NZ621959B2 - Quartet breeding - Google Patents
Quartet breeding Download PDFInfo
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- NZ621959B2 NZ621959B2 NZ621959A NZ62195912A NZ621959B2 NZ 621959 B2 NZ621959 B2 NZ 621959B2 NZ 621959 A NZ621959 A NZ 621959A NZ 62195912 A NZ62195912 A NZ 62195912A NZ 621959 B2 NZ621959 B2 NZ 621959B2
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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
- A01H1/02—Methods or apparatus for hybridisation; Artificial pollination ; Fertility
-
- 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
-
- 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
- A01H1/06—Processes for producing mutations, e.g. treatment with chemicals or with radiation
- A01H1/08—Methods for producing changes in chromosome number
-
- 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
- A01H3/00—Processes for modifying phenotypes, e.g. symbiosis with bacteria
- A01H3/04—Processes for modifying phenotypes, e.g. symbiosis with bacteria by treatment with chemicals
-
- 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
- A01H5/10—Seeds
-
- 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
- C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
- C12N15/62—DNA sequences coding for fusion proteins
-
- 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)
-
- 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)
- C12N15/8201—Methods for introducing genetic material into plant cells, e.g. DNA, RNA, stable or transient incorporation, tissue culture methods adapted for transformation
- C12N15/8209—Selection, visualisation of transformants, reporter constructs, e.g. antibiotic resistance markers
- C12N15/821—Non-antibiotic resistance markers, e.g. morphogenetic, metabolic markers
- C12N15/8212—Colour markers, e.g. beta-glucoronidase [GUS], green fluorescent protein [GFP], carotenoid
-
- 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)
- C12N15/8216—Methods for controlling, regulating or enhancing expression of transgenes in plant cells
- C12N15/8218—Antisense, co-suppression, viral induced gene silencing [VIGS], post-transcriptional induced gene silencing [PTGS]
-
- 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
- C12N15/8287—Phenotypically and genetically modified plants via recombinant DNA technology with agronomic (input) traits, e.g. crop yield for fertility modification, e.g. apomixis
Abstract
Discloses a method for the production of a set of seeds which are genetically identical to the male gametes from which they arise, comprising: a) placing a limited number of paternal gametes that have the form of tetrads or dyads on the stigma of a flower to fertilise maternal egg cells to obtain a number of zygotes, wherein the number of paternal gametes is limited to be equal or lower than the number of egg cells contained in the female reproductive organ carrying the stigma; b) inducing the loss of maternal chromosomes from the zygotes to obtain a seed set containing a limited number of seeds in which the maternal chromosomes are absent. number of zygotes, wherein the number of paternal gametes is limited to be equal or lower than the number of egg cells contained in the female reproductive organ carrying the stigma; b) inducing the loss of maternal chromosomes from the zygotes to obtain a seed set containing a limited number of seeds in which the maternal chromosomes are absent.
Description
QUARTET BREEDING
J:' ill.) Oh' THi'. NViiNT ON
This invention relates to a method for the
production 0: a set 0: seeds which are genetically identical
to ,he male gametes jrom which they arise. This invention
jurther relates to a set 0: seeds containing a limited
number 0: seeds in which the maternal chromosomes are
absent, which set is composed 0" pairs 0" genetically
mentary seeds which when plants grown from the seeds
are crossed result in essentially the same hybrid. The
invention also relates to a method for providing a se, ol
parent plants for the production 0: a plant 0: which the
genetic tution is ially identical to the genetic
constitution 0: its male grandparent.
BACKGROUND
Plant breeding corresponds to the domestication o;
plant species for the bene it o" humans to obtain jood, feed
2O and ‘iber o su t y and quantity. Plant breeding
is a very old occupation o: mankind and only in the course
o: the 2OUlcentury the practical dge received a
scienti lC "oundation. Plant breeding was originally based
on selecting and propagating those plants that were
outper‘orming in local selection ‘ie'ds. With the
rediscovery of the genetic laws and the development or
statistical tools plant breeding became based on knowledge
o: genetics and was technologically supported by methods
such as d haploids (DH) — see e.g. Haploids in Crop
ement eds; Palmer C, Keller W, and Kasha K (2005)
in: 3iotechno'ogy in Agriculture and Forestry 56 -—Idds;
_. Nagata
T, Lorz H, and Widholm J. Springer—Verlag Qerlin leidelberg
New York, S%N 3—500—22224—3 — and molecular markers — see
e.g. De Vienne ed. (2003) Molecular Markers in Plant
Genetics and Biotechnology. Science publishers nc. finfield,
NH USA. S%N l—57808O.
?lant breeding delivers c concepts tailored
to a ic environment which allows its exploitation in
an economic manner. This objective 0' p'ant breeding is
achieved through the e ”icient ation 0: genetic
variation which exists within the germplasm of plant
species. Such genetic concepts comprise combinations 0;
genes which lead to a desirable phenOtype in a particular
environment. This means that the plan, parts which are
harvested are maximised in yield and quality, at the lowest
possible cost ed to grow the plants and t the
product. When plant breeding is applied at a commercial
level, seed produCtion is also an important issue. Seed
production aims at the multiplication of plants by means I]
sexual reproduction, in which the genetic composition is
ved.
In addition, the commercial seeds need to be 0:
2O su "icient quality to allow e "icient germination. The
preservation o : c constitution through sexual
reproduCtion is however a paradox, because sexual
reproduction fundamentally exists to create 0 "spring with
new combinations 0" alle'es. The genetic mechanisms that act
during sexual reproduction have evolved to increase genetic
variation, in order to enhance the chances O" al 0' a
species in a changing environment. Meiotic recombination,
independent chromosome assortment and the mating system are
main contribut ing factors in this respect. Uniformity in
0 "spring thro Jgh sexual reproduction can ore only be
achi v d wh n th par ntal plants are fully homozygous.
Combining game ,es of such plant will lead to the exact
reproduction o: the genetic composition 0: the parent in
each subsequent generation.
In many crops, the commercial seeds result from a
cross 0: two homozygous al lines. This approach
ensures that the F1 hybrid is heterozygous for several loci,
which "
can result in hybrid vigour and uni ormity. a
breeder wishes to improve an existing F’ hybrid variety or
an inbred variety, he will traditionally need to ma<e
crosses and go through several rounds O" empirical selection
to e this objective.
As the knowledge 0: gene function in relation to
plant growth and development is still d, rs
still largely depend upon phenotypic ion. As during
inbreeding many genes are in a heterozygous state,
especially during early generations, the allelic variants I)
the genes responsible for the phenotypic value assigned to
some 0: the individual plants can be lost easily. This is
due to the fact that during sexual reproduction and
inbreeding zygosity and specific gene interactions are
2O lost. Therefore, in plant breeding these mechanisms may act
counterproductively, especially in those cases where
cally heterozygous plants have been identified with
high agronomic, horticultural or ornamental value. Sexual
uction will result in the segregation of the desirable
alleles.
Therefore there is a strong need for technology
that e ”iciently allows the preservation o: the genetic
constitution during sexual reproduction o:_ plants with a
high agronomic, horticultural or ornamental value.
One possibility to perpetuate pl ants while
preserving the genetic constitution is by vegetative
propagation. This allows a complete preservation o: the
genetic composition, as multiplication occurs exclusively
2012/069191
throagh mitosis. Plants have evolved natural mechanisms 0;
vegeoaoive ation, which allow them to swiftly occupy
ts. For example, vegetative propagation can occur
throagh the formation 0' tubers, bulbs or rhizomes. An
alternative is to use in vitro or in vivo culture technology
to prodJce cuttings. A commercial disadvantage of vegetative
propagation technology, when compared to propagation through
seeds, is the fact tha it is labour-intensive and therefore
costly. Furthermore, i is di" ”icult to store plants :or
longer periods ol dime, which poses logistic problems, and
the risks 0 in ec,ions o: the plant material with pathogens
like viruses is considerably larger as compared to a
situation in which plant material is propagated through
seeds.
Alternatively, vegetative propagation may be
achieved through ,he "ormation O" l seeds, which is
genera"y referred to as apomixis. This phenomenon occurs
"y in a number 0:: species, and it may be induced in
ly propagating plant species by genetic engineering.
2O In theory, this can be achieved by making use 0: specific
genes which lly induce the three di "eren, steps or
apomixis, i.e. apomeiosis, par':henogenesis and autonomous
endosperm development. In prac:ice, however, the genes
responsible for ,he di "erent steps have not yet been
fied, and their interaction may be quite complicated.
On the other hand, artificial engineering 0" lhe
apomixis components may be quite feasible. For example, by
modifying di "erent steps during meiosis it has been shown
that meiosis can be essentially converted into mitosis. This
so-called “MiMe approach” makes use 0: a ation 0;
mutations which suppress double strand break formation
-1), induce sister chromatid segregation during
meiosis l (rec8) and skip the second meiotic cell division
2012/069191
(osdl). Combining this approach with parthenogenesis and
autonomous endosperm formation may tely result in
engineered apomixis (d’Trfurth et al: Turning meiosis into
mitosis; PROS Qio'ogy 7009; WO/2010/07943 2). gh since
long the potentia' 0' apomixis technology for plant breeding
has been widely re cognised, proo o concept is still not
available.
As yet another alternative, use can be made 0;
reverse breeding technology (W003/017753). Reverse breeding
is based on the suppression 0'' meiotic recombination through
genetic engineering or al interference, and the
subsequent product ion of doubled haploid plants (3 ls)
derived from spore s ning unrecombined parental
chromosomes. These DHS di" "er with t to their genetic
composition solely as a consequence o: the independent
parental chromosome assor :ment which occurs during meiosis.
Therefore, it is s U ”icient to make use 0 : one co-dominant,
polymorphic marker per chromosome to determine which of the
DHs or lines derived thereo: should be combined through
crossing to reconstruCt the genetic composition of the
original starting plant. As such, application of reverse
breeding technology allows c preservation of any
fertile selected plant h seeds, even i: its genetic
composition is unknown.
A disadvantage of ,his Lechnology is the fact that
complete suppressi OH O" meiOtic recombination results in the
absence 0: ata. This may lead to inappropriate
chromosome segregation during meiosis I, which can
aneup' oidy O" the gametes and thus to reduced gamete
viability and per: ormance. When no chiasmata are formed
during meiosis I, every chromosome has an independent 50%
chance to move to either one o: the poles . This means that
the theoretical chance to make a spore with a full
chromosome complement is (%)n, wherein n represents the
haploid chromosome number. The frequency 0: balanced gametes
therefore decreases with increasing haploid chromosome
number. Although many crop s have a relatively low
chromosome number (e.g. cucumber has 7 chromosomes per
d genome; spinach has only 6) there are also
economically important species with relatively high
chromosome numbers. A good example is tomato, economically
one of the most important vegetable crops, which has 12
chromosomes per haploid genome. This technical constraint
significantly reduces the e ”iciency 0: reverse breeding
technology.
As another alternative ch use can be made
plants regenerated from unrediced spores. This technology
has b n t rm d N ar R v rs 3r ding (WOZOO6/O94773). The
unreduced spores are formed preferentially as a consequence
ol ,he omission of the second meiotic division. This
lly occurring phenomenon is known as Second Division
Restitution (SDR), and it can occur in plants during sexual
2O reproduction concomitant'y with regular meiotic events.
Near Reverse Breeding technology exploits SDR
events by regenerating plants from unrediced spores,
produced through natural or ered SDR. Genes have been
discovered which — when mutated — give rise to SDR, such as
OSDl and TAMI. The resulting plants d SDR—O plants)
are y homozygoas, and they can be subsequently used to
produce traditional DHs. Molecu'ar markers which are
polymorphic between the al and maternal s o: the
starting plant can be used to identify ,hose SDR—O plants
(and DHs derived thereof) that are largely complementary
with respect to their genetic composition.
Crossing of these plants will result in the near—
complete reconstruction o: the c make-up o: the
2012/069191
original starting plant. However, due to meiotic
recombination during the formation "
0 ,he SDR—O events and
during the formation 0' the DHs derived thereof, the
mentarity will not be complete. The reconstructed
hybrids will genetically di "er to some extent, both from
each other and from the original starting hybrid plant.
However, this variation will be strongly reduced when
compared to a ion in which the DHs are derived
directly from a rnglar meiotic event. Moreover, these DHs
are genetically fixed, which means there is no room :OI
r selection.
The advantage 0: integrating an SDR event in this
process is that the selec ,ion for genetic complementarity
occurs in a two-step process. The firs a step is concentrated
on the proximal s 0: the chromosomes, i.e. including
the centromeres. The second step is directed towards the
distal ends 0: the somes, i.e. those regions which
were exchanged due to recombination. This d genetic
fixation reduces the complexity and increases the chances I]
70 finding largely complementary genotypes, especially when
molecular markers are avai "able for selection.
A further advanta ge O: this approach is the fact
aha, SDR can occur natural:_y during sexual reproduction and
tha, i a can be :ed as such without further need CO
interfere with sexual reproduction processes. Methods ":0
further increase the normal ence of S DR events are
{nown in the art, for example through stress treatment with
N20 (as has been previously been bed in lily: Qarba-
Gonzalez et al (2006), Euphytica l48: 303-309; and in tulip:
Okazaki et al. (2005), Euphytica l43: 101-114).
It is an object o: the present invention to
further increase the e ”iciency o: the above-described
methods for preserving the genetic constitution o: a
heterozygous plant with excellent agronomic, ultural
or ornamental proper':ies.
The presen' invention takes advantage 0: the
observation that speci:fic mutations can lead to a defect in
the tion 0' microspores during pol' en formation. This
results in the formation 0 " clusters 0 Jr pollen grains
which remain physically at :ached together throughout their
development. Although the individual pol' en grains in the
clusters remain together in a tetrad a, maturity, they are
fertile and can each per "orm sation and produce seeds
upon pollination. The biological explanaoion "or this so-
called quartet phenotype is the e to dissolve the
pectin layer which is normally only pr s nt b tw n th
microspores, in the early stages of pollen pment.
The invention thus relates to a method for ,he
tion of a set 0: seeds which are cally identical
to the male gametes from which they arise, comprising:
a) placing a limited number 0: paternal gametes
that have ,he "orm o ,etrads or dyads on the stigma o; a
70 flower to "ertilile ,ernal cells to obtain number I)
ma egg a or
zygotes;
b) inducing the loss ol al chromosomes from
the rygotes to obtain a seed set con':aining a limited number
0: seeds in which the maternal chromosomes are absent.
“Genetically identical” means that all chromosomes
of on s d ar th sam as the chromosomes 0: the
corresponding gamete and the combination 0: chromosomes
within a seed is the same as in the corresponding gamete.
In the research leading to the present invention
it was furthermore surprisingly found that combining methods
available in the prior ar with ,he above specific mutations
that lead to a de.fect in ,he separation 0' pores
during pollen formation leads to a great increase in the
e "iciency with which parent plants with an essentially
complementary genetic constitution can be fied, which
a‘ter ng will give rise to a heterozygous plant with
essentially the same genetic constitution as its paternal
grandfather. Such methods with which the invention can be
combined are for example reverse breeding and near reverse
breeding.
The quartet phenotype was for example bed in
Copenhaver et a; (2000) Plant Physiology 124, 7-15.
Mutations in di "eren a non-homologous genes may result in
similar quartet ypes (e.g. grtl, grt2 and grt3 in
Arabidopsis thaliana). The QRT3 gene (in Arabidopsis:
At4g20050)has been molecularly characterised, and it encodes
a member 0: a divergent class 0" polyga'acturonases (Qhee et
al. (2003) Plant Physiology l33: ll70—l'80). These mutations
are use ul "or providing the tetrad jor use in the method
according to the invention.
The individual po'len grains in the clusters 0;
four pollen grains contain the products 0'' a single meiOtic
cell division. When an individua:_ pollen quartet is used to
ise a plant, this idea'ly 'eads to the ‘ormation O" 4
seeds, when the e ”iciency o "ertilisation is l00%. The
jact Lhao ,he "our dua' po'len grains 0" a tetrad
represeno ,he ts 0' a sing'e meiotic ce'l division has
75 interesting implications ‘or the technology which is subject
0: this invention.
At the start of meiosis, the initial process is the
replication 0: the genomic DNA. Subsequently, during
prophase homologous chromosomes align and synaps, to form
the bivalents. During this stage double strand breaks (383s)
are formed which are repaired ising the aligned non-sister
chromatids. The chromosomal ction during repair leads
to the ‘ormation 0' speci.fic soructures called double
holiday junctions, which are resolved. This leads either to
gene conversion or crossing over. The ng over (CO)
events are ultimate" y visible in the form 0" chiasmata,
which are structura' ly required for appropriate gue
segregation during meiosis Wi th respect to this invention
it should be noted that irrespeCtive O: the bution 0;
the COs the products 0" meiosis are always fully
complementary with e ach other, with respect to their allelic
composition. During the second meiotic division the sis:er
chromatids segregate to opposite poles, giving rise to the
final meiotic products, i.e. four haploid ce' ls. Normally
these four meiotic products become ed from each other
during their further development, and they will mingle with
the pollen grains derived from other meiotic events inside
the same anther loca le. However, when the mother plant
ts the quartet phenOtype, the four products or a
single meiotic event will physically remain together.
The set 0 "our pollen grains in a tetrad can
n variable degrees 0: genetic complementarity, which
70 is a function of the number 0: haploid somes. As the
products 0" meiosis are “ul 'y mentary among each
other, the four pollen grains held together in the tetrad
contain at least 50% complementarity. The specific ou':come
for each tetrad is determined by chance, and this chance
follows a distribution which is given by the so-called
?ascal’s Triangle (Figure 1).
For example, cucumber has 7 haploid chromosomes.
The first meiotic di vision results in two fully
complementary meioti c products. During the second meiotic
division the somes can segregate randomly in each '1
the two products 0" meiosis ", which can result in 2D 27
l78 di" "erent products. In general, it can be stated that in
case 0: n chromosome s, a total 0.: 7n di" "erent Letrads can be
obtained from a single meiotic event. The number 0 Fully
complemen':ary events is always 1, i.e. the first number on
each row (Figure 1), while the second number on each row
corresponds to the number 0: haploid chromosomes. The
subsequent numbers in the same row correspond to the
expected number 0: meiotic products having 2, 3, 4, 5 and 6
non—complementary chromosomes in a , respec:ively.
In the example 0: cucumber, with 128 di""erent
meiotic products originating from any given meiotic event,
these numbers are 21, 35, 35, 21 and 7, respec:ively. As the
producos o meiosis are Sully complementary to each other,
the extreme situation that none 0:5 the chromosomes would be
complementary does not exist n a tetrad, e there
will always be complementarity :o the chromosomes of the
other meiosis i product. The number 0: events with one non—
complemen':ary chromosome is there:fore 7 * 2, with two non—
complemen' 21 *
:ary chromosomes 2, etc. "“
e.g. 3 chromosomes
are non—complementary, this implies that the other four are
complementary. The probability (percent chance) 0" "inding a
certain degree 0: complementarity in the four members or a
pollen te':rad is given by the :able in Figure 2. The chance
O: GDCOUH':ering meiotic produC':s having 0, 1, 2 or 3 non—
complemen':ary chromosomes (and hence with 7, 6, 5 or 4
men':ary chromosomes, respectively) within a pollen
tetrad of cucumber is thus ;.6% (=(l+l)/l28), 10.9%
)/;28), 32.8% (=(2l+2;)/l28) and 54.7% (=(35+35)/l28),
respectively.
Importantly, “non—complementary” in this context
ly only re:fers to the telomeric ends 0: these
chromosomes. we e.g. have a situation with 3 non—
complemen':ary chromosomes and only 40% heterozygosity after
ina:ion, 4 of the 7 chromosomes will be completely
complemen':ary, while the other 3 chromosomes are still 60%
2012/069191
complementary. In essence, the tetrad constellation thus
results in a situation in which the pollen grains are always
pairwise at least entirely mentary for 50% O f the
chromosomes - —
I and as a result 0: recombination still
lly complementary for the remaining chromosomes. This
invention thus accomplishes the near-complete titution
O: the geno :ype of a hybrid plant, while still all owing
between 0 and 50% of variation compared to the original
hybrid plan jrom which the pollen tetrads are derived to
carry out the invention.
This method there:fore allows the reconstruction I)
the identical or near—identi cal genetic constituti OH O: a
hybrid plant. The near-identical reconstruCtion ha s definite
advantages, as this allows the tion on the e ecu O__
additional gene':ic variation on the hybrid phenotype o;
interest. This additional genetic variation may either prove
to have an advantageous or disadvantageous e "ect on the
hybrid phenotype, and this will allow jor the further
c improvement 0: a
superior hybrid phenOtype .
ion Ol” "our chromosomes is graphically illustrated in
Figure 3.
An important aspect of the claimed invention is the
use of quartet microspores for the pollination o: a mother
plant which eliminates the maternal genome from it s hybrid
progeny. An e 0: such a plant has been recently
described in Arabidopsis by Maruthachalam and Chan (Haploid
plants produced by centromere-mediated genome elimination;
Nature 464 (2010), 615-619; US patent application
7011008370? u I W070ll044l37), but this example is in no way
limiting the application 0“ this invention, as the ion
can also be carried out wi':h other haploid inducer systems.
The elimination of the maternal genome from hybrid
progeny can thus be achieved by means 0: transgenic
replacement of the endogenous centromere-specific histone
n CENTB by a modified version. In practice, a modified
version 1
of ,he CENHB n is overexpressed in a plant
that lacks a functional endogenous CENH3 gene.
Alternatively, also the CENPC, M2812, NDC8O or NUF2
polypeptides can be used for the same purpose, when
overexpressed in a plant that has a corresponding
inactivated endogenous CENPC, M1812, NDC80 or NUF2 gene.
Suitably one or two alleles of the endogenous CENH3, CENPC,
M1812, NDC80 or NUF2 genomic coding sequence 0: the plant is
inactiva ,ed or knocked-out, and preferably all alleles are
inactiva ,ed or knocked-out. The plant, when crossed with a
wildtype plant, tes for example at least 0.1% haploid
progeny.
Pre ferably the polypeptide is a recombinantly
al tered CENHB polypeptide. The polypeptide may comprise a
logous amino acid ce 0 f at least five amino
acids (or alternatively O" at 1eas: ten amino acids) linked
to a protein comprising a CEN {3 histone- fold domain, wherein
2O the amino acid sequence is ologous go she CENHB
histone-fold domain. Suitably, the said heterologous amino
acid sequence is linked direcoly Lo the CENTB histone—fold
domain and the polypeptide lacks a CENHB tail domain.
Alternatively, the heterologous amino acid sequence may be
linked to the CENHB histone—:fold domain via an intervening
protein ce. This intervening protein sequence may
se a CENHB tail domain or a non—CENHB e H3 tail
domain (and the recombinant protein then corresponds to a
tail-swap version of the CENHB protein).
Suitably, when the intervening protein comprises a
CENHB histone H3 tail domain, the CENHB tail domain may be
heterologous to the CENHB histone-fold domain. When the
polypeptide comprises a CENHB histone-fold domain and a
truncated CL-lJWH3 tail domain, the amino us ol the ,ail
domain is trancated relative to the plant’s endogenous tail
domain.
Pollinating such transgenicall_y complemented plants
with pollen from a wild ,ype "ache r plant results in sterile
progeny, due to the fac, thau ,he Fl progeny is haploid. ln
fact each Fl progeny is ically identical to the pollen
grain that was used O? "ertililation and from which it
originated. Wild type and modi:fied chromosomes are
apparently incompatible in kinetochore assembly in the
zygote. Spontaneous or induced doubling o: somes leads
to the "orma ,ion of DHs. CENH3 is a conserved and probably
single copy gene in plants, and this system can ore
also be applied in crop species. " seed formation would be
problematic due to endosperm imbalance, embryo rescue can be
performed.
In another embodiment, the maternal genome can be
eliminated from the Fl—progeny by means ol O ,her haploid
r systems, or through interspecies crossing (as
described by e.g. 3ains & Howard 1950, Nature 166: 795).
"n a further embodiment, the t mutation can
also be combined with reverse breeding logy
(WOO3/Ol7753; Dirks et al. 2009, Plant Biotech J 7: 837—
845), thereby greatly improving the e ”iciency o: reverse
breeding. In this embodiment, the quartet phenotype is
combined with suppression O" meiotic chromosome
recombination in the :ather plant , by c, transgenic or
al means. While the quartet mutation results in the
physical attachment 0: the 4 products 0" a sing' e meiosis in
a tetrad at pollen maouri vY/ the suppression o;
recombination ensures that these pollen grains contain
unrecombined parental chromosomes. The present invention
thus ensures that DHs with complementary genetic composition
WO 45616
can easily be identified among the four DHs derived from
po'len from a single meiosis, with one co-dominant,
pO' ymorphic marker per chromosome.
A drawback of reverse breeding may be the
occurrence o: unbalanced (aneuploid) spores. It is r
possible to morpho' ogically idenoi "y balanced tetrads (for
example by visually selecting tetrads in which the four
pollen grains are equal in size, which is tive 0' an
equal bution 0“ all chromosomes, or by means 0: e.g.
flow cytometry), and DHs regenerated from such tetrads will
automatically be pairwise complementary. When balanced
tetrads are used for pollinating a mOther plant which
eliminates the maternal genome from its hybrid progeny, this
will give rise to 4 haploid seeds which are pairwise
complemen':ary with respect to their genetic composition.
Subsequent crossing of the complementary DHs or lines
derived thereO“ will result in the truction of the
genetic composition of ,he original starting plant. When the
four progeny plants of ,his cross are nOt genOtyped prior to
2O crossing, the chance 0: obtaining a reconstruCtion of the
genetic composition of ,he original starting plant by
randomly crossing two 0: these four plants is 50%.
In another embodiment, the t phenotype can
be combined wi':h Near Reverse Breeding (WO2006/O94773). In
this embodimen "I the ence 0: second division
restitution (S DR) in a plant that exhibits the quartet
phenOtype will lead to the production 0'' pol'en dyads by the
father plant, which ses two diploid po' len grains with
a perfectly complementary gene':ic composition, including
cal chromosome breaking . Pollinating a mother
plant that eliminates the maternal genome from its hybrid
progeny with such a pollen dyad will result in two diploid
plants, and crossing these two plants with each other will
result in the near-complete reconstitution o: the genetic
composition 0: the original hybrid.
“Near-complete” re fers in this ation to the
fact that together the two plants have the same genetic
material as their father plant (as 1’10 DNA is lost or gained
during a meiotic division), but the relative genomic
position 0: chromosomal segmen':s may be di "erent, asa
result 0; cross-over events during meiosis. The on I]
chromosomal break-points is however identical in the ":WO
plants, as they originated from a sing:_e meiotic event. The
idenoi on O" complemen':ary SDQ—O lines is thus greatly
facilitated by exploiting the quartet ype, and the
omplete reconstitution 0: the genetic composition I]
any given hybrid becomes much easier and e ”icient.
Due to meiotic recombination during ,he formation
of the SDR-O events the recons litu ,ion will no t be 100%
complete, since the reconstruC':ed hybrids will genetically
di" "er to some extent, both from e ach other and from she
original starting hybrid (fa lher) plant, ally at the
2O telomers as a result 0:f COs. This feature thus provides the
additional advantage that additional genetic variation is
being created in a pre-selected superior hybrid plant, by
ing alternative and slightly di "ering c
arrangements while maintaining most 0: the original hybrid
tution. This may lead to a further improvement or a
hybrid phenotype.
"t is a further object o : this invention to
provide an e ”icient method for obtaining a se, ol seeds,
which seeds are genetically identical to the male gametes
from which they arise, and which set 0: seeds is composed I)
pairs 0: genetically essentially complementary seeds which,
when the plants grown from them are crossed, give rise to
essentially the same hybrid plant. This hybrid plant is
genetically essentially iden':ical to the plant that produced
the male gametes from which the said set 0: seeds arose.
“Essentially” as used herein is intended to mean
that the genetic complementarity ol ,he pairs 0: seeds need
not be 100%, as also the near-complete reconstitution o; a
hybrid plant may be desirable, as explained above (because
it may 0 "er the opportunity to further e a hybrid
phenotype). Such a near-comple':ely reconstituted hybrid
plant is only essentially iden':ical to the original hybrid
plant and to other near-comple':ely reconstituted hybrid
plants obtainable by the invention, because although it has
the same or large: y the same genomic material as the
original hybrid p— ant, there may be alternative or slightly
di" "ering genomic ements present in their genomes, as
a result 0 "di" "erent cross—over events, or some c
regions may be gous as a result 0: recombination. When
meiotic cross-over takes place, “essentially” thus relates
to the degree 0: cross-over that occurred during the
‘ormation o: the pollen grains used for pollinating the
haploid-inducer mother plant.
In another contex "I jor example in the absence I]
meiotic recombination, “essen':ially” may also re:fer to the
selection 0" pairs 0" seeds ( from among the set 0:: seeds
obtained by this invention) that are not 100% genetically
complementary to each other. In this embodiment, which is
also intended ,0 al' within the scope of the present
invention, for example a pair O: seeds can be selected ( from
the said se, ol seeds) that are fully mentary to each
other for n—l chromosomes (with n being the hap:_oid
chromosome number 0: the species), and identica' ‘or the
remaining chromosome. The hybrid plant resulting ‘rom the
CIOSS O: the plants grown from this pair 0: seeds will then
be cally cal to the original hybrid plant "01”
2012/069191
all but one chromosome, and di""erent (namely homozygous)
for the remaining chromosome. Overall the plant is thus only
“essentially” genetically identical. SJCh plants can for
example be obtained when carrying out the present invention
in a preferred embodiment, with suppression O“ meiotic
recombination (“Reverse Breeding”). It is to be understood
that the same t can be done for n—2 chromosomes, n—3
chromosomes, etce':era. This concept allows, for example, the
genomic and pheno :ypic analysis 0' a p' ant while ng on
only a subset o: its somes, and while leaving the rest
O: the hybrid genome unchanged.
The invention thus relates to a method for the
production 0: a set 0: seeds which are genetically cal
to the male gametes from which they arise, comprising:
a) placing a limited number 0: al gametes
that have the "orm o tetrads or dyads on the stigma o; a
flower to fertilize ma':ernal egg cells to obtain a number n
zygotes;
b) inducing the loss 0. macernal chromosomes from
2O the zygotes to obtain a seed set con':aining a d number
0: seeds in which the maternal chromosomes are .
In this method competition among pollen tubes for
the "ertilization O" ovules should pre'ferab' y be minimized
or prevented, to avoid that some of the pollen grains
comprised in a tetrad or dyad ail to "erti' ize an ovule.
Therefore a limited pollination is pre'ferab' e, such that
there are at least as many ovules present in the female
reproductive organ 0: the pollinated _ ower as there are
pollen grains deposi:ed onto its stigma. Each pollen grain
should then be able to fer,ilize an ovule.
In one embodimen':, the limited number 0: paternal
gametes is therefore equal to or lower than the number 0;
egg cells contained in the female reproductive organ
carrying the stigma.
The average number 0: egg cells or ovules per
flower, being the preferred upper limit for the number of
paternal gametes that can be successfully used in this
method, is known so she skilled person who is familiar with
a specific crop. "t is generally slightly higher ,han ,he
average number of seeds present in a typical ”rui, o" that
crop. For comato, for example, the average number of egg
cells per flower is about lOO, for arassica species about
, for Arabidopsis about 40—50, for elon about 200,
for grape about 4, for cacumber about 250—300, for sweet
pepper about 100, and for melon about 500. 3urd et al., Am.
J. Bot. 96(6), 1159—ll67 (2009) describes a study on ovule
number per f'ower in ’87 angiosperm species.
A limited number 0: paternal s suitably
comprises any number tha' allows to use the method of the
invention in an e "icien': way. This means that too much
c variation in the male gametes must be avoided, i.e.
2O the number 0: meiOtic events that gave rise to the male
s deposited onto I)
a single stigma should be kept low i;
those meiotic events each genera :ed a large degree 0;
genetic rearrangements in the genome o: the individual
gametes that constitJte the dyad or tetrad (through
some recombination).
In a preferred embodiment the limited number 0;
paternal gametes is two or four (corresponding to the number
O: gametes comprised in a single pollen dyad or tetrad,
respectively, and hence derived from a single s in the
absence OI presence 0 f the second meiotic division,
respectively). This s tra uegy will lead to the formation I]
four seeds (in case a d was used for poll ination) or
two seeds (in case a dyad was used for pollination), which
are geneti cally identical to the pollen grains that
originated from a single meiOtic division. When the gametes
have the f
orm O" dyads, the limited number of pacernal
gametes that allows to use the method of the invention in an
e "icient way may be much higher than two, because the
amount 0: c variation is greatly reduced, as the two
s comprised within a dyad are genetically fully
complementary to each other. Especially when using gametes
that have the form 0" dyads i, is ,hus e ”icient to use any
number 0; gametes that is smaller than the average number I)
egg cells or ovules per flower.
The tetrad or dyad form 0" the male gametes is the
resu't o inter"erence with microspore tetrad separation in
the father plant. In one embodiment, the interference with
microspore tetrad separation ses interference with one
or more target genes involved in the break-down of the
pectin layer n the microspores resulting from a single
meiotic division. The one or more target genes can be
selected from the group consisting of QRTl, QRTZ, QRT3, or
2O their functional homologues. Suitable mutations are the
introducti OH O: stop codons or irame shifts in the target
genes, ami no acid substitutions that t protein
structure and/or function, and insertions 0: genetic
elements such as T—DNA into the coding sequence, er or
other rnglatory sequence of ,he gene. In Arabidopsis, the
qrtl-4 musation results from ,he insertion of a T—DNA into
an exon 0“ she QRTl gene, the quartet mutant phenOtype in
the grtl—5 mutant is caused by a T9DNA insertion into the
QRTl gene’ s promoter, and the grtl—6 mutation is caused by a
T—DNA insertion into an intron 0: the QRTl gene. The qrtZ-l
mutant in Arabidopsis comprises a Valine to Alanine amino
acid subst itution on position 372 (a GTG to GCG mutation) in
WO 45616
the QRT2 protein, which is the underlying cause of the
quartet phenotype in this mutant line.
In another embodiment, interference with
pore tetrad separation comprises inter:ference with the
break-down O: the pectin layer between the microspores
resulting jrom a single meiotic division by chemical means.
The QQT gene produC':s are enzymes that play a role in the
breakdown ol the pectic ccharide (peCtin) layer that
is pr s nt b 'ZW 1’1 th individual male gametes (microspores)
that arise from the meiotic division 0: a pollen mother
cell. " this pectin layer is not degraded, the four male
gametes (microspores) remain physically attached to each
other in a tetrad form.
"nter‘ering with one or more target genes involved
in microspore tetrad separation can be achieved by a number
0" di" "erent approaches. The inter:fering with a target gene
can consist o: preventing transcription thereo . "n one
embodiment transcription ol a Large t gene can be prevented
by means 0:_ RNA oligonucleotides, DNA ucleotides or
2O RNAi molecules directed agains the target gene promoter.
In another embodimen transcription is prevented
by means 0:f the expression O: a negatively acting
transcription ‘actor acting on the target gene er.
Furth rmor r: rir wi
, th int g th the target gene can also
consist of destabilizing tt e targe t gene mRNA or ript.
This can be achieved by mea HS 0' Jcleic acid molecules that
are complementary to the La rge t gene mRNA or transcript,
selected from the group cor sis ting of antisense RNA, RNAi
molecules, Virus-Induced Gene Silencing (V lGS) molecules,
pressor molecules, RAA oligonucleotides or DNA
oligonucleotides.
"nter‘ering with the target gene can also consist
O: inhibiting the target gene expression product, by means
O: one or more dominant negative c acid constructs, OI
by means 0: one or more al compounds.
In yet another ment, the interfering with
the target gene t S O: the introduCtion 0: one or more
ons into ,he target gene, leading to perturbation o;
its bio'ogical "uncoion. The one or more mutations can
ei ther be introduced randomly - by means 0: one OI more
chemical compounds (such as ethyl methanesulphonate,
ni trosomethylurea, hydroxylamine, profl avine, N—methyl—N—
ni trosoguanidine, N—ethyl—N—nitrosourea , N—methyl—N—nitro—
ni trosoguanidine, diethyl sulphate, e thylene imine, sodium
az ide, formaline, urethane, , e thylene oxide) and/or
physical means (such as UV—irradiation, fast-neutron
exposure, X—rays, gamma irradiation) and/or insertion o;
genetic ts (such as transposons, T—DNA, retroviral
elements) - or speci -:-iC al' y, by means 0 : homologous
recombination or oligonuc:_eotide-based mutation induction.
Chemical mean s to inter‘ere w ith microspore tetrad
separation comprise the use 0: chemical inhibitors that
2O reduce the aCtivity (or the stability) oj she QRT gene
products, OI the use 0; chemicals that — directly or
indireCtly - reduce the expression leve l of the QQT gene
products, resulting in the persistence or ,he peCtin layer
between the tour microspores resulting ‘rom a single meiotic
event. The enzyme activity o: QRT prote ins can be inhibited
by means O: chemical tors, such that treatment or a
flower bud during the stage 0" normal microspore separation
(or a preceding stage) with the inhibit ing chemical leads to
the persistence o: the pectin layer be':WGeD the microspores
that are d from a single meiosis, and thus to the
persistence o: microspore tetrads during later developmental
stages and at anthesis.
In a preferred embodiment, the father plant, which
produced the said male gametes (in the form 0 a tetrad or a
dyad) exhibits — in addition to the quartet ype -
suppression o: chromosome recombination, which abolishes
chromosome crossing-over and leads to the intact
transmission 0" entire chromosomes. In this embodiment the
chance 0" identi"ying two genetically complementary genomes
among the individual pollen grains 0" a tetrad is 50
t. When the father plant which produced the said male
gametes exhibits suppression o: chromosome ination,
this suppression o: chromosome recombination is achieved by
interfering with one or more target genes involved in
recombination.
In one embodiment the target gene is ed in
double strand breaks, and it can be selected from the group
consisting 0" SP077, MHKl, MHKQ, MRHQ, MH/4, KHClOQ, RPC704,
RPC774, MFKl/MRR4, RPDl, HOPl, RAD50, MREll, XRS2, or their
functional homologues.
In another embodiment the target gene is involved
2O in some pairing and/or strand exchange, and it can be
selected from the group consisting of RHD54/TID1, DMCl,
SAE3, REDl, HOPl, HOP2, REC8, MPRl, MRPQ, qui, HTPQ, MRT5,
RAD51, RAD52, RAD54, RAD55, RAD57, RPAl, SMC3, SCCl, MSHZ,
MSH3, MSH6, PMSl, SOLODANCERS, HIM6, CHKZ, or their
onal homologues.
In yet anOther embodiment the target gene is
involved in the meiOtic recombination process, and it can be
selected from the group consisting o: SGSl, MSH4, MSH5, ZIPl
and HTPQ, or their functional homologues.
In r embodiment the target gene is selected
from the group consisting of BKDl, BKDZ, BKDB, BHSl, NBSl,
COMl, MNDl, MEK3/KCK, uiy3, uiy4, ETD, SHOCl, ZYPl, MLHi,
MLH3, or their functional homologues.
"n,er "ering with one or more target genes involved
in ina:ion "
can be achieved by number a 0 di""erent
approaches. The interfering with a target gene can consist
0: preventing transcription thereo;.
In one ment transcription 0: a target gene
can be prevented by means 0: RNA oligonucleotides, DNA
ucleotides or RNAi mo'ecules directed against the
target gene promoter. In another embodiment transcription is
prevented by means of the expression 0: a negatively acting
transcription ‘actor acting on the target gene promoter.
Furth rmor th int r: rir g wi
, uh ,he target gene can also
consist of destabilizing tt e target gene mRNA or transcript.
This can be achieved by mea n S O" n Jcleic acid molecules that
are complementary to the La rge u gene mRNA or transcript,
selected from the group cor S is ting 0: antisense RNA, RNAi
molecules, Induced Gene Silencing (VZGS) molecules,
co-suppressor molecules, RkA oligonucleotides or DNA
oligonucleotides. "nter‘ering with the target gene can also
consist 0: inhibiting the target gene expression product, by
2O means 0: one or more dominant nega :ive c acid
constructs, or by means 0: One OI more chemical compounds.
In yet another embodiment, the interfering with
the target gene ts o: the introduCtion o: one OI more
mutations into ,he target gene, leading to perturbation o;
75 its biological UHC ,ion. The one or more mutations can
either be introduced randomly - by means 0: one OI more
chemical nds (s JCh as ethyl methanesulphonate,
ni trosomethylurea, hydroxylamine, proflavine, N—methyl—N—
ni trosoguanidine, N—ethyl—N—nitrosourea, N—methyl—N—nitro—
ni trosoguanidine, l sulphate, e thylene imine, sodium
azide, formaline, urethane, phenol, e thylene oxide) and/or
physical means (such as UV-irradiation, eutron
exposure, X—rays, gamma irradiation) and/or insertion I]
genetic elements (such as transposons, T—DNA, retroviral
elements) - or specifical'y, by means of homologous
recombination or oligonucleotide-based mutation induction.
In another pre:ferred ment, ,he father plant
which produced the said male gametes exhibits — in addition
to the quartet phenotype - second on restitution (SDR)
during meiosis. In this ment, the father plant
produces male game':es which are 2n and which have the form
0: dyads, because the second meiotic division does not take
place. The two male gametes comprised within one dyad are
genetically fully complementary, and the chance 0;
idenoifying two genetically complementary genomes among the
two individual pollen grains 0"_ a dyad is thus 100 percent.
When the father plant, which produced the said
male gametes, ts second division restitution during
meiosis, this second on restitution can occur
spontaneoasly, without interference with the starting
organism. In another embodiment, second division restitution
is induced by means 0: genetic modification. This genetic
modification can be transient, or it can be achieved by
stab'e incorporation into the genome o: a genetic element
(such as a transgene, mutation , oson, retroviral
element, T—DNA) increasing the number 0: second division
restitution events in the organism.
In yet another embodiment second division
restitution is achieved by subjecting the father plant to
nmental stress, such as temperature , NO2 I
nitrous oxide (N20) I or combinations thereo: (Zhang et al.
(2002) Journal of ultura 7 Science & Biotechnology 78:
84-88; wo 2006/ 094773; 3arba-Gonzalez et al. (2006),
Euphytica L48: 303—309; Okazaki et al. (2005), Euphytica
143: lOl-ll 4).
The loss 0: maternal chromosomes from the zygote -
to obtain a seed set containing a limited nmeer 0: seeds in
which the maternal chromosomes are absent - can be achieved
in di "erent manners. In one embodiment, a haploid inducer
line can be used as the female. A haploid inducer line is a
plant in which the chromosomes 0: one ol the parents are
eliminated from the genome ol the Aygote formed alter
"ertililation 0" an egg cell by pollen. The female can e.g.
be a plan, 0" a di""erent species, as has been bed by
e.g. 3ains & Howard 1950, Nature 166: 795. In anOther
embodiment the loss 0: maternal chromosomes from the Aygote
results from the use 0: a transgenic plant as the mother
organism, which transgenic plant comprises a logous
transgene expression cassette, the expression cassette
comprising a promoter operably lin<ed to a cleotide
encoding a recombinantly altered CTNHB, CENPC, M"S’7, NDC8O
or NUF2 polypeptide, and having a corresponding inactivated
endogenous CENH3, CENPC, M1812, NDC80 or NUF2 gene as
described in W07011/O44137.
2O The present invention also relates to a se, ol
seeds containing a limited number 0: seeds in which the
maternal somes are absent, which set is composed I)
pairs 0: essentially genetically complementary seeds which
when crossed result in essentially the same hybrid, and
which set 0: seeds is obtainable by the method 0: the
invention. The seeds ol this set 0: seeds a" have the same
lather, because they originated from the po"ination 0' a
mOther plant with a limited number 0: paternal s that
have the form 0 s or dyads, which paternal s
had been collected from a single father plant. Because 0;
this, and because of the elimination of the maternal
chromosomes from the Aygotes, from a genetic point 0: view
the seeds of the said set 0: seeds only have one male
grandparent and one female grandparent, namely the s
0.- their tather. This is schematically represen':ed in Figure
The t invention also relates to a set 0;
parent plants for the tion " which
0' a p' ant o_ the
genetic constitution is essentially identical to the genetic
constitution o: its male grandparent, comprising growing
plants jrom seeds 0: the se, O__ seeds 0: the invention,
a fter or prior to doubling the chromosome number of the
seeds, and iden oi Lying two genetica" y complemen':ary plan'
as the parent plants. Such genetica' 'y complemen':ary plan'
can be identi:fied by means 0.- molecu— ar ic) markers
for which the jather p' ant (who produc d th mal gam t s)
was heterozygous, and :or which the two paternal
arents had di erenL alleles. These markers can be
scored with a number 0 di "erent approaches, such as direct
quencing o: speci:fic genomic regior Sr AFLP, RFLP, SSR,
QAP3, KASPar (K3ioscience), InvaderTM OI Invader PlusTM (see
e.g. De Vienne ed. (2003) Mo" ecular Markers in Plant
2O Genetics and Biotechnology. Science publishers DC. file-Id,
NH USA. S %N 1—578080).
The invention further relates to a method :OI
screening the set 0: seeds or the plants grown thereo 01”
their gene':ic constitution, to identi:fy a plan, O j which the
c consti:ution is essentially identical uO ,he gene':ic
constitution of its paternal grand:father, and to identify
another plant 0: which the genetic consti all ,ion is
ially iden':ical to the genetic cons oi oution o: its
paternal grandmO':her.
A plant 0: which the genetic constitution is
essentially iden':ical to the genetic constitution 0: its
paterna' grand a ,her can subsequently be crossed to another
plant 0: which the genetic constitution is essentially
identical to the genetic constitution of its paternal
grandmother, in order to obtain progeny plants 0: which the
genetic constiouoion is essentially identical to the genetic
tJtion ol oheir own grandfather. With ‘their own
grandla,her’ the (hybrid) plant is meant, which produced the
po"en tetrads or pollen dyads that were used :or
po"ination O" the haploid inducer line. This pedigree is
graphically i'lustrated and clarified in Figure 4.
The invention further re'ates to the use 0: the
said set or seeds, alter or prior to doubling the chromosome
number ol ,he seeds, for the identification 0" two
genetically mentary plants as the parenos for a cross.
Crop species on which this invention can be
sed include for example o, poplar, sugar beet,
oilseed rape, soybean, tomato, cucumber, gherkin, corn
salad, spinach, pepper, petunia, potato, eggplant, melon,
elon, carrot, radish, vegetable Brassica species
(cabbage, lower, broccoli, kohlrabi, Brussels
sprouts), bean, pea, onion, strawberry, table beet,
2O gus, and grape vine.
The present invention is further described in the
following clauses.
CLAUSES
This invention relates to:
l. A method for ,he production 0: a se, ol seeds which are
genetically identical to the male gametes from which they
arise, sing:
a) placing a limited number 0: paternal gametes
that have ,he "orm o tetrads or dyads on the stigma o; a
flower to fertilize maternal egg cells to obtain a number I)
zygotes;
b) inducing the loss of macernal somes from
the rygotes to obtain a s eed set containing a limited number
O: seeds in which the maternal chromosomes are .
2. A method according to clause 1, wherein the limited
number of paternal gamete s is equal to or lower than the
number 0: egg cells contained in the female reproductive
organ ng the stigma.
3. A method according to clause 1 or 2, wherein the limited
number 0: paternal gametes is two or four.
4. A method according to any combination 0: the clauses 1-3,
wherein the paternal game ,es that have the form 0" tetrads
or dyads are the result 0 inuer"erence with microspore
tetrad separation.
. A method according to clause 4, wherein interference with
microspore tetrad separat ion comprises interference with one
or more target genes invo lved in the down of the
pectin layer between the microspores ing from a single
meiotic divi sion.
6. A method according to clause 5, n the one or more
2O targ t g n s ar s l c, d from the group consisting of QRTl,
QRT2, QRT3, or their finctional homologues.
7. A method according to clause 4, wherein interference with
microspore tetrad separation is achieved by chemical means
8. A method according to any combination 0: clauses 1—7,
wherein the father plant exhibits suppression o: chromosome
recombination.
9. A method according to any combination of the s 1-7,
wherein the fa,her plant exhibits second division
restitution (SDR) during meiosis.
lO. A method according to clause 8, wherein suppression o;
chromosome recombination is achieved by inuerfering with one
or more target genes involved in recombination.
ll. A method according to clause 10, wherein the target gene
2012/069191
is involved in double strand breaks.
12. A method according to clause ll, wherein the target gene
is selected jrom the group consisting O" S?Oll, fiRl, MfiR7,
MRO, M4. 4, 7, R'icio4, R'ic114, MiiK'/M+'.4, R01, HO?l,
RAD50, {111, XRS7, or their tunctional homologues.
L3. A method according to cLause LO, wherein the target gene
is ed in chromosome pairing and/or strand exchange.
L4. A method according to cLause L3, wherein the target gene
is selected jrom the group consisting o: R{D54/TLDl, DMCL,
SAi'.3, Razai, HOLDl, HOP2, REC8, *ZRl, MR0, '. pi, '. P7, Mi: 5,
RAD5l, QAD52, QAD54, RADSS, RAD57, RPA, SMC3, SCCL, MSH2,
MSiB, MSH6, PMSL, SOLODANCjRS, HLM6, CHK2, or their
functional homoLogues.
L5. A method according to cLause LO, wherein the target gene
is involved in the meiOtic recombination process.
L6. A method ing to cLause L5, wherein the target gene
is selected jrom the group consisting of SGSl, MSl4, MSH5,
ZLPl and H"P7, or their tunctional homoLogues.
17. A method according to clause 5 and/or 10, wherein the
70 inter‘ering with the one or more target genes consists o;
preventing ription thereor.
18. A method according to clause 17, n transcription
is prevented by means 0: RNA oligonucleOtides, DNA
oligonucleotides or RNAi molecules direCted against the
target gene promoter.
19. A method according to clause 17, wherein transcription
is prevented by means of the expression 0: a negatively
acting transcription tactor acting on the target gene
promoter.
20. A method according to clause 5 and/or 10, wherein the
interfering with the target consists I)
one or more genes o;
destabilizing the target gene mRNA or transcript.
21. A method according to clause 20, wherein the target gene
mRNA is destabilized by means 0“ c acid molecules that
are complementary to the Larges gene mRNA or transcript,
selected from the group consisting of antisense RNA, RNAi
molecules, Virus-Induced Gene ing (VZGS) molecules,
co-suppressor molecules, RNA oligonucleotides or DNA
oligonucleotides.
22. A method according to clause 5 and/or 10, wherein the
ering with the one or more target genes consists o;
inhibiting the target gene expression product.
23. A method according to clause 22, n the target gene
expression product is inhibited by means of the expression
product(s) or one or more dominant ve nucleic acid
construc:s.
24. A method according to clause 22, wherein the target gene
sion product is inhibited by means 0: one or more
chemical compounds.
. A method according to clause 5 and/or 10, wherein the
interfering with the one or more target genes consists o;
2O the introduction 0: one or more mutations into the target
gene, leading to bation o i,s ical runction.
26. A method according to clause 25, wherein the one or more
mutations are introduced randomly by means 0: one or more
chemical compounds and/or physical insertion I)
means and/or 0;
genetic elements.
27. A method according to clause 26, wherein the one or more
chemical compounds the I)
are selected from group consisting or
ethyl methanesulphonate, nitrosomethylurea, hydroxylamine,
prO' avine, N-methyl—N—nitrosoguanidine, N—ethyl—N—
nitrosourea, N-methyl-N-nitro—nitrosoguanidine, diethyl
sulphate, ethylene imine, sodium azide, formaline, urethane,
phenol and ethylene oxide.
28. A method according to clause 26, wherein the physical
means are selected from the group ting 0: UV—
irradiation, fast-neutron re, X-rays, gamma
irradiation.
29. A method according to clause 26, wherein the genetic
element is selected from the group consisting of
osons, T—DNA, retroviral elements.
. A method according to clause 25, wherein the one or more
mutations are introduced specifically by means of homologous
lO recombination or oligonJcleotide-based mutation induction.
31. A method according to clause 9, wherein second division
restitution occurs spontaneously, in particular without
erence with the starting organism.
32. A method ing to clause 9, wherein second division
restitution is d by means of genetic modification.
33. A method according to clause 32, wherein the genetic
modi”ica,ion is transient.
34. A method according to clause 32, wherein the genetic
modifica,ion is achieved by stable incorporation into the
genome of a genetic element increasing the number of second
division restitution events in the organism.
. A method according to clause 9, wherein second division
restitution is achieved by subjecting the father plant to
environmental stress.
36. A method according to clause 35, wherein the
environmental stress is selected from temperature ,
N02, nitrous oxide (N20), or combinations f.
37. A method according to any combination of ,he clauses l-
36, wherein the loss of maternal chromosomes from ,he 2ygote
is induced by using a haploid inducer line as the female.
38. A method according to clause 37, wherein the female is a
plant of a di""erent species.
39. A method ing to any combination 0: clauses l-37,
wherein the female plant is a transgenic plant that
comprises a heterologous transgene expression cassette, the
expression te comprising a promO':er operably linked to
a polynucleotide encoding a recombinan':ly altered C:NHB,
CENPC, MlSlZ, NDC8O or NUF2 ptide, and having a
corresponding inactivated endogenous CENH3, CENPC, M1812,
NDC80 or NUF2 gene.
40. Se, of seeds containing a d number 0: seeds in
which the maternal chromosomes are absent, which set is
composed O" pairs 0" genetically complementary seeds which
when plants grown from the seeds are crossed result in
essentially the same hybrid, and which seed set is
obtainable by to I]
a method according any combination 0;
clauses l-39.
4;. A method for providing a se, ol parent plan ,s for the
production 0: a plant of which the genetic cons ,ituuion is
essentially identical to the genetic cons:itution "
o: its
male grandparent, comprising growing plan as from seeds 0;
the set 0: seed according to clause 40, a fter or prior CO
2O doubling the chromosome number ol ,he seeds, and identifying
two cally complementary plan':s as the parent plants.
42. A method according to clause 41, wherein the se, ol
seeds or the plants grown thereo: are screened for uheir
c constitution, to identi fy a plan, O f which the
genetic consoiou ,ion is essential ly identical to the genetic
constitution of its paternal grandfather, and to identi:5y
another plant 0: which the genetic consti all ,ion is
essentially identical to the genetic cons oi oution
0; its
paternal grandmOther.
43. A method according to any ation 0 : clauses 40-42,
wherein a plant of which the genetic cons oi ,ion is
essentially identical to the genetic cons oi all ,ion 0; its
paternal grand a lher, is crossed to another plant of which
the genetic constitution is ially iden':ical to the
genetic constitution 0: its paternal O':her, in order
to obtain progeny plan,s ol which the genetic constitution
is essentially identical to the genetic constitution o;
their own grandfather.
The inventior will be ‘urther illustrated in the
Examples that follow and that are not intended to limit the
invention in any way. In the Txamples, re‘erence is made to
she "ollowing tigures:
Figure 1: the so-called Pascal’s Triangle,
depicting the specific outcome 0: chromosome complementarity
for each pollen tetrad, in on 0‘ the number 0;
somes of the species. From top to bottom the number or
haploid chromosomes increases, and the sum 0: the numbers on
each row always equals 2“, being tt e total ntmber o;
di""erent meiotic products that can arise from a meiosis in
which n somes are involved. "5
we ta<e the seventh row
as an example (for e.g. cucumber, with 7 haploid
somes, n = 7), it can be seen that the number 0" "ully
2O complementary events is always 1, i.e. ,he jirst number on
the row, while the second number on the row corresponds to
the number 0: haploid chromosomes. The uent numbers in
the same row correspond to the expected number 0: meiotic
products having 2, 3, 4, 5 and 6 non-complementary
chromosomes in a tetrad, respectively. The total number 0;
events with one non-complementary chromosome is 7 * 2, with
two non-complementary chromosomes 21 * 2, etc. "“
e.g. 3
chromosomes are non—complementary, this implies that the
other four somes are complementary. Importantly, “non—
complementary” in this context actual'y on'y re‘ers to the
telomeric ends ol ,hese chromosomes. wee .g. have a
situation with 3 non—complemen':ary somes and only 40%
heterozygosioy ajter recombination, 4 of the 7 chromosomes
will be completely complementary, while the other 3
chromosomes are still 60% complementary.
Figure 2: this table shows the probability
(percent chance) 0 g a certain degree 0;
mentarity in the four members 0: a pollen tetrad, as a
‘unction E
0' the haploid chromosome number. For e.g. er
(with n = 7) the chance 0: encoun :ering c products
having 0, l, 2 or 3 non—complemen :ary chromosomes (and hence
with 7, 6, 5 or 4 mentary chromosomes, respectively)
within a pollen tetrad of cucumber is thus 1.6%
(=(1+1)/128), 10.9% (=(7n7)/128), 32.8% (=(21+21)/128) and
54.7% (=(35+35)/128), respectively.
The probability (percent chance) 0" "inding a
certain degree of complementarity in the four members of the
quartet is given by the table in figure 2. The chance of
encoun':ering meiotic products having 0, 1 2
, or 3 non—
complementary chromosomes (and hence with 7, 6, 5 or 4
complementary somes, tively) within a pollen
tetrad of cucumber is thus 1.6% (=(1+l)/1 28), 10.9%
(=(7+7)/l28), 32.8% (=(21+2l)/128) and 54 .7% (=(35+35)/128),
respectively.
Figure 3: graphical representation 1
0: a meiOtic
event with 4 haploid chromosomes (n = 4). One parent 0: the
hybrid plant contributed blue chromosomes, while the Other
paren: contributed red chromosomes to the hybrid. "n a ‘irst
step the genome doubles from 2n to 4n, and subsequently
crossing-over can take pl_ace between the gous regions
Ol sister chromatids, as illustrated here with a single
cross-over event per Chromosome. During the first meiotic
division two dip:_oid daughter cells are produced, which are
genetically completely complementary (i.e .
if both their
genomes are taken together the 4n genomic composition from
be fore the division is obtained). "n this ‘igure only one
2012/069191
possible example of he s "
t e 0" is shown.
During the second meiotic division the s (in this
context: microspores or pollen grains) are ed, and the
chromosomes can randomly s gr gat to ith r daughter cell.
This leads to 7“"1 di "erent pairs 0: daughter cells
(gametes). For the diploid cell on the lej, the jigure shows
one possible pair 0: gametes, while for the diploid cell on
the right all 8 possib'e pairs 0" gametes are shown (= 23 =
211—1) .
When uently doubled haploid plants are
regeneraoed jrom the di "erent gametes (for example by the
method 0: the invention, by generating haploid plants and
doubling their genome), these plants can be crossed to each
other. The numbers just below the di "erent chromosome sets
correspond to the number 0: chromosomes that are
complemenoary to the chromosome set on the tar le t o the
tigure. "or example the plant containing ,he jour
chromosomes that are ed on the tar le a (i.e. the :our
entirely lee chromosomes) would be crossed to a plant
2O containing ,he jour entirely red chromosomes jrom the jirs,
ol ,he eight chromosome pairs on the right, then all 4
somes would be complementary. This cross would result
in the exact reconstitution o: the original hybrid plant
that had produced the gametes. Similarly, crossing the same
plant with the four blue chromosomes with plants containing
the other possible chromosome sets displayed on the right
(more precisely: the left chromosome set 0: each of the
eight pairs) wil' either resu't in the complete
reconstitution ol she origina' hybrid plant (when all 4
chromosomes are entirely complementary), Or in the near-
complete reconsti tition o: the original hybrid plant (when
one or two ol the Sour chromosomes are not entirely
complementary). The situation that more than two chromosomes
would not be complementary does not exist, because the
s originated from the same meiotic even' In addition,
it is clear from the drawing that a large par O__ the “non—
complementary” somes is in fact complementary, and
that crossing wil:_ lead to a highly heterozygous progeny;
the only non—comp:_ementary chromosome parts are due to the
cross-over events at the chromosomes’ telomeres, which
cross-over regions would become homozygous in the resulting
progeny. When the numbers below the chromosome pairs are
added up to group the events that have 0, l or 2 non—
complementary somes in comparison to the chromosome
set on the _CaT‘ 1e.:t, this leads to the 2 — 8 — 6
distribution for n = 4, which can also be found in the
‘ourth I]
row 0' the triangle 0 "igure 1 (where they are
displayed as — 4 _6_4_ l).
On the far right "
0 ohis ”figure a second possible
pair 0: gametes is depicted, that can be derived from the
lej,—most diploid cell during meiosis The numbers listed
at the bootom or the jigure represen, ,he number 0;
2O complementary chromosomes when one or ,he gametes from this
pair is combined with any 0: the 16 s derived from the
right—most diploid cell. Again the same outcome can be
observed: 0: the 16 s 2 are fully complementary (i.e.
4 complementary chromosomes), 8 have one non-complementary
chromosome and 6 have two non-complementary chromosomes. 3y
g the four ts derived from a single meiotic
event cogether, and by providing a means to obtain progeny
plants thao are cally identical to these four meiotic
prodJcts, ,he present invention maximizes the chance or
iden,i Lying pairs 0: progeny plants that upon crossing can
give rise to the origina' hybrid plant, or to a hybrid that
is genetically essential:_y the same as the original hybrid.
Figure 4: simplified overview 0: a pedigree
according to the present invention, assuming tha'I DO
recombination occurs. A hybrid plant, resulting from the
CIOSS Ol ,wo (homozygous) parental lines (with genotypes AA
and %%, respectively) produces pollen grains in ,he "orm 0'
tetrads. When a single tetrad is used to a:e a haploid
inducer mOther plant (with random genOtype) the progeny
resulting from this cross will consist o: a set 0 "our
haploid seeds. Genetically these seeds are A, A, 3 and 3 (in
the absence 0: recombination), and there is no genetic
contribution from the mOther plant. Hence these four haploid
seeds only have two grandparen':s, namely the parental lines
of the hybrid "ather p'ant tha': produced the pollen tetrad.
Aj,er genome doubling four doubled haploid plants can be
obtained, which — in the e 0: ination - will
always be pairwise genetically “ul 'y complementary. Crossing
the two genetically mentary plants from any of the
pairs leads to the reconstitution o: the original hybrid
plant. The situation is more ex when recombination does
2O occur, as illustrated by ‘igures ’, 7 and 3. When
recombination occurs the chance 0 ”inding a pair 0 Fully
complementary plants among the progeny o: a pollen ,eorad
decreases in on o: the haploid chromosome number, but
in the absence 0: recombination the chromosome number has no
e "ect on the outcome.
EXAMPLES
EXAMPLE 1
Tdentification of guartet—pollen—shedding Brassica plants
An essential resource ‘or ng out this
invention is a plant or the species ol interest that sheds
its pollen grains in a tetrad form, whereby the four
products from a meiotic division remain physically attached
to each other. Such a plant can either be obtained in a
mutant screen or through a transgenic approach. This example
illusurates the jirst option, while the second option will
be explained in subsequent examples.
"n order to iderti‘y a plant exhibiting the quartet
pollen phenotype, Brassica oleracea EMS-mutant population
was ed phenotypically, to detect the occurrence 0;
pollen grains with the quartet phenotype (i.e. pollen
tetrads) in the anthers o " individual . In a bulk—
approach, pollen from multiple plants was pooled together
and diluted in solution so that individual po'len grains
could be clearly discerned. These pollen pools were then
screened by eye under a binocular, bat atively this
screen is also possible with ow cytometry or by "ilvra,ion
(with a "i'ter that has a pore size that is larger than the
diameter 0 an individual pol'en grain, but smaller than the
diameter ol a pollen tetrad). Upon detecting the desired
quartet phenotype in a pollen pool, all plants that
contributed pollen to that pool were screened individually,
2O until a t mutant plant was positively identi‘ied. "n
the next generation the transmissibility O" the quartet
phenotype was confirmed.
EXAMPLE 2
Creating a Brassica plant that eliminates the al
genome from its Pl-progeny
A publication by Maruthachalam & Chan (Nature 464,
615-619; 2010) teaches that the ,rans"ormation 0'
Arabidopsis thaliana cenh3 mutant plants with an
overexpression construct for a NH3—tailswap protein
results in an aberrant mitotic division in the zygote,
ing ization. During this aberrant mitosis the
al chromosom s ar s l ctiv ly liminated jrom the
dividing zygote. As the CENHB protein is universal in
eukaryotes and its function is very wel' conserved this
strategy "rom Arabidopsis is widely app:_icable in Other
plant species.
In order to create a Brassica ea plant in
whose Fl progeny the maternal genome is selectively
ated, a ca plant was created that lacks a
'Jnctional version of the protein that is orthologous to
C?NH3 from opsis. This was ed by means 0; an
QWAi approach. This plant was subsequently genetically
transformed by means 0: Agrobacterium in:fection, with the
GFP-CENHB-tailswap construct described by Maruthachalam &
Chan (Nature 464, 615—619; 20l 0). Due to the lethality o:
the homozygous cenh3 mutant plant (as is the case in
Arabidopsis), it was necessary to transform a heterozygous
silenced plant with this ht. Transformant plants were
subsequently selected based on the construct’s selection
marker, and the presence and correct expression of the GFP—
CENHB—tailswap fusion protein could be detected with
2O fluorescence microscopy during mitotic division.
EXAMPLE 3
Combining the quartet phenotype with maternal genome
e7imination in Arabidopsis
This example illustrates how the genotype I)
0; a
hybrid plant can be e ”iciently reconstituted.
A transgenic Arabidopsis thaliana plant 0: the Ler
ion was created, harbouring a single copy (in
gous state) ol an RNAi construct that targets the QRTl
gene (At5g55590), driven by the CaMV 358 constitutive
er. Alternatively other techniques such as artificial
micro—RNAs (amiRNAs) can be used for this purpose. This
plant was then crossed to a wild-type Arabidopsis thaliana
plan, ol the Ws accession.
The resulting F1 generation consisted 0: hybrid
plants with a mixed Ler/Ws background, which were hemizygous
for the QNAi construct. Because the RNAi construct aCts
sporophytically and in a dominant manner, al' F’ plants
exhibited the quartet pollen phenotype. An F’ p'ant —
exhibiting the quartet pollen phenotype — was then d
as a father with an Arabidopsis thaliana cenh3 mutant plant
o: the Col-O accession, which had been genetically
transformed with the GFP—CENH3-tailswap construct as
reported by Maruthachalam & Chan (Nature 464, 9;
2010). This cross resu'ted in the elimination o: the
al chromosomes during the first mitotic division in
the zngte, leading to the "ormation O" haploid seeds.
"n preparation for the crossing, nearly dehiscent
anthers of the father plant were opened under a lar
cope to allow the colleCtion 0" individual, ripe
pollen tetrads. Each pollen tetrad was carefully ted
2O onto the pistil o: a mother plant, using an eyelash or a
fine brush hair, and the four pollen grains were allowed to
"ertilixe "our . The four seeds resul ling from this
limited pollination with a single pollen te':rad were allowed
to mature, and were subsequently harvested and allowed to
germinate. Alternatively, more than one tetrad can be
deposited onto the pistil o: the mother plant, but care
should be taken that the number 0: pollen grains does not
xc d th av rag number 0: ovules in the female
reproductive par, ol the species. The use 0: more than one
tetrad "or pollination will namely reduce the e "iciency
with which genetically complementary progeny plants can be
identified.
The ploidy o: the seedlings resulting from the
d po" ination o _ the transgenic Col-O mother plant was
tested by _ ow cytome'try. Their ploidy was n, except in some
cases in which spontaneous genome doubling to 2n had
meanwhile occurred. For haploid individuals genome doubling
was subsequently accomplished by standard methods known to
the skilled person (e.g. colchicine treatment). Once the
four ngs resu' ting from this cross were 2n, their
genomic DNA was isolated and genetically analysed for
genetic markers covering the entire opsis genome.
ally markers polymorphic between Col-O and Ler and
between Col-O and Ws were tested , to distinguish the
contribution 0: both paren':al genomes to the four progeny
plants. Due to the ation o : the maternal genome from
the rygo ,es ,he four progeny plants only contained
recombined chromosomes from the hybrid father plant, and
h nc th y t st d n gative for all Col—O—specific markers.
Figure 2 shows that the occurrence rate 0: progeny
plants with a certain number 0: complementary chromosomes
2O within a pollen tetrad is dependent on the haploid
some number (n). opsis has five chromosomes, and
because of ,he quartet pollen phenotype in the al
father plan ,he chromosome constellation of the four
seedlings relets from a single meiotic division. This
implies ,hat ,here is a theoretical chance of l in 16 (6.3%)
for two "u' ly complementary genomes to be present in a
single pol:_en tetrad. The chance is 3l.3% for having two
genomes that have one non-complementary chromosome, and
62.5% for having two genomes that have two non-complementary
chromosomes. In all cases the individual pollen grains in a
tetrad are there:fore at least 50% complementary to each
other. "mportant' le _ ination results in e.g. 40%
heterozygosity, the overall complementarity between the
2012/069191
genome o: the individual pollen grains will always be higher
than 50%, because even the “non-complementary” somes
would then still be 60% complementary to each other.
Therefore, in theory only l6 individual crosses
with a pollen tetrad are required on average to identify two
Arabidopsis seedlings that have essentially complementary
sets 0: chromosomes. In practice, however, more are needed
because the e ”iciency o: the pollination, seed formation,
and plant germination and al is generally below 100
percent. As a rule 0: thumb 10 times more crosses were done
with single tetrads, i.e. 160 in this case, to maximize the
chance 0: success.
After fication, two genetically essentially
complementary plants were grown to anthesis and then
crossed. The genetic constitution of the Fl y
resu'ting "rom this cross was experimentally shown to be
essentially identical to the genetic tution 0: its
paternal grand ather, i.e. the grtl mutant plant with a Ler/
Ws hybrid background.
EXAMPLE 4
Combination of the quartet phenotype with maternal genome
elimination in Arabidopsis, with non—transgenic progeny
In Example 3 the F1 progeny remained transgenic,
because it ed the RNAi construct targeting the QRTl
gene, and hence also the quartet pollen phenotype. r,
when a GFP reporter te that specifically expresses the
Green Fluorescent Protein in mature pol'en grains is
integrated into the RNAi construct used in Example 3, this
allows another approach, in which the progeny plants are not
transgenic. The T—DNA construct then also contains a GFP
protein with a nuclear localization signal under a late-
pollen—specific promoter (the LAT52 promoter; Twell et al,
1990, Development L09: 705-713), which allows the easy
visual ion 0: this construct in mature pollen grains.
In anther es o: the Ler/Ws hybrid plant
mentioned in Example 3 ygous for the RNAi construct
targeting QRTl), pollen tetrads were selected in which two
of the "our pollen grains did not express GFP in their
nucleus, either visually (using a fluorescence binocular or
microscope) or by FACS (fluorescence—activated cell
sorting). Only two of the "our pol'en grains thus contained
the RNAi construct targeting the QRTl gene. Pollination o;
the above-mentioned Col-O mother plant - which induced the
elimination of the al chromosomes during the first
mitotic division in the zygote - with s JCh a pollen tetrad
gave rise to two transgenic haploid progeny plants
(harbouring the RNAi construct) and to :wo non-transgenic
haploid progeny plants (not harbouring the RNAi construct).
The non—transgenic progeny plants per definition
lacked the Ler chromosome fragment harbouring the RNAi—
construct for QRTl, and the crossing of these two plants can
2O thus never lead ,0 the exact reconstitution o: the original
Fl , e the reconstituted plants will be
homozygous for chromosome ]
a, least one Ws region, namely :or
the chromosome region which corresponds :o the chromosome
region that contains the RNAi-construct for QRTl in the Ler
parent plant.
EXAMPLE 5
Combining the quartet pollen phenotype with second division
restitution in sweet pepper (Capsicum annuum)
When second division restitut ion (SDR) occurs, the
second meiotic division does not take place, and the result
o: meiosis will be two diploid po'len grains, instead 0;
four haploid pollen grains. Th r for wh n
, th m iotic
2012/069191
products remain physically attached to each other — as is
the case with the quartet pollen phenotype — a plant will
produce pollen dyads when SDR occurs. "n this preferred
embodiment o: the current invention, the two diploid meiotic
products remain physically attached to each other, and
because their chromosomes have identical recombination break
points the two pollen grains are 100% genetically
complementary to each other.
A sweet pepper plant (Capsicum annuum) exhibiting
the quartet pollen phenotype was obtained through an RNAi
approach, similarly as described in Example 3. A progeny
plant thereo: — homozygous for the quartet phenotype — was
subjeCted to cold stress, in order to se the frequency
0: unreduced microspore (gamete) formation, as described by
Zhang et al. (2002) 7 of Horticu7tura7 Science &
Biotechnology 78: 84-88 and in examp'e 2 of ).
Up to 25% of the microspores and pollen ed in the
anthers of ,he cold-ureaued plant had ,he "orm O" a dyad.
Isolated microspore fracuions were fur,her enriched for
2O dyads by microscopic analysis (alternative'y flow cytometry
can be used). Using this approach, the app'ication referred
to as Near-Reverse Breeding () could be
enabled in a preferred embodiment.
For this purpose, a second sweet pepper plant was
created which eliminates the maternal genome from its
zngtes during the first mitotic division, “o'lowing the
experimental approach outlined in e 2. This transgenic
sweet pepper plant was ated with a single pollen dyad
derived from the mentioned cold-tr at d sw t p pp r
plant, and the resulting two diploid seeds were harvested
and germinated. The pollen dyad was ed manually in an
anther squash from among the pollen quartets that resulted
from non—SDR c events.
The plants grown from these two diploid seeds were
subsequently crossed, and — using genetic mar<ers — the
genetic composition 0: the progeny plants or ,his cross
could be confirmed as being essentially identical to the
c composition 0: the sweet pepper plant that produced
the po"en dyad we used for pollination. However, due to
cross-over events that had occurred during the ‘ormation 0'
the po"en dyads some telomeric variation had been
introduced, which provided onal genetic ion in
the selected hybrid ound.
Thus, the sweet pepper plant created in this
example by pollinating a haploid inducer mother plant with a
pollen dyad produced by another sweet pepper plant was
genetically only “essentia"y identical” to the sweet pepper
plant that ed the po"en dyad for pollination, because
additional genetic ion had been introduced at the
telomeres, as a resu't O" cross—over events that had
occurred during the ‘ormation o: the pollen dyads. All
genetic material 0: ,he Lather plant had been maintained,
2O but some paros or it had been rearranged through cross-over
events, and this rearrangement may cause additional
phenotypic e ecos.
This e thus allows jor ,he introduction I)
additional genetic variation in a seleCted ) hybrid
plant. This additional variation may have positive or
negative additional phenotypic e "ecLs, when compared to the
original hybrid phenOtype, and it thus provides an
interesting opportunioy to jurther improve (and/or fine—
tune) a hybrid ype, without losing the combination I)
selected traits comprised in the original hybrid.
Alternatively, the sweet pepper plant exhibiting
the quartet phenotype can be crossed with a sweet pepper
plant that naturally exhibits an above-average degree or
SDR. Their progeny will then naturally produce an above-
average percentage 0“ pol 'en dyads. Another strategy is to
mutagenize a tion 0: sweet pepper plants that
naturally exhibit an above-average degree o: 83?, and to
screen for plants displaying the t pollen phenotype in
this mucano population, in a ‘orward genetics approach.
In each and every dyad the chance is 100% that the
two pollen grains are genetically essentially complementary
to each other (with identical somal break-points). The
two microspores comprised in a dyads are per definition
genetically essentially complementary, and crossing the two
plants that can be derived from any one o: these dyads will
always result in a hybrid plant that is essentially
genetically identical to the original hybrid p— ant that
produced the dyads. This embodiment thus greatly improves
the e ”iciency o: th N ar R v rs 3r ding technology.
Generally, in this embodiment o: the invention a
plant carrying a genetic jeature that causes the elimination
O: the al chromosomes from its geny is
2O pollinated through limited pollination. The pollen used in
this cross is a single pollen dyad obtained from a hybrid
plant 0: the same species, which exhibits the quartet pollen
phenotype in combination with SDR. This pollen dyad is
obtained by visually screening squashed anthers and by
subsequently selecting a dyad cons ,ellation jrom among the
tetrad constellations (which resul ,ed jrom meiotic divisions
during which SDR had not occurred), or by ing a pollen
"raction "or dyads — in a more high-throughput g — by
means 0 "low cytometry or cell sorting.
A‘ter pol" ination E
0' the mother plant ng a
genetic jeature tha causes the elimination o: the maternal
chromosomes from its Fl—progeny, each 0. the ,wo diploid
pollen grains sed in the dyad jer,ilise an ovule, and
seed is allowed ,0 form and mature. Upon ripeness the two
seeds resu'ting rom ,his cross are harvested and
germinated. The ing seedlings are then tested for
their ploidy level by means 0 "low try, to confirm
that they are indeed 2n, as would be expeCted.
Subsequently, genomic DNA is isolated from the two
ngs, and genetic markers covering the entire genome
are tested in both individuals. Due to the elimination o;
the maternal chromosomes from the zygote, both seedlings are
expeCted only to possess paternal chromosomes. Due to the
fact ,hat the chromosomes from both seedlings originated in
a single meiotic division, all chromosome break points are
identical, and their genomes are 100% complementary. This is
confirmed by the genome-wide marker analysis.
The seedlings are subsequently grown to maturity
and d with each other. Their Fl progeny is genetically
essentially identical to the original starting hybrid plant
that was used as a laoher in the first cross, except for
cross-over events that have occurred during the "orma,ion I]
2O the SDR gametes. These cross-over events introduce some
telomeric ion, which provides additional genetic
variation in the selected hybrid ound.
The xact reconstruction of the (hybrid)
genotype 0: the al grandfather organism was achieved
in only two generations’ time and without the need :or
intermediate regeneration or genome doubling steps or tissue
culture.
EXAMPLE 6
Combining the quartet pollen phenotype with suppression of
some recombination and maternal genome elimination in
Arabidopsis
From a cross between an Arabidopsis plant that
exhibits the quartet pollen phenotype and anOther
Arabidopsis plant in which chromosome recombination is
partially or completely ssed (either by enic,
mutational or al means), an F2 progeny plant can be
selected in which both properties are combined: the four
po'len grains resulting "rom a single meiotic division
remain physically attached to each other to the time I)
up o;
anthesis and pollen shedding, and during s the
recombination o: homologous chromosomes is suppressed.
This progeny plant allows the application 0;
Reverse Breeding (WO 03/017753; Dirks et al 2009) in a more
e "icient way. Because the meiotic products remain
physically attached to each other, the chance 0" identi‘ying
two pollen grains with essentially complementary sets ol
2O chromosomes is greatly increased. The number 0" di""erent
tetrads is a on 0‘ the chromosome number ol the
species, but within a single tetrad, however, the chance
that two pollen grains have fully complementary sets 0;
chromosomes is always 50%, as the tour pollen grains are
pairwise complementary. Within each and every tetrad the
chance 0 g two pairs 0: complementary pollen grains
is thus lOO%.
As described in Example 3, an Arabidopsis thaliana
Ler plant was created, harbouring a single copy (in
homozygous state) 0: an RNAi construct that targets the QRTl
gene, driven by the CaMV 358 constitutive promoter. This
plant was then crossed with an opsis thaliana plant I)
the Ws accession which harboured I)
a homozygous single copy 0;
an RNAi construct that targets the DMCl gene, also driven by
the CaMV 358 constitutive er.
The resulting F1 generation consisted of hybrid
plants with a mixed Ler/Ws background, which were all
hemizygoas for both BNAi construCts. Because the RNAi
constructs both junction sporophy':ically and in a dominant
, the Fl plants exhibi':ed the quartet pollen phenotype
and suppression o: chromosome recombination during meiosis.
As an undesired side-e ect the suppression o: chromosome
recombination also ed in the ence 0: unbalanced
pollen tetrads (alongside balanced tetrads), because in the
absence 0 su "icient UHC ,ional DMCl protein each
chromosome is randomly dis:ributed over the daughter cells
0: a division. However, balanced tetrads could be selected
from s experimentally (through visual inspection
and/or flow try).
Balanced pollen tetrads derived from an Fl plant —
exhibiting the quartet pollen pheno type in combination with
suppression o: chromosome recombina :ion, being hemizygous
for both transgenic cons:ructs — were subsequently used to
pollinate Arabidopsis thaliana cenh3 mutant plants ol the
Col-0 accession (as crea:ed and ed by Maruthachalam &
Chan, 2010), which had been genetically trans formed with the
GFP—CENH3-tailswap construct reported by Maruthachalam &
Chan (2010), which results in the ation of the
maternal chromosomes during the ll”S mitotic division in
the zygote.
When 1
a single balanced pol: _en tetrad was used :or
pollination O" a pistil O the mother plant, this cross
ideally resulted in tour haploid progeny seeds. The four
y seeds were allowed to germinate, and the seedlings
were genetically tested with s. Because no chromosome
recombination had occurred during meiosis (due to the RNAi
construct targeting DMCl all chromosomes were passed onto
the next generation in their entirety), only very few
markers needed to be tested for each chromosome, to
determine r it was inherioed from the Ler grandparent
or from the Ws grandparent (in fac, a single rphic
mar<er per chromosome would be su "icient; in our
experimental approach we used one marker per chromosome arm,
i.e. two markers per chromosome).
To ensure that the mother plant had not contributed
genetically to the progeny also Col-O specific markers were
, but no Col-O c material could be identified,
as was also the case in Example 3.
The four progeny plants were found to be pairwise
perfectly genetically complementary, and based on the
genetic marker ana'ysis these pairs could be e ”iciently
idenoified. Crossing such a pair 0: genetically
complementary progeny plants to each other resulted in the
e "icient genetic reconstitution o: the original hybrid
plant that produced the pollen tetrad that was used :OI
pollination, i.e. the Ler/Ws hybrid plant gous :OI
both RNAi construC' Figure 4 illustrates the pedigree I]
:s. o;
the plants used in this experiment.
Claims (33)
1. Method for the production of a set of seeds which are genetically cal to the male s from which they arise, comprising: a) placing a limited number of paternal gametes that have the form of tetrads or dyads on the stigma of a flower to fertilize maternal egg cells to obtain a number of s, wherein the number of al gametes is limited to be equal or lower than the number of egg cells contained in the female reproductive organ carrying the stigma; b) inducing the loss of maternal chromosomes from the zygotes to obtain a seed set containing a limited number of seeds in which the maternal chromosomes are absent.
2. Method as claimed in claim 1, wherein the limited number of paternal gametes is equal to or lower than the number of egg cells contained in the female reproductive organ carrying the stigma.
3. Method as claimed in claim 1 or 2, wherein the limited number of paternal gametes is two or four.
4. Method as claimed in any one of the claims 1-3, wherein the paternal gametes that have the form of tetrads or dyads are the result of erence with microspore tetrad separation.
5. Method as claimed in claim 4, wherein interference with microspore tetrad separation comprises interference with one or more target genes involved in the break-down of the pectin layer between the microspores resulting from a single meiotic division.
6. Method as claimed in claim 5, wherein the one or more target genes are selected from the group consisting of QRT1 , QRT2 , QRT3 , or their functional homologues.
7. Method as claimed in claim 4, wherein interference with microspore tetrad separation is achieved by chemical means.
8. Method as claimed in any one of the claims 1-7, n the father plant exhibits suppression of some recombination.
9. Method as claimed in any one of the claims 1-7, wherein the father plant ts second division restitution (SDR) during s.
10. Method as claimed in claim 8, wherein suppression of chromosome recombination is ed by interfering with one or more target genes involved in recombination.
11. Method as claimed in claim 10, wherein the one or more target genes are involved in double strand breaks, such as SPO11 , MER1 , MER2 , MRE2 , MEI4 , REC102 , REC104 , REC114 , MEK1 /MRE4 , RED1 , HOP1 , RAD50 , MRE11 , XRS2 , or their functional homologues, or wherein the one or more target genes are involved in chromosome pairing and/or strand exchange, such as RHD54 /TID1 , DMC1 , SAE3 , RED1 , HOP1 , HOP2 , REC8 , MER1 , MRE2 , ZIP1 , ZIP2 , MEI5 , RAD51 , RAD52 , RAD54 , RAD55 , RAD57 , RPA , SMC3 , SCC1 , MSH2 , MSH3 , MSH6 , PMS1 , SOLODANCERS , HIM6 , CHK2 , or their functional homologues, or wherein the one or more target genes are involved in the meiotic ination process, or their functional homologues, or wherein the one or more target genes are selected from the group consisting of PRD1 , PRD2 , PRD3 , PHS1 , NBS1 , COM1 , MND1 , MER3/RCK , ZIP3 , ZIP4, PTD , SHOC1 , ZYP1 , MLH1 , MLH3 , or their functional homologues.
12. Method as claimed in claim 11, wherein the one or more target genes involved in the meiotic recombination process are SGS1, MSH4, MSH5, ZIP1 and/or ZIP2.
13. Method as claimed in claim 5 or 10, wherein the interfering with the one or more target genes consists of ting transcription thereof.
14. Method as claimed in claim 13, wherein ription is prevented by means of RNA oligonucleotides, DNA oligonucleotides or RNAi molecules directed against the target gene promoter, or wherein transcription is prevented by means of the expression of a negatively acting transcription factor acting on the target gene promoter.
15. Method as claimed in claim 5 or 10, wherein the interfering with the one or more target genes ts of destabilizing the target gene mRNA or transcript, or wherein the interfering with the one or more target genes consists of inhibiting the target gene expression product.
16. Method of claim 15, wherein the target gene mRNA or transcript is destabilized by means of nucleic acid molecules that are complementary to the target gene mRNA or transcript, selected from the group consisting of nse RNA, RNAi molecules, Virus-Induced Gene Silencing (VIGS) molecules, pressor molecules, RNA oligonucleotides or DNA oligonucleotides.
17. Method of claim 15, wherein inhibiting the target gene expression product is by means of the expression product(s) of one or more dominant negative nucleic acid constructs.
18. Method of claim 15, wherein inhibiting the target gene expression product is by means of one or more chemical compounds.
19. Method as claimed in claim 5 or 10, wherein the ering with the one or more target genes consists of the introduction of one or more mutations into the target gene, leading to perturbation of its biological function.
20. Method as claimed in claim 19, n the one or more mutations are introduced randomly by means of one or more chemical compounds, and/or by physical means, and/or by insertion of genetic elements and/or wherein the one or more mutations are introduced ically by means of homologous recombination or oligonucleotide-based mutation induction.
21. Method as claimed in claim 20, n the one or more chemical compounds selected from methanesulphonate, nitrosomethylurea, hydroxylamine, proflavine, N-methyl-N- nitrosoguanidine, N-ethyl-N-nitrosourea, N-methyl-N-nitronitrosoguanidine , diethyl sulphate, ethylene imine, sodium azide, formaline, urethane, phenol and ethylene oxide.
22. Method as claimed in claim 20, wherein the al means comprise UV-irradiation, fast-neutron exposure, X-rays, gamma irradiation.
23. Method as claimed in claim 20, wherein the insertion of genetic elements includes transposons, T-DNA, iral elements.
24. Method as claimed in claim 9, wherein second division restitution occurs spontaneously, in particular without interference with the starting organism.
25. Method as d in claim 9, wherein second division restitution is induced by means of genetic modification, wherein the genetic modification is transient, or n the genetic modification is achieved by stable oration into the genome of a genetic t increasing the number of second division restitution events in the organism, or wherein second division restitution is achieved by subjecting the father plant to environmental stress, such as ature stress, NO2, nitrous oxide (N2O), or combinations thereof.
26. Method as d in any one of the claims 1- 17, wherein the loss of maternal chromosomes from the zygote is induced by using a haploid inducer line as the female.
27. Method as claimed in claim 26, wherein the female is a plant of a ent species.
28. Method as claimed in any one of the claims 1- 26, wherein the female plant is a transgenic plant that comprises a heterologous ene expression cassette, the expression te comprising a promoter operably linked to a polynucleotide encoding a recombinantly altered CENH3, CENPC, MIS12, NDC80 or NUF2 polypeptide, and having a corresponding inactivated endogenous CENH3 , CENPC , MIS12 , NDC80 or NUF2 gene.
29. Set of seeds containing a limited number of seeds in which the maternal chromosomes are absent, which set is composed of pairs of genetically complementary seeds which when plants grown from the seeds are crossed result in essentially the same hybrid, and which seed set is obtainable by a method as claimed in any one of the claims 1-28.
30. Method for providing a set of parent plants for the production of a plant of which the genetic constitution is essentially identical to the c constitution of its male grandparent, comprising growing plants from seeds of the set of seed as claimed in claim 29, after or prior to doubling the chromosome number of the seeds, and identifying two genetically complementary plants as the parent plants.
31. Method as claimed in claim 30, n the set of seeds or the plants grown thereof are screened for their genetic constitution, to identify a plant of which the genetic constitution is essentially identical to the genetic constitution of its paternal ather, and to identify another plant of which the genetic constitution is essentially identical to the genetic constitution of its paternal grandmother.
32. Method as d in any one of the claims 29- 31, wherein a plant of which the genetic constitution is ially identical to the genetic constitution of its paternal grandfather, is crossed to another plant of which the genetic tution is essentially identical to the genetic constitution of its paternal grandmother, in order to obtain progeny plants of which the genetic constitution is essentially identical to the c constitution of their own grandfather.
33. A method according to claim 1, substantially as herein described with reference to any one of the accompanying examples and/or figures thereof.
Applications Claiming Priority (3)
Application Number | Priority Date | Filing Date | Title |
---|---|---|---|
EP11183362A EP2574234A1 (en) | 2011-09-29 | 2011-09-29 | Quartet breeding |
EP11183362.0 | 2011-09-29 | ||
PCT/EP2012/069191 WO2013045616A1 (en) | 2011-09-29 | 2012-09-28 | Quartet breeding |
Publications (2)
Publication Number | Publication Date |
---|---|
NZ621959A NZ621959A (en) | 2016-08-26 |
NZ621959B2 true NZ621959B2 (en) | 2016-11-29 |
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ID=
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