EP3849297A1 - Downy mildew resistant impatiens - Google Patents
Downy mildew resistant impatiensInfo
- Publication number
- EP3849297A1 EP3849297A1 EP18933227.3A EP18933227A EP3849297A1 EP 3849297 A1 EP3849297 A1 EP 3849297A1 EP 18933227 A EP18933227 A EP 18933227A EP 3849297 A1 EP3849297 A1 EP 3849297A1
- Authority
- EP
- European Patent Office
- Prior art keywords
- plant
- impatiens
- snp
- downy mildew
- seed
- Prior art date
- Legal status (The legal status 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 status listed.)
- Pending
Links
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Classifications
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
- A01H1/12—Processes for modifying agronomic input traits, e.g. crop yield
- A01H1/122—Processes for modifying agronomic input traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
- A01H1/1245—Processes for modifying agronomic input traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, e.g. pathogen, pest or disease resistance
- A01H1/1255—Processes for modifying agronomic input traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, e.g. pathogen, pest or disease resistance for fungal resistance
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
- A01H1/04—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection
- A01H1/045—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection using molecular markers
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H5/00—Angiosperms, i.e. flowering plants, characterised by their plant parts; Angiosperms characterised otherwise than by their botanic taxonomy
- A01H5/02—Flowers
-
- A—HUMAN NECESSITIES
- A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
- A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
- A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
- A01H6/16—Balsaminaceae, e.g. Impatiens
- A01H6/165—Impatiens
Definitions
- the present disclosure relates to the field of plant breeding and, more specifically, to the development of downy mildew resistant Impatiens plants and seeds and hybrids thereof.
- Impatiens downy mildew caused by Plasmopara obducens , is a destructive foliar disease of Impatiens walleriana that is capable of causing complete defoliation or plant collapse, especially in landscape plantings under moist conditions and cool nights.
- Hosts include all cultivars of Impatiens walleriana , the common garden impatiens, and interspecific hybrids with an I walleriana parent are susceptible. A few wild species of impatiens are also susceptible; however, there are no other bedding plant species that are known hosts. Both vegetative propagated and seed-raised I walleriana are susceptible but there is no evidence of seedborne transmission of P. obducens. New Guinea impatiens, Impatiens hawkeri , including Meaning, Celebration, Celebrette, and Sunpatiens series have high resistance to this disease.
- Young plants and immature plant tissues are especially susceptible to infection. Symptoms are often first observed on terminal growth. Seedling cotyledons are highly susceptible to infection. Early symptoms include light-green yellowing or stippling of leaves, downward curling of infected leaves, and white downy-like fungal growth on the undersides of leaves. Advanced symptoms include stunting in both plant height and leaf size when infected at an early stage of development, leaf and flower drop resulting in bare, leafless stems, and infected stems become soft and plants collapse under continued wet and cool conditions as found in landscape plantings. (Warfield C., Impatiens Downy Mildew; Guidelines for Growers, 2014; Warfield, C. Downy Mildew of Impatiens, GrowerTalks, 2011).
- the present disclosure provides an Impatiens plant, for example an Impatiens walleriana plant, having resistance to downy mildew relative to a wild type plant, wherein the Impatiens plant comprises the genetic source for downy mildew resistance (DMR) found in Impatiens sp. T041.
- DMR downy mildew resistance
- a representative sample of seed comprising the genetic source of resistance from Impatiens sp. 7511 has been deposited under ATCC Accession No. PTA-123803.
- the deposited Impatiens sp. 7511 seed has the downy mildew resistance trait from Impatiens sp. T041.
- the present disclosure additionally provides an Impatiens walleriana plant of a cultivated variety comprising in its genome an introgressed locus that confers resistance to downy mildew relative to a wild-type plant, wherein the locus comprises a marker as set forth in or having the sequence of SEQ ID NO:24 or SEQ ID NO:27, and wherein a representative a sample of seed comprising the locus has been deposited under ATCC Accession No. PTA-123803.
- the locus further comprises a marker as set forth in or having the sequence of SEQ ID NO: 18, SEQ ID NO: 13, SEQ ID NO:4 or SEQ ID NO:5.
- the locus is inherited from Impatiens sp. T041.
- the Impatiens plant having downy mildew resistance comprises a transgene.
- the plant is inbred, while in yet other embodiments the plant is hybrid.
- the plant is a cultivated ornamental variety of Impatiens.
- the present disclosure further provides a plurality of Impatiens plants having resistance to downy mildew grown in a field.
- the present disclosure also provides a plant part of an Impatiens plant having resistance to downy mildew, wherein the plant part comprises at least one cell of the plant.
- the plant part is a leaf, pollen, a meristem, a cell, a seed, or an ovule.
- the present disclosure additionally provides a seed that produces an Impatiens plant having resistance to downy mildew.
- the present disclosure further provides a method of producing a downy mildew resistant Impatiens seed, the method comprising crossing a downy mildew resistant Impatiens plant with itself or a second Impatiens plant.
- the method comprises crossing the downy mildew resistant Impatiens plant with a second, distinct Impatiens plant to produce an Fl hybrid Impatiens seed.
- the present disclosure also provides an Fl hybrid Impatiens seed produced by this method.
- the method further comprises crossing a plant grown from the Fl hybrid Impatiens seed with itself or a different Impatiens plant to produce a seed of a progeny plant of a subsequent generation, growing a progeny plant of a subsequent generation from the seed of a progeny plant of a subsequent generation and crossing the progeny plant of a subsequent generation with itself or a second plant to produce a progeny plant of a further subsequent generation, and repeating steps (a) and (b) using the progeny plant of a further subsequent generation from step (b) in place of the plant grown from the Fl hybrid Impatiens seed in step (a), wherein steps (a) and (b) are repeated with sufficient inbreeding to produce an inbred Impatiens plant.
- the present disclosure also provides a method of identifying an Impatiens plant having resistance to downy mildew relative to a wild-type plant, comprising obtaining a biological sample from an Impatiens plant, and screening the biological sample for the presence of an SNP 26 marker as set forth in or having the sequence of SEQ ID NO:24 or an SNP 29 marker as set forth in or having the sequence of SEQ ID NO:27, wherein the presence of the SNP 26 or SNP 29 marker identifies the Impatiens plant as having downy mildew resistance relative to a wild-type plant.
- the biological material is also screened for the presence of an SNP 20 marker as set forth in or having the sequence of SEQ ID NO: 18, an SNP 14 marker as set forth in or having the sequence of SEQ ID NO: 13, an SNP 4 marker as set forth in or having the sequence of SEQ ID NO:4, or an SNP 5 marker as set forth in or having the sequence of SEQ ID NO:5 wherein the presence of the SNP 20, SNP 14, SNP 4 or SNP 5 marker further identifies the Impatiens plant as having downy mildew resistance relative to a wild-type plant.
- the Impatiens plant comprises an introgression that confers resistance to downy mildew that is found in Impatiens sp.
- the Impatiens plant is an Impatiens walleriana plant. In other embodiments the Impatiens plant is an inbred or hybrid plant.
- FIG. 1 shows a pedigree chart for IMS 16-675 DMR Impatiens plant.
- FIG. 2 shows a pedigree chart for IMS 16-730 DMR Impatiens plant.
- FIG. 3 shows a pedigree chart for IMS 17-578 DMR Impatiens plant.
- FIG. 4 shows a pedigree chart for IMS17-514 OMR Impatiens plant.
- FIG. 5 shows a pedigree chart for IMS 16-555 OM Impatiens plant.
- FIG. 6 shows a pedigree chart for IMS16-176 OMR Impatiens plant.
- FIG. 7 shows a pedigree chart for IMS 16-706 OMR Impatiens plant.
- FIG. 8 shows a pedigree chart for double-type Impatiens plant 8017-2.
- FIG. 9 shows a pedigree chart for double-type Impatiens plant 6179-4.
- FIG. 10 shows a pedigree chart for double-type Impatiens plant 8018-2.
- FIG. 11 shows an overview of part of the anchoring results for 21 large scaffolds.
- FIG. 12 shows an overview of KASPar markers (SNP 1 to SNP 9) in the T041 region and the KASPar marker genotypes of the parental lines in the mapping populations.
- A homozygous as the resistant parental line;
- B homozygous as the susceptible parental line;
- H heterozygous.
- FIG. 13 shows calculation of the disease indices (at time points T4, T5, T6) from the frequency of observations in the F3 families per recombinant F2 individual.
- FIG. 14 shows localization of the T041 gene among the markers in the T041 region on the basis of disease indices at three different time points T4, T5, T6.
- A homozygous as the resistant parental line
- B homozygous as the susceptible parental line
- H heterozygous
- C B or H
- D A or H
- U missing genotype.
- FIG. 15 shows a summary of the preprocessing and mapping results in number of reads and % of reads and resulting genome coverage.
- FIG. 16 shows a Summary of the number of variants per variant type per sample.
- FIG. 17 shows the integration of the genetic map of the T041 region with the sequence scaffolds in Pseudo chromosome 2.
- the most probable location of the T041 gene is in the SNP6- GAP-SNP1-SNP5 region. This region is divided over scaffolds 10 and 24 with a gap in between.
- cM distances are based on the genetic map used for anchoring, which shows other cM distances than the genetic map of the mapping population used for the mapping of T041; the main difference is the number of individuals in both populations: 250 and 70, respectively.
- FIG. 18 shows the selection of 25 new SNPs in the region between SNP 6 (Position 57705221) and SNP 1 (Position 58710645).
- the boundary between scaffolds 10 and 24 is in between genes IW.l.0_gl3372 and IW. l.0_gl3373.
- the given gene number, annotation and SNP impact are indicated as well as the genotyping on the basis of the resequencing data of the 5 resistant (in bold) and 5 susceptible genotypes.
- 0/0 homozygous as the resistant reference (IMl6_847)
- 1/1 homozygous alternative allele
- 0/1 heterozygous
- FIG. 19 shows an overview of marker scores for 7 putative new diagnostic markers among the 25 new KASPar markers.
- New markers are placed among existing markers SNP 3, 6, 1, 5 and 4.
- original parental lines of the mapping populations are IMS17-226, P25.1, P3.2 and P4.2.
- FIG. 20 shows an overview of marker scores in susceptible (0) and resistant (1) germplasm for the 6 best diagnostic markers (the last 2 in Scaffold 10 and the first 4 in Scaffold 24) in a wider context of associated markers in the region (SBG genotypes are shown for all except the 3 new markers, SNP 20, 26 and 29). Also SNP marker 14 is indicated here as diagnostic marker since it is diagnostic with one exception in line TIMS 16-851. In the sample list, lines (TIMSl6_224, TIMS16 851 and TP3.2) seem to narrow down the T041 region to the region between markers 14 and SBG marker l6090l87_Impatience_SBG_372239_7. On top the scaffolds harboring the markers are indicated. Diagnostic markers are present both on scaffolds 10 and 24. A: homozygous as the resistant parental line; B: homozygous as the susceptible parental line; H: heterozygous; U: missing genotype.
- FIG. 21 shows marker scores in germplasm for SNP markers 14, 20, 26, 29 and 4, among earlier marker scores for SNP markers 8, 3, 1, 5 and 2.
- the phenotypic scores were taken at 7 different time points after infection. Resistant, susceptible, intermediate (R/S) or questionable phenotypes (?) are indicated.
- FIG. 22 shows marker scores in parental lines and hybrids for SNP markers 14, 20,26, 29 and 4, among earlier marker scores for SNP markers 8, 3 and 5 and 4 (twice used).
- the phenotype score (Final score) was a single end point evaluation. All plants were either resistant (4) or showed intermediate resistance (3).
- One aspect of the current disclosure concerns methods for producing seed of downy mildew resistant Impatiens plants as described herein.
- a downy mildew resistant Impatiens plant may be crossed with itself or with any second plant.
- Such methods can be used for propagation of downy mildew resistant (DMR) Impatiens plants or can be used to produce plants that are derived from the downy mildew resistant Impatiens plants disclosed herein.
- Plants derived from the downy mildew resistant Impatiens plants disclosed herein may be used, in certain embodiments, for the development of new Impatiens varieties.
- novel varieties may be created by crossing downy mildew resistant Impatiens plants followed by multiple generations of breeding according to such well known methods.
- New varieties may be created by crossing with any second plant. In selecting such a second plant to cross for the purpose of developing novel lines, it may be desired to choose those plants which either themselves exhibit one or more selected desirable characteristics or which exhibit the desired characteristic(s) when in hybrid combination.
- inbreeding and selection take place to produce new varieties. For development of a uniform line, often five or more generations of selling and selection are involved.
- Backcrossing can be used to improve a variety, and may be used, for example, to introduce a desired allele or trait into the plant genetic background of any plant that is sexually compatible with a plant of the present disclosure.
- Backcrossing transfers a specific desired trait from one inbred or non-inbred source to a variety that lacks that trait. This can be accomplished, for example, by first crossing a variety of a desired genetic background (recurrent parent) to a donor inbred (non recurrent parent), which carries the appropriate allele or loci for the desired trait(s) in question. The progeny of this cross are then mated back to the recurrent parent, followed by selection in the resultant progeny for the desired trait to be transferred from the non-recurrent parent.
- the process is repeated, for example for five or more backcross generations with selection for the desired trait, until a plant is obtained wherein essentially all of the desired morphological and physiological characteristics of the recurrent parent are recovered in the converted plant, in addition to the single transferred locus from the nonrecurrent parent.
- the progeny thus have the characteristic being transferred, but are like the superior parent for most or almost all other loci.
- the last backcross generation can be selfed to give true-breeding progeny when the trait being transferred is introgressed into a true-breeding variety.
- the recurrent parent therefore provides the desired genetic background, while the choice of the particular nonrecurrent parent will depend on the purpose of the backcross. One of the major purposes is to add some commercially desirable trait to the plant. The exact backcrossing protocol will depend on the characteristic or trait being altered and the genetic distance between the recurrent and nonrecurrent parents. Although backcrossing methods are simplified when the characteristic being transferred is a dominant allele, a recessive allele or an additive allele (between recessive and dominant) may also be transferred. In this instance it may be necessary to introduce a test of the progeny to determine if the desired characteristic has been successfully transferred.
- Modified backcrossing may also be used with plants of the present disclosure. This technique uses different recurrent parents during the backcrossing. Modified backcrossing may be used to replace the original recurrent parent with a variety having certain more desirable characteristics or multiple parents may be used to obtain different desirable characteristics from each.
- the plants of the present disclosure are particularly well suited for the development of new lines based on the genetic background of the plants.
- a second plant to cross with a downy mildew resistant Impatiens plant disclosed herein for the purpose of developing novel Impatiens lines it will typically be preferred to choose those plants which either themselves exhibit one or more selected desirable characteristics or which exhibit the desired characteristic(s) when in hybrid combination.
- desirable traits may include, in specific embodiments, high flower yield, flower quality, high seed germination, seedling vigor, disease resistance, and adaptability for soil and climate conditions such as drought or heat.
- Consumer-driven traits, such as flower color, shape, and texture, even aroma and taste are other examples of traits that may be incorporated into new lines of Impatiens plants developed by this disclosure.
- the present disclosure provides methods of vegetatively propagating a plant of the present disclosure.
- Such a method may comprise the steps of: (a) collecting tissue capable of being propagated from the plant; (b) cultivating the tissue to obtain proliferated shoots; and (c) rooting the proliferated shoots to obtain rooted plantlets.
- such a method may further comprise growing downy mildew resistant Impatiens plants from the rooted plantlets.
- a plant of the present disclosure is propagated by seed, wherein a plant may be used as either a female or a male parent for producing progeny seed and plants.
- such an allele may be inherited from or introgressed from Impatiens sp. T041 or Impatiens sp. 7511, or a progeny or progenitor of any generation thereof comprising the allele.
- Impatiens sp. 7511 is a family of siblings created from self-crosses of Impatiens sp. T041, which comprises the genetic source for downy mildew resistance.
- the deposited Impatiens sp. 7511 seed has the downy mildew resistance trait from Impatiens sp. T041.
- Single locus traits have been identified that are not regularly selected for in the development of a new inbred but that can be improved by backcrossing techniques.
- Single locus traits may or may not be transgenic; examples of these traits include, but are not limited to, resistance to bacterial, fungal, or viral disease, or herbicide or insect resistance. These comprise genes generally inherited through the nucleus.
- Direct selection may be applied where the single locus acts as a dominant trait.
- the progeny of the initial cross are assayed for viral resistance and/or the presence of the corresponding gene prior to the backcrossing.
- Selection eliminates any plants that do not have the desired gene and resistance trait, and only those plants that have the trait are used in the subsequent backcross. This process is then repeated for all additional backcross generations.
- the present disclosure provides the genetic complement of a downy mildew resistant Impatiens plant as described herein.
- Genetic complement refers to the aggregate of nucleotide sequences, the expression of which sequences defines the phenotype of, in the present case, a downy mildew resistant Impatiens plant, or a cell or tissue of that plant.
- a genetic complement thus represents the genetic makeup of a cell, tissue or plant, and a hybrid genetic complement represents the genetic make-up of a hybrid cell, tissue or plant.
- the genetic complement of a downy mildew resistant Impatiens plant as disclosed herein may be identified by any of the many well-known techniques in the art. For example, one can utilize a suitable genetic marker which is closely genetically linked to a trait of interest. One of these markers can be used to identify the presence or absence of a trait in the offspring of a particular cross, and can be used in selection of progeny for continued breeding. This technique is commonly referred to as marker-assisted selection.
- Any other type of genetic marker or other assay which is able to identify the relative presence or absence of a trait of interest in a plant can also be useful for breeding purposes.
- Procedures for marker-assisted selection are well known in the art. Such methods will be of particular utility in the case of recessive traits and variable phenotypes, or where conventional assays may be more expensive, time consuming or otherwise disadvantageous.
- Types of genetic markers which could be used in accordance with the present disclosure include, but are not necessarily limited to, Simple Sequence Length Polymorphisms (SSLPs), Randomly Amplified Polymorphic DNAs (RAPDs; Williams, et al. , Nucleic Acids Res.
- DAF DNA Amplification Fingerprinting
- SCAR Sequence Characterized Amplified Regions
- AP-PCR Arbitrary Primed Polymerase Chain Reaction
- AFLPs Amplified Fragment Length Polymorphisms
- SNPs Single Nucleotide Polymorphisms
- one, two, three or four genomic loci may be integrated into a line via this methodology.
- this line containing the additional loci is further crossed with another parental line to produce hybrid offspring, it is possible to then incorporate at least eight separate additional loci into the hybrid.
- additional loci may confer, for example, such traits as disease resistance, drought or heat tolerance, or a flower quality trait.
- each locus may confer a separate trait.
- loci may need to be homozygous and exist in each parent line to confer a trait in the hybrid.
- multiple loci may be combined to confer a single robust phenotype of a desired trait.
- Many useful traits that can be introduced by backcrossing, as well as directly into a plant are those which are introduced by genetic transformation techniques. Genetic transformation may therefore be used to insert a selected transgene into a plant of the present disclosure or may, alternatively, be used for the preparation of transgenes which can be introduced by backcrossing. Methods for the transformation of plants that are well known to those of skill in the art and applicable to many plant species include, but are not limited to, electroporation, microprojectile bombardment, Agrobacterium- mediated transformation and direct DNA uptake by protoplasts.
- friable tissues such as a suspension culture of cells or embryogenic callus or alternatively one may transform immature embryos or other organized tissue directly.
- pectolyases pectolyases
- An efficient method for delivering transforming DNA segments to plant cells is microprojectile bombardment.
- particles are coated with nucleic acids and delivered into cells by a propelling force.
- Exemplary particles include those comprised of tungsten, platinum, and preferably, gold.
- cells in suspension are concentrated on filters or solid culture medium.
- immature embryos or other target cells may be arranged on solid culture medium.
- the cells to be bombarded are positioned at an appropriate distance below the microprojectile stopping plate.
- An illustrative embodiment of a method for delivering DNA into plant cells by acceleration is the Biolistics Particle Delivery System, which can be used to propel particles coated with DNA or cells through a screen, such as a stainless steel or Nytex screen, onto a surface covered with target cells. The screen disperses the particles so that they are not delivered to the recipient cells in large aggregates. Microprojectile bombardment techniques are widely applicable, and may be used to transform virtually any plant species.
- Agrobacterium- mediated transfer is another widely applicable system for introducing gene loci into plant cells (Marion, et al, Nature 277: 129-131, 1978).
- An advantage of the technique is that DNA can be introduced into whole plant tissues, thereby bypassing the need for regeneration of an intact plant from a protoplast.
- Modem Agrobacterium transformation vectors are capable of replication in E. coli as well as Agrobacterium , allowing for convenient manipulations (Nester, et al. , Basic Life Sci. 30:815-822, 1985).
- recent technological advances in vectors for Agrobacterium- mediated gene transfer have improved the arrangement of genes and restriction sites in the vectors to facilitate the construction of vectors capable of expressing various polypeptide coding genes.
- the vectors described have convenient multi-linker regions flanked by a promoter and a polyadenylation site for direct expression of inserted polypeptide coding genes.
- Agrobacterium containing both armed and disarmed Ti genes can be used for transformation.
- Agrobacterium- mediated transformation In those plant strains where Agrobacterium- mediated transformation is efficient, it is the method of choice because of the facile and defined nature of the gene locus transfer.
- the use of Agrobacterium- mediated plant integrating vectors to introduce DNA into plant cells is well known in the art (Fraley, et al. , Plant Mol. Biol. 3:371-378, 1984; U.S. Patent No. 5,563,055).
- Transformation of plant protoplasts also can be achieved using methods based on calcium phosphate precipitation, polyethylene glycol treatment, electroporation, and combinations of these treatments (see, e.g., Potrykus, et al., Mol. Gen. Genet. 199: 183-188, 1985; Omirulleh, et al. , Plant Mol. Biol. 21 :415-428, 1993; Fromm, et al, Nature 312:791-793, 1986; Uchimiya, et al, Mol. Gen. Genet. 204:204, 1986; Marcotte, et al. , Nature 335:454, 1988).
- a number of promoters have utility for plant gene expression for any gene of interest including, but not limited to, selectable markers, scoreable markers, genes for pest tolerance, disease resistance, or any other gene of agronomic interest.
- constitutive promoters useful for plant gene expression include, but are not limited to, the cauliflower mosaic virus (CaMV) P-35S promoter, which confers constitutive, high-level expression in most plant tissues (see, e.g. , Odel, et al. , Nature 313:810, 1985), including in monocots (see, e.g. , Dekeyser, et al. , Plant Cell 2:591, 1990; Terada and Shimamoto, Mol. Gen. Genet.
- CaMV cauliflower mosaic virus
- P-eFMV FMV promoter
- a variety of plant gene promoters that are regulated in response to environmental, hormonal, chemical, and/or developmental signals can also be used for expression of an operably linked gene in plant cells, including promoters regulated by (1) heat (Callis, et al, Plant Physiol.
- hormones such as abscisic acid (Marcotte, et al., Plant Cell 1 :969-976, 1989), (4) wounding (e.g., wunl, Siebertz, et al., Plant Cell 1 :961-968, 1989); or (5) chemicals such as methyl jasmonate, salicylic acid, or Safener.
- organ-specific promoters e.g., Chen, et al, Genetics 116:469-477, 1987; Schernthaner, et al, EMBO J. 7: 1249-1255, 1988; Bustos, et al, Plant Cell 1 :839-853, 1989).
- Exemplary nucleic acids which may be introduced to plants of this disclosure include, for example, DNA sequences or genes from another species, or even genes or sequences which originate with or are present in the same species, but are incorporated into recipient cells by genetic engineering methods rather than classical reproduction or breeding techniques.
- exogenous is also intended to refer to genes that are not normally present in the cell being transformed, or perhaps simply not present in the form, structure, etc., as found in the transforming DNA segment or gene, or genes which are normally present and that one desires to express in a manner that differs from the natural expression pattern, e.g. , to over-express.
- exogenous gene or DNA is intended to refer to any gene or DNA segment that is introduced into a recipient cell, regardless of whether a similar gene may already be present in such a cell.
- the type of DNA included in the exogenous DNA can include DNA which is already present in the plant cell, DNA from another plant, DNA from a different organism, or a DNA generated externally, such as a DNA sequence containing an antisense message of a gene, or a DNA sequence encoding a synthetic or modified version of a gene.
- genes for insect tolerance such as a Bacillus thuringiensis (B.t.) gene
- pest tolerance such as genes for fungal disease control
- herbicide tolerance such as genes conferring glyphosate tolerance
- quality improvements such as environmental or stress tolerances, or any desirable changes in plant physiology, growth, development, morphology or plant product(s).
- structural genes would include any gene that confers insect tolerance including but not limited to a Bacillus insect control protein gene as described in WO 99/31248, herein incorporated by reference in its entirety, U.S. Patent No. 5,689,052, herein incorporated by reference in its entirety, U.S. Patent Nos. 5,500,365 and 5,880,275, herein incorporated by reference in their entirety.
- the structural gene can confer tolerance to the herbicide glyphosate as conferred by genes including, but not limited to Agrobacterium strain CP4 glyphosate resistant EPSPS gene (aroA:CP4) as described in U.S. Patent No. 5,633,435, herein incorporated by reference in its entirety, or glyphosate oxidoreductase gene (GOX) as described in U.S. Patent No. 5,463,175, herein incorporated by reference in its entirety.
- the DNA coding sequences can affect these phenotypes by encoding a non-translatable RNA molecule that causes the targeted inhibition of expression of an endogenous gene, for example via antisense- or co-suppression-mediated mechanisms (see, for example, Bird, et al. , Biotechnol. Genet. Eng. Rev. 9:207-227, 1991).
- the RNA could also be a catalytic RNA molecule (i.e., a ribozyme) engineered to cleave a desired endogenous mRNA product (see for example, Gibson and Shillitoe, Mol. Biotechnol. 7: 125-137, 1997).
- a catalytic RNA molecule i.e., a ribozyme
- any gene which produces a protein or mRNA which expresses a phenotype or morphology change of interest is useful for the practice of the present disclosure.
- Allele Any of one or more alternative forms of a gene locus, all of which alleles relate to one trait or characteristic. In a diploid cell or organism, the two alleles of a given gene occupy corresponding loci on a pair of homologous chromosomes.
- Backcrossing A process in which a breeder repeatedly crosses hybrid progeny, for example a first generation hybrid (Fl), back to one of the parents of the hybrid progeny. Backcrossing can be used to introduce one or more single locus conversions from one genetic background into another.
- Fl first generation hybrid
- Crossing The mating of two parent plants.
- Cross-pollination Fertilization by the union of two gametes from different plants.
- Diploid A cell or organism having two sets of chromosomes.
- Emasculate The removal of plant male sex organs or the inactivation of the organs with a cytoplasmic or nuclear genetic factor or a chemical agent conferring male sterility.
- Enzymes Molecules which can act as catalysts in biological reactions.
- Fl Hybrid The first generation progeny of the cross of two non-isogenic plants.
- Genotype The genetic constitution of a cell or organism.
- Haploid A cell or organism having one set of the two sets of chromosomes in a diploid.
- Hybrid Fl progeny produced from crossing two non-identical parental lines. Parental lines may be related or unrelated.
- a “hybrid” may refer to Impatiens plants comprising downy mildew resistance as described herein.
- Inbred Line A group of genetically and phenotypically similar plants reproduced by inbreeding.
- Linkage A phenomenon wherein alleles on the same chromosome tend to segregate together more often than expected by chance if their transmission was independent.
- Phenotype The detectable characteristics of a cell or organism, which characteristics are the manifestation of gene expression.
- a plant part refers to a part of a plant of the present disclosure.
- a plant part may be defined as comprising a cell of such plant, such as a cutting, a leaf, a floret, an ovule, pollen, a cell, a seed, a flower, an embryo, a meristem, a cotyledon, an anther, a root, a root tip, a pistil, a stalk, a stem, and a protoplast or callus derived therefrom.
- Quantitative Trait Loci Quantitative trait loci (QTL) refer to genetic loci that control to some degree numerically representable traits that are usually continuously distributed.
- Regeneration The development of a plant from tissue culture.
- a regenerated Impatiens plant as described herein would comprise a downy mildew resistance allele that confers downy mildew resistance.
- Resistance The ability of an Impatiens variety to restrict the growth and development of downy mildew or the damage it causes when compared to susceptible Impatiens varieties under similar environmental conditions and pressure from downy mildew. Resistant Impatiens varieties may exhibit some disease symptoms or damage under heavy pressure from downy mildew.
- Self-pollination or self-fertilization The transfer of pollen from the anther to the stigma of the same plant.
- a "self-pollinated” or “self-fertilized” seed refers to a seed arising from fusion of male and female gametes produced by the same plant. In hybrid seed production, self-pollinated or self-fertilized seed refers to that portion (e.g, less than 1%) of the seed that was the result of self- pollination.
- Susceptibility The inability of an Impatiens variety to restrict the growth and development of downy mildew.
- Tissue Culture A composition comprising isolated cells of the same or a different type or a collection of such cells organized into parts of a plant.
- a tissue culture in accordance with the present disclosure may originate from or comprise cells or protoplasts from a plant part selected from the group consisting of embryos, meristems, cotyledons, pollen, leaves, anthers, roots, root tips, pistil, flower, florets, seed, stems, and protoplasts or callus derived therefrom.
- Impatiens sp. 7511 is a family of siblings created from self-crosses of Impatiens sp. T041 (see below). The deposited Impatiens sp. 7511 seed has the downy mildew resistance trait from Impatiens sp. T041.
- the sporangial suspension was applied to adaxial and abaxial leaf surfaces as a fine mist. Plants were immediately bagged after inoculation to maintain 100% relative humidity and placed into a l7°C, dark growth chamber overnight resuming a 23°C days and l7°C nights and 12 hour light/dark schedule the following morning. Plants were evaluated 14 days after inoculation. The total number of leaves per plant, the number of leaves or cotyledons with visible sporulation and the degree of sporulation, the number of leaves with internal gray discoloration and the number of abscised leaves and cotyledons was recorded.
- Plasmopara obducens causes downy mildew of Impatiens.
- a seedling assay was designed to test for resistance in impatiens against this obligate parasite. The assay is conducted in a greenhouse under controlled environmental conditions.
- Impatiens seeds were sown into 128 cell plug trays filled with a peat-based, soilless potting mix. Trays were placed in a 25°C mist chamber with continuous light (ca. 50 micromol/s) for approximately 4 to 6 days. Trays were transferred to an enclosed greenhouse and maintained at approximately 20°C average day temperature with 14 hours of light per day (ca. 50 micromol/s light).
- the three week old seedlings were inoculated with a suspension of P. obducens sporangia (ca. 1x105 sporangia/ml).
- the isolate of P. obducens used for inoculations was obtained from naturally-infected Impatiens walleriana plants grown in an outdoor field trial in Holland and subsequently maintained on I walleriana plants enclosed in plastic bags and grown in a greenhouse. Inoculum was prepared by vigorously rinsing sporulating impatiens leaves in water. After adjusting the concentration, the sporangial suspension was applied to leaves of the seedlings using a hand-pump spray bottle. Each tray was transferred into a clear plastic bag, tied closed to maintain 100% humidity and placed in the dark for 18 hours at l7°C.
- Seedlings were visually evaluated for visible sporulation on the abaxial leaf surfaces as well as for internal leaf discoloration. Seedlings were rated on a scale of 1-4 based on the incidence and severity of the disease as described below in Table 1.
- Table 1 Rating Scale for Disease Incidence and Severity
- Seedlings rated 2 through 4 were transplanted into 9-cm pots filled with soilless potting mix and placed back into the greenhouse for 14 days and grown using standard practices known to those skilled in the art. After 14 days plants were transferred back into individual clear plastic bags to increase the humidity to 100% and promote sporulation for a second time. After two days, plants were removed from the bags and evaluated using the rating scale previously described in Table 1. Plants rated 3 or 4 were maintained for use in the breeding program, and those rated 1 or 2 were discarded.
- a Ball Horticultural Company proprietary Impatiens sp. breeding line coded T041-1-B-50 was crossed as the female parent with a Ball Horticultural Company proprietary Impatiens walleriana inbred breeding line coded G0008Q as the male parent.
- the Fl population was screened for downy mildew resistance as described in Example 2 and rated as highly resistant.
- One Fl plant coded IMC-211 was selected and self-crossed.
- the resulting F2 population was screened for downy mildew resistance, and plant ratings were as follows: 9/16 High Resistance; 3/16 Moderate Resistance, 3/16 Low Resistance, and 1/16 No resistance.
- the resistant phenotype is characterized as plants at 14 to 30 days after inoculation exhibiting no or sparse sporulation and/or internal discoloration of the leaf tissue of one or two leaves. Plants without resistance are characterized at 14 to 30 days after inoculation as having leaf yellowing, dense sporulation on the abaxial leaf surfaces, extensive leaf abscission and eventual collapse of the plant.
- Impatiens sp. selection T041 was used in an introgression breeding program to introduce genetic downy mildew resistance into Impatiens walleriana. Individual plants selected from the method, as described in Example 2, are listed below in Table 2. All resistant plants have selection T041 Impatiens sp. in their pedigree.
- Pedigrees illustrating the introgression of genetic downy mildew resistance from Impatiens sp. selection T041 into Impatiens walleriana are shown in Figures 1 through 10. Breeding examples include introgression of the resistance into multiple colors of standard commercial Impatiens walleriana and introgression of the resistance into multiple double-flowered breeding lines.
- mapping populations were developed in Impatiens.
- Resistant parental lines (25) were chosen on the basis of disease response in the seedling assay.
- One susceptible parental line was chosen as the other parent (G0008Q).
- Crosses between the 25 resistant lines and the susceptible line resulted in 25 independent Fl's, that were selfed to produce 25 F2 mapping populations.
- All Fl's and small F2 populations were evaluated for the disease response, and on the basis of the segregation pattern one population was chosen for the initial mapping of the disease resistance locus and for marker development (IMC243).
- the mapping population used for marker development (IMC243) consisted of 70 F2 individuals. For marker validation also a germplasm panel was included, consisting of 74 samples, including 4 parental lines and 3 Fl hybrids in duplicate. Leaf samples from population IMC243 were collected before disease assays were started, leaf samples from germplasm were collected from a greenhouse. For this material disease resistance scores were communicated as qualitative scores (Resistant or Susceptible). The leaf samples were used for the isolation of DNA and for subsequent SBG genotyping. [00105] The panel of 144 samples was used for the preparation of SBG libraries with PstVMsel as the enzyme combination with two selective nucleotides added to the primers (+0/+GT).
- the libraries were subsequently sequenced in 4 lanes of the Illumina HiSeq (single read sequencing). After sequencing Illumina reads were filtered on the basis of quality, presence of sample identification tags and the Pstl restriction site motif. Subsequently, reads from all samples were used to generate a reference sequence and the produced clusters were mined for SNPs. In this step also a preliminary genotype score file was constructed.
- genotypic data of samples of IMC243 and their parental lines was selected from the total dataset as the dataset that was used for mapping. For this dataset markers were selected that were segregating as expected for an F2 mapping population.
- a QTL mapping was performed using the data of the six traits individually and the genotypic data of the IMC243 population. QTL were identified for all traits on Linkage Group 2 (LG2) and/or Linkage Group 5 (LG5). The QTL on LG5 was observed in the early stages of disease development and the QTL on LG2 was observed during the later stages of disease development when also a clear separation between susceptible and resistant individuals was observed. Since there was little correlation between the early response QTL and the later response QTL the later QTL seemed more meaningful. Therefore, the correlation between genotype and phenotype was investigated for the LG2 QTL region. [00110] The association of the LG2 QTL region with the disease response at timepoints 3, 4 and 5 was recorded.
- the germplasm panel consisted of 67 samples, including 4 parental lines (T041-1-B50 alias TP25-1, T041-1-B3 alias TP3-2, T041-1-B4 alias TP4-2 as resistant lines, G0008Q alias TP26-1 and their 3 Fl hybrids TF1-24B, TF1-3B and TF1-4B, respectively).
- disease resistance scores were communicated as qualitative scores (Resistant or Susceptible).
- For the association analysis only the mapped markers were selected from the total dataset. In addition, filtering was done for ⁇ 10% missing data and ⁇ 90% Major Allele Frequency, resulting 2424 mapped markers in the data set for association analysis.
- markers were selected in the T041 resistance associated region on chromosome 2 on the basis of the genetic map and were converted to KASPar markers. Names and position of the markers are provided in Table 6, SNP sequences are provided in Table 7 (the resistant allele (T041- B-50) is shown as the first letter in the SNP position, the susceptible allele (IMS 17-226) is shown as the second letter in the SNP position). Markers were selected for two purposes: 1) Validation of markers to select for T041 mediated resistance; 2) Validation of markers at the borders of the best associated region to select for recombinants in the region as part of the T041 gene isolation project.
- Table 8 also shows the results of a BUSCO search, which is used as QC in assemblies to assess the gene completeness based on near- universal single-copy orthologs selected from OrthoDB v9 (BUSCO v2; Felipe, el al., Bioinformatics 31 :3210-3212, 2015). Busco results were highly similar in both assemblies, indicating that only around 10% of the 1440 genes was missing in both assemblies.
- HQ isoforms were used for the evidence based annotation of the reference sequence, generated using the same genotype as used for the genome reference sequence: Impatiens walleriana IMS 16-847. Seedlings of IMS 16-847 were grown in a greenhouse, samples from different tissues were harvested, and after RNA isolation samples were pooled into 2 pools. After library prep, samples were sequenced in 6 SMRT Cells on the PACBio Sequel. A more detailed report of the transcript analysis is provided below.
- the PacBio IsoSeq pipeline was used to process the data.
- the PacBio IsoSeq pipeline includes three steps. The first step is to obtain "reads of insert," which are the sequences between SMRTbell adapters. If a transcript is sequenced several passes in a single PacBio raw read, a consensus sequence is generated using the arrow algorithm. The second step is to generate full length and non-chimeric reads. In this step, a few criteria are used: 5'primer identified; 3 'primer identified; poly- A tail identified; and no artificial concatemer. If reads of insert fulfill all of the criteria, the reads are classified as full length and non-chimeric reads.
- the reads of insert are classified as not full length and non-chimeric reads.
- the minimum read length of 50 bp is used to further filter the sequences. 5' and 3'primers and polyA tails in full length and non-chimeric reads are trimmed off for the next step in the process.
- the third step is to generate high quality and non- redundant full length transcripts.
- the full length non-chimeric reads are clustered based on the sequence similarity and consensus sequences (also named isoforms) are called per cluster. After that, the not full length non-chimeric reads are mapped to the isoforms and polished using a program called Quiver. Furthermore, the polished isoforms are classified as high quality (HQ) isoforms if the polished accuracy is above 0.99, as low quality (LQ), if the polished accuracy is lower than 0.99.
- HQ high quality
- LQ low quality
- Table 11 shows the results generated from the PacBio Isoseq analysis pipeline. About 48% of reads of insert were full length non-chimeric reads, which was according to expectation. After isoform polishing, high quality (HQ) isoforms and low quality (LQ) isoforms were separated. The analysis generated more than 110,000 HQ isoforms. The generated HQ isoforms are unique on the sequence level, however, these isoforms could still be redundant on the transcript level because of PCR errors and some sequencing errors resulting in different isoforms for the same transcripts. The redundancy in the HQ isoforms is, however, not a problem for the purpose of improving genome annotation, because the redundant isoforms are most likely aligned to the same genes on the genome.
- Table 13 shows the additional KASPar markers 1 1 to 16 with the original SBG marker name and their order in relation to KASPar markers 1 to 9. For some markers in the region it was not possible to design KASPar markers due to insufficient flanking sequence next to the SNP position.
- leaf material was harvested from the F2 plants and DNA was isolated.
- DNA was isolated.
- recombinants in the region were selected to be able to just phenotype the recombinants between either SNP 8 (for populations IMC243 and 223) or SNP 3 (for population IMC222) and SNP2, that were flanking the QTL region.
- SNP 8 for populations IMC243 and 223
- SNP 3 for population IMC222
- SNP2 for population IMC222
- FIG. 12 shows an overview of the position of KASPar markers SNP1 to SNP9 in the T041 region and the KASPar marker genotypes of the parental lines of the mapping populations.
- assays SNP8, SNP3, SNP5 and SNP2 were selected for the recombinant screening.
- P25 1 scored H for SNP8 F2 type segregation for SNP 8 was observed in population IMC 243: therefore SNP8 was also used in the selection of recombinants for this population.
- In total 107 recombinants were identified among the 3 times 250 F2 individuals. Due to fertility issues in Impatiens only 70 plants produced seeds: only those recombinants were available for phenotyping as F3 families.
- Phenotyping of the recombinants (as F3 families) for the 3 mapping populations was performed at 6 time points, starting 2 weeks after infection of 4 week old seedlings. The 6 time points were divided over 3 weeks with 3 to 4 day intervals. Differences between susceptible and resistant material started from time point 4, therefore time points 4, 5 and 6 were selected for further analysis.
- An overview of the phenotyping results at time points 4, 5 and 6 of a selection of recombinants is shown in FIG. 13. Per time point the number of individuals with a disease score from 1 (severe symptoms or dead) to 5 (no disease) are shown.
- a disease index was calculated per timepoint per recombinant F2 individual by multiplying the disease scores with the number of individuals with that score divided by the total number of F3 individuals scored.
- QTL mapping using the disease index per time point for time points 4, 5 and 6 and the genotypes of the recombinants placed the T041 resistance gene among SNP markers 1 and 6 for all 3 time points, however after visual inspection the T041 gene was placed in a wider region between markers 6 and 5.
- T041 gene illustrates localization of the T041 gene among the markers in the T041 region on the basis of disease indices at three different time points T4, T5, T6 (with regard to disease severity, the higher numbers indicate resistance, while lower numbers indicate susceptibility) on the basis of genotypes of a selection of recombinants for the 3 populations IMC222, 223, and 243.
- Marker 14 in population IMC222 marks the start of the introgression segment from the R-gene source (P3) in this population.
- Impatiens breeding lines were selected for re-sequencing, consisting of 5 T041 resistant (including IMS 16-847 the breeding line used for generating the reference sequence) and 5 susceptible lines.
- the other resistant lines were: 1934 advanced breeding line, candidate genotype for the KMB population for gene validation; 2004 advanced breeding line, candidate genotype for the KMB population for gene validation; SM1819 T041-1-B3, parental line of mapping population IMC222; and GM1821 T041-1-B50, parental line of mapping population IMC243.
- the susceptible lines were: A8996G, IM15-313-1, J3453Q, M3804Q and Super Elfin, all breeding lines.
- Re-sequencing was done by Whole Genome Shotgun (WGS) sequencing of the 10 genotypes: one Paired-end WGS library of 550 bp insert size per genotype was generated and sequenced (2 x 125 nt) to at least 30x raw read coverage.
- IMS 16-847 was sequenced to 68x coverage in 4 lanes of the Illumina HiSeq 2500, the other 9 lines were sequenced in 12 lanes to 39 - 70x coverage per line.
- Results of the re-sequencing analysis were used in this project to detect in-gene variants separating the 5 resistant and the 5 susceptible genotypes in the T041 region.
- Genalice version 2.4.14 (doi.org/l0. l073/pnas. l7l3830H4) was utilized for mapping of high quality reads and calling of high quality variants.
- the analysis included the following steps: 1) pre-processing raw sequencing data such as trimming adapters; 2) mapping of pre-processed reads against the Anthurium reference genome; 3) variant calling on the mapped data and annotation; and 4) post-processing raw variant data (such as QC filtering). These steps are explained in greter detail below.
- Read pre-processing the reads were trimmed using minimum base quality PHRED score of 17, while allowing a maximum of 10 bases with missing quality scores. After trimming, reads of at least 75 nt and containing less than 5 undetermined nucleotides (Ns) were retained.
- Genome reference mapping read pairs that passed the filtering were mapped against the Impatiens whole genome reference sequence IW.1.0 PSC. This reference with a total genome size of 1,631,493,185 bp consisted of 8 pseudo chromosomes and an additional Chr_0 containing the scaffolds that could not be integrated with the genetic map.
- FIG. 15 presents a summary of the pre-processing and the mapping steps.
- Variant calling The reads with a mapping quality score of at least 60 were used for variation detection. A total of 28,151,123 raw variants were mined using gaVariant. The raw variants were subsequently filtered on allele quality of >20, sample quality of >20 and minimum allele depth of 7X. In addition, SNPs identical in all samples were discarded. After high quality filtering, a total of 21.146.844 high quality variants were retained.
- FIG. 16 presents a summary of variant types per sample.
- Variant annotation the filtered variants were annotated using SnpEff Table 15 presents the number of annotated variants per annotation type. Note: it is possible that variants have more than one annotation type.
- the 1 Mb of sequence between SNP 6 and SNP 1 was used to develop new SNP markers (as KASPar assays).
- 25 in-gene SNPs were chosen separating the 5 Resistant and 5 Susceptible germplasm lines.
- the SNPs are listed with the annotation of the genes harboring the SNPs and the genotypes on the basis of the re-sequencing data.
- the boundary between scaffolds 10 and 24 is in between genes IW. l .0_gl3372 and IW. l .0_gl3373.
- the SNP sequences are provided in Table 16 (the resistant allele (T041-B-50) is shown as the first letter in the SNP position, the susceptible allele (IMS 17-226) is shown as the second letter in the SNP position).
- SNPs were tested on the recombinants from populations IMC 222, 223, and 243. Out of the 25 KASPar assays tested, 14 yielded unambiguous genotypes that fit perfectly in the region between SNP 1 and SNP 6. The 14 new SNPs were almost co-segregating (as expected): only 2 recombinations within the region covered by the 14 SNPs were detected in recombinants, better specifying the earlier detected recombination between SNP 6 and 1 in those two individuals (individual 229-075 from population IMC222, and individual 231-123 from population IMC243; FIG. 14). Those SNPs will become important when the homozygous F4 recombinants have been phenotyped. Additional SNP assays are also being developed for the SNP 1 - SNP 5 region.
- SNP were also tested for their diagnostic value in germplasm.
- 7 putative new diagnostic markers were identified.
- 3 SNP markers SNP 20, 26 and 29
- SNPs 5, and 4 SNPs 26, 29, 5 and 4 are all present in the sequence of scaffold 24, only SNP20 is present in the scaffold 10 sequence. All diagnostic SNPs are therefore present in the proposed location of the T041 gene. It was earlier found that, although tightly linked to the T041 locus in mapping populations, SNPs 6 and 1 are not diagnostic in germplasm due to detection of similar alleles in both susceptible and resistant germplasm. Results are shown in FIG. 19.
- New diagnostic SNPs were also placed in the context of additional associated markers in the region, illustrating that all diagnostic markers are in the region bordered by 2 different germplasm lines: TIMS 16-851 and TIMS 16-224 that are together showing the maximal region to harbor the T041 gene, between marker 14 and l6090l87_Impatience_SBG_372239_7. This implies that the maximal region on the basis of the germplasm analysis starts in scaffold 10 and ends in scaffold 24. Results are shown in FIG. 20.
- FIG. 21 shows marker scores in germplasm for SNP markers 14, 20, 26, 29 and 4, among earlier marker scores for SNP markers 8, 3, 1, 5 and 2 in relation to phenotypic scores.
- the phenotypic scores were taken at 7 different timepoints after infection. Genotypes generated with the new markers are highly consistent with the genotypes generated with the earlier markers. Only marker 26 generated some inconsistent scores in IMS16-555 samples. In this panel of samples new SNPs 14, 20, 29 have the same diagnostic value as SNP 5.
- FIG. 22 shows marker scores in parental lines and hybrids (see Table 17) for SNP markers 14, 20, 26, 29 and 4 among earlier marker scores for SNP markers 8, 3 and 5 and 4 (twice used). All material is resistant or partly resistant, since it all survived disease pressure. Disease response scores were only taken at the end of the trial.
- Genotypes generated with the new markers are highly consistent with the genotypes generated with the earlier markers.
- SNP markers 3 and 26 generated identical genotypes, which are, however, not completely consistent with the other marker genotypes.
- Marker 29 generated some inconsistent scores in IM-2139 samples.
- SNP 14 and 20 generate the most consistent results and have the same diagnostic value as SNP 5.
- compositions and/or methods disclosed and claimed herein can be made and executed without undue experimentation in light of the present disclosure. While the compositions and methods of this disclosure have been described in terms of preferred embodiments, it will be apparent to those of skill in the art that variations may be applied to the compositions and/or methods and in the steps or in the sequence of steps of the method described herein without departing from the concept, spirit and scope of the present disclosure. More specifically, it will be apparent that certain agents that are both chemically and physiologically related may be substituted for the agents described herein while the same or similar results would be achieved. All such similar substitutes and modifications apparent to those skilled in the art are deemed to be within the spirit, scope and concept of the present disclosure as defined by the appended claims.
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