra-fast transformation technique for monocotyledons
AU780117B2 (en) 1999-08-26 2005-03-03 Basf Plant Science Gmbh Plant gene expression, controlled by constitutive plant V-ATpase promoters
US20110131679A2 (en) * 2000-04-19 2011-06-02 Thomas La Rosa Rice Nucleic Acid Molecules and Other Molecules Associated with Plants and Uses Thereof for Plant Improvement
JP2005185101A (en) * 2002-05-30 2005-07-14 National Institute Of Agrobiological Sciences VEGETABLE FULL-LENGTH cDNA AND UTILIZATION THEREOF
WO2004065596A2 (en) 2003-01-21 2004-08-05 Cropdesign N.V. Use of the regulatory sequence of the rice gos2 gene for the gene expression in dicotyledonous plants or plant cells
DE602004006477T2 (en) 2003-02-04 2008-02-14 Cropdesign N.V. PROMOTER FROM RICE
US20060150283A1 (en) * 2004-02-13 2006-07-06 Nickolai Alexandrov Sequence-determined DNA fragments and corresponding polypeptides encoded thereby
US20070277269A1 (en) * 2006-04-17 2007-11-29 Ceres, Inc. Nucleotide sequences and polypeptides encoded thereby useful for modifying plant characteristics
US20120159672A1 (en) * 2004-02-06 2012-06-21 Nickolai Alexandrov Sequence-determined DNA fragments and corresponding polypeptides encoded thereby
US20060075522A1 (en) * 2004-07-31 2006-04-06 Jaclyn Cleveland Genes and uses for plant improvement
CN101022719B (en) 2004-09-16 2010-06-09 克罗普迪塞恩股份有限公司 Root evaluation method and device
AR052059A1 (en) 2004-12-21 2007-02-28 Bayer Cropscience Gmbh CANE SUGAR PLANTS WITH INCREASED CONTENT OF STORAGE CARBOHYDRATES
EP1820391A1 (en) 2006-02-17 2007-08-22 CropDesign N.V. Method and apparatus to determine the start of flowering in plants
AU2009294651B2 (en) 2008-09-16 2016-03-17 Basf Plant Science Gmbh Method for improved plant breeding
US8952219B2 (en) 2009-06-25 2015-02-10 Syngenta Participations Ag Methods for Agrobacterium-mediated transformation of sugar cane

Patent Citations (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2009141824A2 (en) * 2008-05-22 2009-11-26 Evogene Ltd. Isolated polynucleotides and polypeptides and methods of using same for increasing plant yield, biomass, growth rate, vigor, oil content, abiotic stress tolerance of plants and nitrogen use efficieny
WO2010086221A1 (en) * 2009-01-28 2010-08-05 Basf Plant Science Company Gmbh Plants having enhanced yield-related traits and a method for making the same

Non-Patent Citations (3)

* Cited by examiner, † Cited by third party
Title
DATABASE GENBANK [online] 7 August 2009 (2009-08-07), XP003032756, accession no. NCBI Database accession no. BAF15103.1 *
IRSHAD M. ET AL.: "A new picture of cell wall protein dynamics in elongating cells of Arabidopsis thaliana: Confirmed actors and newcomers.", BMC PLANT BIOLOGY, vol. 8, no. 94, 16 September 2008 (2008-09-16), pages 1 - 16, XP021042608 *
See also references of EP2681323A4 *

Cited By (2)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2023154887A1 (en) * 2022-02-11 2023-08-17 Northeast Agricultural University Methods and compositions for increasing protein and/or oil content and modifying oil profile in a plant
WO2023151007A1 (en) * 2022-02-11 2023-08-17 Northeast Agriculture University Methods and compositions for increasing protein and/or oil content and modifying oil profile in a plant

Also Published As

Publication number Publication date
EP2995622A1 (en) 2016-03-16
AU2012222993A2 (en) 2013-12-05
EP2681323A1 (en) 2014-01-08
BR112013021836A2 (en) 2019-01-08
US20130340120A1 (en) 2013-12-19
ZA201307172B (en) 2014-12-23
EP2681323A4 (en) 2015-03-18
AR085505A1 (en) 2013-10-09
MX2013009749A (en) 2013-10-01
EA201391243A1 (en) 2014-07-30
CN103492573A (en) 2014-01-01
CA2826591A1 (en) 2012-09-07
DE112012001017T5 (en) 2013-12-19
US20180291393A1 (en) 2018-10-11
AU2012222993A1 (en) 2013-09-19

Similar Documents

Publication Publication Date Title
US20180291393A1 (en) Plants having enhanced yield-related traits and producing methods thereof
CA2852617A1 (en) Plants having enhanced yield-related traits and a method for making the same
EP2596105A2 (en) Plants having enhanced yield-related traits and a method for making the same
US20150322449A1 (en) Plants Having Enhanced Yield-Related Traits And Methods For Making The Same
US20140123344A1 (en) Plants Having Enhanced Yield-Related Traits and Method for Making the Same
US20140053298A1 (en) Plants Having Enhanced Yield-Related Traits and Method for Making the Same
US20140068816A1 (en) Plants Having Enhanced Yield-Related Traits and Producing Methods Thereof
US20140325708A1 (en) Plants having enhanced yield-related traits and method for making the same
US20140298545A1 (en) Plants Having Enhanced Yield-Related Traits and a Method for Making the Same
US20130125262A1 (en) Plants having enhanced yield-related traits and a method for making the same
US20150007367A1 (en) Plants having enhanced yield-related traits and method for making the same
EP2707490A1 (en) Plants having enhanced yield-related traits and method for making the same
US20140304858A1 (en) Plants having enhanced yield-related traits and producing methods thereof
US20160076049A1 (en) Plants having enhanced yield-related traits and method for making thereof
US20140165229A1 (en) Plants Having Enhanced Yield-Related Traits and a Method for Making the Same
US20140250548A1 (en) Plants Having Enhanced Yield-Related Traits and a Method for Making the Same

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 12751992

Country of ref document: EP

Kind code of ref document: A1

ENP Entry into the national phase

Ref document number: 2826591

Country of ref document: CA

WWE Wipo information: entry into national phase

Ref document number: 2012751992

Country of ref document: EP

WWE Wipo information: entry into national phase

Ref document number: MX/A/2013/009749

Country of ref document: MX

WWE Wipo information: entry into national phase

Ref document number: 14001804

Country of ref document: US

Ref document number: 12013501769

Country of ref document: PH

WWE Wipo information: entry into national phase

Ref document number: 2013002475

Country of ref document: CL

Ref document number: 1301004751

Country of ref document: TH

Ref document number: 1120120010175

Country of ref document: DE

Ref document number: 112012001017

Country of ref document: DE

ENP Entry into the national phase

Ref document number: 2012222993

Country of ref document: AU

Date of ref document: 20120227

Kind code of ref document: A

WWE Wipo information: entry into national phase

Ref document number: 201391243

Country of ref document: EA

WWE Wipo information: entry into national phase

Ref document number: A201311465

Country of ref document: UA

REG Reference to national code

Ref country code: BR

Ref legal event code: B01A

Ref document number: 112013021836

Country of ref document: BR

ENP Entry into the national phase

Ref document number: 112013021836

Country of ref document: BR

Kind code of ref document: A2

Effective date: 20130827