WO2017025627A1 - Résistance à la variante australienne de a. candida race 9 dans le broccoli - Google Patents

Résistance à la variante australienne de a. candida race 9 dans le broccoli Download PDF

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Publication number
WO2017025627A1
WO2017025627A1 PCT/EP2016/069241 EP2016069241W WO2017025627A1 WO 2017025627 A1 WO2017025627 A1 WO 2017025627A1 EP 2016069241 W EP2016069241 W EP 2016069241W WO 2017025627 A1 WO2017025627 A1 WO 2017025627A1
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Prior art keywords
snp
seq
plant
allele
resistance
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PCT/EP2016/069241
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English (en)
Inventor
Pierrick BERTHY
Perrine DAVID
Pierre HURRIER
Grégoire MARANDEL
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Vilmorin & Cie
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Priority claimed from AU2015255211A external-priority patent/AU2015255211B2/en
Application filed by Vilmorin & Cie filed Critical Vilmorin & Cie
Priority to EP16753890.9A priority Critical patent/EP3334273A1/fr
Priority to JP2018527016A priority patent/JP6954903B2/ja
Priority to AU2016305521A priority patent/AU2016305521B2/en
Publication of WO2017025627A1 publication Critical patent/WO2017025627A1/fr

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    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/12—Processes for modifying agronomic input traits, e.g. crop yield
    • A01H1/122—Processes for modifying agronomic input traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance
    • A01H1/1245—Processes for modifying agronomic input traits, e.g. crop yield for stress resistance, e.g. heavy metal resistance for biotic stress resistance, e.g. pathogen, pest or disease resistance
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H1/00—Processes for modifying genotypes ; Plants characterised by associated natural traits
    • A01H1/04—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection
    • A01H1/045—Processes of selection involving genotypic or phenotypic markers; Methods of using phenotypic markers for selection using molecular markers
    • A—HUMAN NECESSITIES
    • A01—AGRICULTURE; FORESTRY; ANIMAL HUSBANDRY; HUNTING; TRAPPING; FISHING
    • A01H—NEW PLANTS OR NON-TRANSGENIC PROCESSES FOR OBTAINING THEM; PLANT REPRODUCTION BY TISSUE CULTURE TECHNIQUES
    • A01H6/00—Angiosperms, i.e. flowering plants, characterised by their botanic taxonomy
    • A01H6/20—Brassicaceae, e.g. canola, broccoli or rucola
    • A01H6/203—Brassica oleraceae, e.g. broccoli or kohlrabi
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6888—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms
    • C12Q1/6895—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for detection or identification of organisms for plants, fungi or algae
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates to resistance in plants of Brassica oleracea to white blister rust caused by the oomycete Albugo Candida race 9, especially to the Australian variant of Albugo Candida race 9.
  • the resistance is provided by DNA sequences, introgressed in the genome of a Brassica oleracea plant, on chromosome 4.
  • the introgressed sequences can be present homozygously or heterozygously in the genome of a Brassica oleracea plant.
  • a particularly preferred resistant plant is broccoli.
  • the present invention further relates to a method for providing B. oleracea plants which are resistant to white blister rust, DNA markers for white blister rust resistance and their use in identifying plants resistant to white blister rust caused by the oomycete Albugo Candida race 9, especially to the Australian variant.
  • Kuntze is an obligate biotrophic pathogen of the Brassicaceae family, also known as the crucifer family, and causes the widespread disease known as white rust (also known as white blister, white blister rust, staghead, A. cruciferum or A. cruciferatum). This disease is destructive to many vegetable and oilseed crops such as broccoli, cabbage, rape, mustard and radish.
  • White rust has been observed worldwide, in countries as geographically and environmentally diverse as India, Canada, Europe and Australia. In Australia, white blister rust has spread to Brassicaceae crops in southern parts of the country.
  • Candida is highly specialized, grows between living host cells and causes a range of symptoms that can be the result of local or systemic infection.
  • the genus Albugo includes several species that cause white rust on a range of hosts and within A.
  • Candida various host- specialized forms have been reported.
  • One of the characteristics of A. Candida is thus its high degree of host specificity.
  • Candida leads to two types of infections, local or systemic. Local infection is characterised by white or creamy-yellow pustules of zoosporangia that form under the epidermis of the host. These usually develop on the lower (abaxial) surface of the leaf and to a lesser extent on the upper (adaxial) surface and occur more commonly on mature leaves. However, they may be localized on any aerial host organ. Initially, the pustules are small and discrete but eventually become large and confluent. Once the pustule is fully developed, the host epidermis ruptures to release a dry, powdery burst of zoosporangia. Subsequently, necrosis of the surrounding leaf tissue may occur.
  • Local infection is characterised by white or creamy-yellow pustules of zoosporangia that form under the epidermis of the host. These usually develop on the lower (abaxial) surface of the leaf and to a lesser extent on the upper (adaxial) surface and occur more commonly on
  • Systemic infection does not usually result in extensive yield loss but would still lead to unmarketable products.
  • Systemic infection can have a severe impact on the productivity of crops grown for seed or floral parts.
  • Systemic infection appears to trigger sexual reproduction of the oomycete and causes distortion, hyperplasia and hypertrophy of the inflorescences, stems and leaves. It can also result in sterility if the flower petals, ovules and pollen grains are malformed as a result of the disease.
  • Candida grows best at moderate temperatures of between 10 and 20°C and in moist conditions. A leaf wetness period of 2.5 hours is sufficient to result in infection, which becomes symptomatic after an incubation period of 10 to 14 days.
  • Brassica is a plant genus in the family Brassicaceae (formerly referred to as Cruciferae).
  • the genus Brassica comprises a number of important agricultural and horticultural crops, including rape, cauliflower, broccoli and turnip. Almost all parts of these plants can be used as food. Rape and rape seed are also used for oil, both for consumption and for fuel. Some species with white or purple flowers or distinct colour or shaped leaves are cultivated for ornamental purposes.
  • the Brassicaceae family occurs worldwide and comprises annuals, biennials and perennials. The family also comprises a large number of wild species.
  • Candida is now subdivided into several races that are specialised to infect specific hosts.
  • Race refers to a variety of a pathogen that can infect some species of a host genus and not others whereas in most pathosystems it is taken to mean a variety of pathogen that can infect some varieties of a host species but not others.
  • Brassica rapa L campestris, Chinese Mustard, Chinese Cabbage, Pak pekinensis, chinensis) Choi, Field and Black Mustard
  • Candida race 9 has spread to B. oleracea var. italica (broccoli) and B. oleracea var. botrytis (cauliflower) crops in southwest Australia, making this pathogen the number one concern for broccoli and cauliflower breeding in Australia.
  • This oomycete pathogen is growing on Broccoli leaves, stem or curds showing white spot symptoms on leaves and transforming buds into white erected pin heads that affect the curd quality and shelf life.
  • the Australian A. Candida strain infecting B. oleracea differs from the A.
  • Candida race 9 generally encountered in other parts of the world, and referred to as European variant; this European variant causes disease essentially on cabbage.
  • race 9 is in some experiments more aggressive towards broccoli than towards cabbage while in Europe, the race 9 appears to be more aggressive towards cabbage and Brussels sprouts. It is therefore reported that race 9 comprises at least two variants, the European variant, more aggressive towards cabbage and the Australian variant more aggressive towards broccoli (Petkowski et al, Proc. Vth IS on Brassica & XVIth Crucifer Genetics WS: 133-141 ; 2010); for example Iron CMS and Belstar commercial varieties show resistance to the European variant but are susceptible to the Australian variant, as reported in WO2010/135782.
  • Candida in broccoli Brassica oleracea var. italica
  • Such resistance would not only increase the stability of crop protection, but would also result in a reduced, or eliminated, requirement for environmentally harmful, and not always effective, fungicide applications.
  • Such resistance could also be beneficial to other B. oleracea plants such as cauliflower, Brussel sprouts, white cabbage, savoy cabbage, etc.
  • WO2008133503 illustrates B. oleracea plants allegedly containing a monogenic dominant resistance gene to A. Candida, but not to the Australian variant of A. Candida race 9.
  • WO201 1036108 illustrates B. oleracea plants allegedly containing a monogenic semi- dominant resistance gene to A. Candida, present on chromosome 2 but not conferring resistance to the Australian variant.
  • WO2010135782 illustrates B. oleracea plants containing a monogenic dominant resistance gene to A.
  • Candida located on chromosome 1. This gene has been able to confer resistance to some strains of the Australian variant of A. Candida race 9 but appears to be unable to generally confer resistance to white rust caused by A.
  • Candida race 9 Australian variant irrespective of the strain.
  • Tyson Minchinton et al, Australian Plant Pathol 2013; 42:169-178
  • Candida race 9 appears to be unable to generally confer resistance to white rust caused by A.
  • Candida race 9 Australian variant irrespective of the strain, as illustrated in the examples (see Ex. 6 and 7).
  • the present inventors have identified a resistance to the Australian variant of the A. Candida race 9 pathogen and have been able to introgress this resistance into B. oleracea plants, thus obtaining resistant B. oleracea plants, more specifically broccoli resistant plants.
  • the resistance of the present invention is imparted by the newly discovered sequences conferring the resistance, said resistance being of monogenic and dominant nature and transferable to different B. oleracea genetic backgrounds.
  • the present invention provides introgressed sequences conferring, when present in homozygous or in heterozygous state, the phenotype of resistance to the Australian variant of the A. Candida race 9.
  • the invention also provides B. oleracea plants that display resistance to Australian variant of the A. Candida race 9, especially broccoli plants, as well as methods that produce or identify B. oleracea plants that display resistance to Australian variant of the A. Candida race 9 as well as seeds, roots and other plant parts such as pollen and ovules containing the introgressed sequences conferring the resistance.
  • the invention also discloses molecular genetic markers, especially SNPs, linked to the introgressed sequences conferring the resistance, i.e. linked to the resistance locus which is of dominant nature.
  • Candida race 9 Australian variant plant may be selected from the group consisting of B. oleracea convar. Botrytis var. italica (broccoli), B. oleracea convar. botrytis var. botrytis (cauliflower), B. oleracea convar. botrytis var. asparagoides (sprouting broccoli), B. oleracea convar. oleracea var. gemnifera (Brussels sprouts), B. oleracea convar. capitata var. alba (white cabbage, oxheart cabbage), B. oleracea convar.
  • Candida biological races established by Pound and William in 1963 (Pound and William, 1963, Phytopathology 53:1 146-1 149), which is further characterized as being more aggressive towards broccoli than towards cabbage by opposition to the European variant race 9 which is more aggressive towards cabbage and Brussels sprouts.
  • the Australian variant is also known as being the variant responsible for the white blister rust outbreaks in Contemporary broccoli and cauliflower crops in the summer 2001 -2002 and the subsequent spread of disease to all Australian broccoli and cauliflower cropping areas (Petkowski et al, Proc. Vth IS on Brassica & XVIth Crucifer Genetics WS: 133-141 ).
  • Candida race 9 Australian variant co-exist, inter alia during field infection, which may have different virulence on the infected plants.
  • the term "Resistance” is as defined by the ISF (International Seed Federation) Vegetable and Ornamental Crops Section for describing the reaction of plants to pests or pathogens, and abiotic stresses for the Vegetable Seed Industry.
  • resistance it is meant the ability of a plant variety to restrict the growth and development of a specified pest or pathogen and/or the damage they cause when compared to susceptible plant varieties under similar environmental conditions and pest or pathogen pressure. Resistant varieties may exhibit some disease symptoms or damage under heavy pest or pathogen pressure.
  • Susceptibility The inability of a plant variety to restrict the growth and development of a specified pest or pathogen.
  • Candida race 9 Australian variant is for example the commercially available plant 'Belstar' or 'Fiesta' from Bejo, the variety 'Rumba' from HM. Clause, the varieties 'Patriot' and 'Green Belt' from Sakata or the variety 'Monaco' from Syngenta. All the commercially available varieties of B. olearacea broccoli are, to date, susceptible to white rust caused by A.
  • Candida race 9 Australian variant apart Booster variety of HM. Clause SA and Tyson variety of Syngenta, which are however not resistant to all infections by A.
  • Candida race 9 Australian variant is for example the commercially available plant 'Belstar' or 'Fiesta' from Bejo, the variety 'Rumba' from HM. Clause, the varieties 'Patriot' and 'Green Belt' from Sakata or the variety 'Monaco' from Syngenta. All the commercially available varieties of
  • a plant according to the invention has thus at least improved resistance to A.
  • an offspring plant refers to any plant resulting as progeny from a vegetative or sexual reproduction from one or more parent plants or descendants thereof.
  • an offspring plant may be obtained by cloning or selfing of a parent plant or by crossing two parents plants and include selfings as well as the F1 or F2 or still further generations.
  • An F1 is a first-generation offspring produced from parents at least one of which is used for the first time as donor of a trait, while offspring of second generation (F2) or subsequent generations (F3, F4, etc.) are specimens produced from selfings of F1 's, F2's etc.
  • An F1 may thus be (and usually is) a hybrid resulting from a cross between two true breeding parents (true-breeding is homozygous for a trait), while an F2 may be (and usually is) an offspring resulting from self-pollination of said F1 hybrids.
  • cross refers to the process by which the pollen of one flower on one plant is applied (artificially or naturally) to the ovule (stigma) of a flower on another plant.
  • genes refers to any segment of DNA associated with a biological function.
  • genes include, but are not limited to, coding sequences and/or the regulatory sequences required for their expression.
  • Genes can also include nonexpressed DNA segments that, for example, form recognition sequences for other proteins.
  • Genes can be obtained from a variety of sources, including cloning from a source of interest or synthesizing from known or predicted sequence information, and may include sequences designed to have desired parameters.
  • the term "genotype” refers to the genetic makeup of an individual cell, cell culture, tissue, organism (e.g., a plant), or group of organisms.
  • heterozygote refers to a diploid or polyploid individual cell or plant having different alleles (forms of a given gene or sequences) present at least at one locus.
  • heterozygous refers to the presence of different alleles (forms of a given gene or sequences) at a particular locus.
  • homolog or “homologue” refer to a nucleic acid or peptide sequence which has a common origin and/or functions similarly to a nucleic acid or peptide sequence from another species.
  • homozygote refers to an individual cell or plant having the same alleles at one or more loci on all homologous chromosomes.
  • homozygous refers to the presence of identical alleles at one or more loci in homologous chromosomal segments.
  • hybrid refers to any individual cell, tissue or plant resulting from a cross between parents that differ in one or more genes.
  • locus refers to any site that has been defined genetically.
  • a locus may be a gene, or part of a gene, or a DNA sequence, and may be occupied by different sequences.
  • a locus may also be defined by a SNP (Single Nucleotide Polymorphism), or by several SNPs.
  • introgression it is meant the infiltration of the genes or of genomic sequences of one species, variant or strain, into the gene pool of another one from an initial hybrid between these species, variants or strains.
  • the present invention is directed to B. oleracea plants, and preferably to B. oleracea broccoli plants that display resistance to Australian variant of A. Candida race 9, as well as methods that produce or identify B. oleracea, especially broccoli plants that display resistance to infection by Australian variant of A. Candida race 9.
  • the present invention also discloses molecular genetic markers, especially SNPs, linked to the resistance locus. The inventors have also shown that the sequences responsible for the resistance can be introgressed into different genetic backgrounds and still confer the resistance phenotype (as demonstrated inter alia in example 1 with different F2 populations and example 4 with 2 inbred lines).
  • the seeds and plants according to the invention have been obtained from an initial cross between a Romanesco plant, the introgression partner displaying the phenotype of interest, and an inbred line of broccoli, the recurrent susceptible parent, followed by backcross and a dihaploidization program.
  • a sample of this Brassica oleracea var italica (broccoli) BROCCO- C4 seed has been deposited by HM. Clause S.A. Rue Louis Saillant, Z.I.
  • the plants grown from these deposited seeds are broccoli plants resistant to white blister rust caused by any Australian variant of A. Candida race 9 and are commercially acceptable phenotype.
  • the present invention is thus directed to a B. oleracea plant or seed, which is resistant to white blister rust caused by the oomycete Albugo Candida race 9 Australian variant, comprising in its genome introgressed sequences or interval conferring said resistance to white blister rust.
  • Said introgressed sequences confer the resistance to a B. oleracea plant or seed when present either homozygously, or heterozygously.
  • the introgressed interval acts as a single dominant allele of a resistance gene responsible for the phenotype (i.e. the resistance trait is monogenic and dominant). Plants homozygous and heterozygous for the introgressed interval both fully exhibit the white rust resistance phenotype. This phenotype can be used to identify progeny that bear the claimed introgressed sequences or interval.
  • the introgressed interval acting as a resistance gene confers the phenotype of interest and is unexpectedly unlinked to negative features incompatible with marketability of the plants, seed or head, such as presence of leaflets on the petioles or "cat- eyes", i.e. the presence of some beads which prematurely break into yellow flowers.
  • Candida race 9 Australian variant infection is advantageously determined by comparison to a susceptible (commercial) line, for example Belstar, Fiesta or Rumba, or to a line resistant to only some strains, for example Booster or Tyson.
  • the resistance may be determined by the pathological test described in example 1 , preferably 15 days after inoculation.
  • a score of "1 " corresponds to leaves with more than 75% of the surface with sporulation
  • a score of "3" corresponds to between 51 and 75% of the surface with sporulation
  • a score of "5" is 26 to 40% of the surface with sporulation
  • a score of "7” is 13 to 25%
  • a score of "8” is 1 to 12%
  • "9" corresponds to the absence of sporulation on the leaves.
  • a plant having a score of 9, i.e. without sporulation on the leaf surface is to be considered as resistant, and more specifically highly resistant.
  • the introgressed sequences are preferably to be found on chromosome 4 in the B. oleracea genome and thus confer resistance to white blister rust caused by the oomycete A.
  • Candida race 9 Australian variant when they are present on either one or both homologous chromosomes 4.
  • the introgressed sequences conferring the resistance are more preferably located within the chromosomal region of chromosome 4 which is delimited on one side by the SNP BO- 0108436 (SEQ ID No:5) and on the other side by the SNP BN-0067793 (SEQ ID No:15), and preferably between SNP BO-0108436 (SEQ ID No:5) and SNP BO-0108751 (SEQ ID No: 1 1 ).
  • SNP BO- 0108436 SEQ ID No:5
  • SNP BN-0067793 SEQ ID No:15
  • SNP BO-0108436 SEQ ID No:5
  • SNP BO-0108751 SEQ ID No: 1 1 1 .
  • the introgressed sequences or interval conferring the resistance are preferably chosen from the introgressed sequences present in the genome of a plant of B. oleracea var. Italica - BROCCO-C4, representative seeds of which are deposited at the NCIMB under the accession number NCIMB 42433. They are especially chosen from the introgressed sequences present on chromosome 4 of said B. oleracea var. Italica -BROCCO-C4. Indeed, the deposited seeds comprise, on one chromosome 4 homologue, introgressed sequences conferring the phenotype of interest, wherein said introgressed sequences are also conferring the phenotype in B. oleracea genetic background. A sample of this B.
  • oleracea var. Italica -BROCCO-C4 seed has been deposited with the National Collection of Industrial, Food and Marine Bacteria (NCIMB), (NCIMB Ltd, Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen AB21 9YA, United Kingdom), on 9 th July 2015, under accession number NCIMB 42433.
  • NCIMB National Collection of Industrial, Food and Marine Bacteria
  • NCIMB Ltd Ferguson Building, Craibstone Estate, Bucksburn, Aberdeen AB21 9YA, United Kingdom
  • accession number NCIMB 42433 accession number
  • the deposited seeds are hybrid seeds, they bear the introgression sequences, conferring the resistance, on only one chromosome 4 homologue.
  • the resistance sequences can be easily identified inter alia by the markers disclosed in the application.
  • sequences conferring the resistance are present in the genome of all deposited seeds; as such the genome of these deposited seeds thus represent a reservoir of introgressed sequences in the B. oleracea genome conferring resistance to white rust caused by A.
  • a plant or seed of the invention comprises in its genome introgressed sequences which are chosen from this reservoir.
  • this introgressed fragment may slightly vary in length between the seeds.
  • the present invention is thus also directed to a B. oleracea seed or plant, preferably a cultivated B. oleracea seed or plant, most preferably a broccoli seed or plant, having in its genome introgressed sequences conferring resistance to white rust caused by A. Candida race 9 Australian variant, wherein said introgressed sequences conferring the resistance are chosen from the introgressed sequences present in the genome of a seed of B. oleracea var. Italica -BROCCO-C4 corresponding to NCI MB 42433 deposit.
  • introgressed sequences or intervals at a given locus or “introgressed sequences or intervals present/found at a given locus”
  • the genomic interval found at this given locus has not the same sequence as the corresponding genomic interval found in the B. oleracea broccoli germplasm before introgression, but has, at this locus, the sequence found in the corresponding genomic interval of B. oleracea var. Italica -BROCCO-C4 (NCIMB 42433) at the same locus; the introgressed sequences are thus exogenous with respect to a plant of the invention.
  • a genomic interval under test has the same sequence, in the sense of the invention, as the corresponding genomic interval found in the B. oleracea var. Italica -BROCCO-C4 at the same locus, if said genomic interval under test is also capable of conferring resistance to white rust caused by A. Candida race 9 Australian variant.
  • GISH genetic in situ hybridization
  • GISH is indeed a powerful technique for detection of the introgression of chromatin material from one species or strain onto another species or strain.
  • the advantage of GISH is that the introgression process is visualized by means of 'pictures of the introgressed genome'. With this technique, it is also possible to establish if a particular region of the genome is homozygous or heterozygous, thanks to the use of molecular cytogenetic markers which are co-dominant. By this technique, it is also possible to determine in which chromosome an introgressed gene of interest is present.
  • the introgressed sequences conferring the resistance phenotype of the invention i.e. resistance to white blister rust caused by the oomycete Albugo Candida race 9 Australian variant, are introgressed from a romanesco B. oleracea plant.
  • the introgressed sequences conferring the resistance, and which are also to be found in the genome of the deposited seeds, are introgressed on chromosome 4 of a B. oleracea plant according to the invention, preferably broccoli, they are more precisely within the chromosomal region of chromosome 4 which is delimited on one side by the SNP BO-0108436 (SEQ ID No:5) and on the other side by the SNP BN-0067793 (SEQ ID No: 15), and more preferably between SNP BO-0108436 (SEQ ID No:5) and SNP BO-0108751 (SEQ ID No: 1 1 ).
  • SNP BO-0108436 SEQ ID No:5
  • SNP BN-0067793 SEQ ID No: 15
  • SNP BO-0108436 SEQ ID No:5
  • SNP BO-0108751 SEQ ID No: 1 1
  • the section on chromosome 4 within the region delimited on one side by the SNP BO-0108436 (SEQ ID No:5) and on the other side by the SNP BN-0067793 (SEQ ID No: 15), comprises sequences which are responsible for the resistance to white rust caused by A.
  • Said introgressed sequences are preferably from a romanesco B. oleracea plant.
  • the introgressed sequences present in the genome of a plant or seed of the invention are to be found at one or more of the following loci:
  • locus encompassing SNP BN-0067786 (SEQ ID No: 14), and / or
  • the locus encompassing SNP BO-0108746 is highly preferred.
  • SNPs identified by their flanking sequences, present in all B. oleracea genomes, especially B. oleracea var. Italica and Romanesco B. oleracea, to discriminate between introgressed and endogenously residing sequences and to track down the introgressed sequences from Romanesco in the B. oleracea broccoli genome.
  • the present inventors have identified that introgressed sequences essential for the phenotype of interest, i.e. white rust caused by A.
  • Candida race 9 Australian variant are to be found in the vicinity of the SNP BN-0067786 (SEQ ID No: 14) or preferably in the vicinity of SNP BO- 0108746 (SEQ ID No:6), or in the vicinity of both SNPs.
  • the introgressed sequences are to be found in a locus encompassing the position of SNP BO-0108746. It is to be noted that the locus of SNP BN-0067786 and SNP BO-0108746 are located within the chromosomal region defined above, i.e. delimited on one side by the SNP BO-0108436 and on the other side by the SNP BN-0067793 on B. oleracea chromosome 4.
  • the allele of SNP BN-0067786 is the allele of SNP BN- 0067786 found in the Romanesco introgression partner, and also in the deposited resistant B. oleracea var. Italica -BROCCO-C4, and demonstrated in the experimental section as genetically linked to the resistance, i.e. allele T of SNP BN-0067786.
  • the 5' flanking region of SNP BN-0067786, or the 3' flanking region of SNP BN-0067786, or both regions, are also identical B. oleracea var.
  • the SNP BN-0067786 may form part of the 3' border or 5' border of the introgressed interval, or may be within the introgressed interval conferring the desired phenotype.
  • the allele of SNP BO-0108746 is the allele of SNP BO- 0108746 found in the Romanesco introgression partner, and also in the deposited resistant BROCCO-C4, and demonstrated in the experimental section as genetically linked to the resistance i.e. allele C of SNP BO-0108746.
  • the 5' flanking region of SNP BO-0108746, or the 3' flanking region of SNP BO-0108746, or both regions, are also identical to B. oleracea var. Italica -BROCCO-C4 sequences in this region. Therefore, the SNP BO-0108746 may form part of the 3' border or 5' border of the introgressed interval, or may be within the introgressed interval conferring the desired phenotype.
  • the presence of the introgressed sequences of interest can indeed be revealed by the presence of specific alleles of given SNPs, wherein said alleles are characteristic of the introgression partner, thus associated with the resistance, and distinct from the allele of the recurrent B. oleracea broccoli parent for these SNPs, associated with the susceptibility.
  • the alleles of given SNPs can thus reflect the presence of the introgression sequences of the
  • SNP BO- 0108436 SEQ ID No:5
  • SNP BO-0108746 SEQ ID No:6
  • SNP BO-0108747 SEQ ID No:7
  • SNP BO-0108748 SEQ ID No:8
  • SNP BO-0108749 SEQ ID No:9
  • SNP BO-0108750 SEQ ID No:10
  • SNP BO-0108751 SEQ ID No:1 1
  • SNP BN-0067786 SEQ ID No:14
  • SNP BN-0067793 SEQ ID No:
  • alleles, associated with the resistance are inter alia allele G of SNP BO- 0108436 (SEQ ID No:5); allele C of SNP BO-0108746 (SEQ ID No:6); allele G of SNP BO- 0108747 (SEQ ID No:7); allele A of SNP BO-0108748 (SEQ ID No:8); allele C of SNP BO- 0108749 (SEQ ID No:9); allele A of SNP BO-0108750 (SEQ ID No:10); allele G of SNP BO- 0108751 (SEQ ID No:1 1 ); allele C of SNP BO-0108752 (SEQ ID No:12); allele C of SNP BO-
  • Table 1 1 discloses for the 1 1 SNPs of the invention the allele which is associated with the resistance phenotype, i.e. the allele which co-segregates with the resistance phenotype, and the allele which is associated with the susceptibility.
  • a plant or seeds of the invention is preferably characterized by allele C of BO-0108746, preferably in combination with at least one, preferably at least two, 3, 5 or all of allele G of BO- 0108436, allele G of BO-0108747, allele A of BO-0108748, allele C of BO-0108749, allele A of BO-0108750, allele G of BO-0108751 , allele C of BO-0108752, allele C of BO-0108753, allele T of BN-0067786 and allele G of BN-0067793.
  • allele C of BO- preferably in combination with at least one, preferably at least two, 3, 5 or all of allele G of BO- 0108436, allele G of BO-0108747, allele A of BO-0108748, allele C of BO-0108749, allele A of BO-0108750, allele G of BO-0108751 , allele C of BO-0108752, allele C of BO-0108753, allele T of BN-
  • the introgressed sequences present in the genome of a plant or seed of the invention are to be found at one or more of the following loci:
  • introgressed sequences are to be found at the loci encompassing SNP BO-0108436, SNP BO-0108746, SNP BO-0108747, SNP BO-0108748,
  • a resistant plant or seed of the invention may also be characterized by the allele T of SNP BN-0067786, or preferably by allele C of SNP BO-0108746, or both. They may also be characterized in addition to allele C of BO-0108746, by at least one of the following alleles: allele G of SNP BO-0108436; allele G of SNP BO-0108747; allele A of SNP BO-
  • the presence of the introgressed sequences can also be revealed by genie amplification of sequences in the proximity of the SNPs defined in the present invention, especially SNP BO-
  • the introgressed sequences conferring the phenotype of interest are in linkage disequilibrium with the allele of SNP BO-0108746.
  • the allele of SNP BO-0108746 is "C”.
  • the allele T of SNP BN- 0067786 and allele C of SNP BO-0108746 are in linkage disequilibrium with the introgressed sequences conferring the resistance. Linkage disequilibrium indeed is used to describe
  • the linkage disequilibrium score may be any positive score, meaning that the association of SNP BO-0108746 with the introgressed sequences is not random.
  • said introgressed sequences are preferably to be found in the genome at a genetic distance of less than 20 cM, preferably less than 15 cM, most preferably less than 10 cM, and even preferably less than 5 cM from the locus corresponding to SNP BO-0108746.
  • the introgressed sequences are to be found in the genome of a plant or seed of the invention in the vicinity of both SNPs BO-0108746 and BN-0067786, preferably at less than 20 cM from both SNPs, or preferably less than 15 cM from both; for example the introgressed sequences are located at less than 5 cM from the locus corresponding to SNP BO-0108746 and at 15 cM or less from SNP BN-0067786.
  • a seed or plant of the invention is characterized by the presence of allele C of SNP BO-0108746 on chromosome 4, optionally in combination with absence of allele A of said SNP.
  • presence of allele C of SNP BO-0108746 confirms the presence of introgressed sequences at the locus of SNP BO- 0108746 and thus of the resistance; moreover the absence of allele A indicates that the introgressed sequences are homozygously present, i.e. present on all the homologues of chromosome 4.
  • a seed or plant of the invention preferably a broccoli seed or plant, is characterized by the presence of both alleles C and A of SNP BO-0108746 on chromosome 4, confirming the heterozygous presence of the introgressed sequences.
  • the introgressed sequences or interval present in the genome of a seed or plant of the invention are at least 5 kilobases long, and preferably at least 8, 10 or 15 kb long.
  • the introgressed sequences or intervals are however not too long in order to avoid introgression of non-commercial features associated with Romanesco introgression partner. It is thus preferred according to the invention that the introgressed sequences mentioned above are less than 25 cM in length, preferably less than 20 cM or less than 15 cM. According to more preferred embodiments, the introgressed sequences are less than 10 cM or even less than 5 cM in length and most preferably less than 5 cM in order to avoid or limit linkage drag. According to a preferred embodiment, said introgressed sequences are minimized to contain as few as possible sequences unrelated to the desired phenotype.
  • the resistance according to the invention is a resistance to white rust caused by A.
  • Candida race 9 Australian variant infection irrespective of the strain of Australian variant, contrary to the plant Booster, referred to in Petkowski et al and described in WO2010/135782 or the plant Tyson, referred to in Minchinton et al.
  • white rust infection is generally due to a plurality of different strains of A.
  • Candida race 9 Australian variant stressing the importance of a resistance irrespective of the strain of Australian variant.
  • the seed or plant according to this aspect of the invention is preferably highly resistant to A.
  • Candida race 9 Australian variant inter alia it remains free of symptoms till the end of the season when grown under natural infection conditions.
  • a seed or plant of the invention which is resistant to A.
  • Candida race 9 Australian variant has less than 25% of the leave surface with sporulation, and preferably less than 10% according to the pathology test described in example 1 , and even preferably no sporulation on the leaf surface. Plants or seeds of the invention, resistant to A. Candida race 9 Australian variant, are also preferably resistant or tolerant to another pest, especially to pest of major agricultural importance.
  • Plants or seeds of the invention preferably also comprise other white rust resistance genes, preferably the monogenic dominant gene on chromosome 1 as disclosed in WO2010/135782, more preferably said plants or seeds comprise in their genome SEQ ID NO:1 and/or SEQ ID NO:2 as defined in WO2010/135782.
  • the invention is directed to B. oleracea plants, preferably broccoli plants, resistant to A. Candida race 9 Australian variant infection, as well as to seeds giving rise to those plants.
  • a B. oleracea plant according to the invention may be a commercial plant or line or variety, preferably cultivated for its head. Such a commercial plant or line gives rise to head which are marketable, when grown in suitable conditions.
  • the plant according to invention may be an inbred or a dihaploid plant or a hybrid, and preferably a broccoli. It is preferably a cultivated B. oleracea.
  • the plant according to the invention may also be cytoplasmic male sterile, for example having the Ogura mitochondrial sterility.
  • Broccoli plants (6. oleracea var. Italica).
  • the invention also concerns other B. oleracea plants, which are known as host for A. Candida race 9 Australian variant, namely cauliflower (B. oleracea convar. botrytis var. botrytis), Brussels sprouts ⁇ B. oleracea convar. oleracea var. gemnifera), white cabbage, oxheart cabbage ⁇ B. oleracea convar. capitata var. alba) and savoy cabbage (B. oleracea convar. capitata var. sabauda).
  • the introgressed sequences, conferring the resistance can be transferred from a resistant broccoli, inter alia BROCCO-C4, to another B. oleracea plants, by a breeding program using the markers exemplified in the examples.
  • a plant or seed of the invention is advantageously not a Romanesco plant or seed.
  • a plant or seed according to the invention may be a progeny or offspring of a plant grown from the deposited seeds of B. oleracea var. Italica -BROCCO-C4, NCIMB 42433. Plants grown from the deposited seeds are indeed resistant to A. Candida race 9 Australian variant, they thus bear in their genome the introgressed sequences conferring resistance. They can be used to transfer these sequences in another background by crossing and selfing and / or backcrossing, and selecting the plants of interest.
  • the invention is also directed to the deposited seeds B. oleracea var. Italica -BROCCO-C4 (NCIMB 42433) and to plants grown from one of these seeds. These seeds contain heterozygously the introgressed sequence conferring the phenotype of interest.
  • the presence of the introgressed sequences according to the invention can be revealed by the sequencing of the SNP identified by the inventors, and more specifically by allele C of SNP BO-0108746.
  • the heterozygous status of the genome of a plant, seed or plant part with respect to the introgressed sequences of interest can be brought to light by the simultaneous presence of alleles C and A of SNP BO-0108746.
  • the homozygous status of the genome of a plant, seed or plant part with respect to the introgressed sequences of interest can be brought to light by the presence of only allele C of SNP BO-0108746.
  • the invention also concerns any plant likely to be obtained from seed or plants of the invention as described above, preferably a broccoli seed or plant, and also plant parts of such a plant, and most preferably explant, scion, cutting, seed, root, rootstock, pollen, ovule, embryo, siliqua, protoplast, leaf, anther, stem, petiole, head and any other plants part, wherein said plant, explant, scion, cutting, seed, root, rootstock, pollen, ovule, embryo, siliqua, protoplast, leaf, anther, stem, petiole, head and/or plant part is obtainable from a seed or plant according to the first aspect of the invention, i.e.
  • the introgressed sequences are thus preferably chosen from those present in the genome of a plant corresponding to the deposited material B. oleracea var. Italica -BROCCO-C4 (NCIMB accession number 42433) and conferring the resistance. They are advantageously characterized by the presence of allele T of SNP BN-0067786 (SEQ ID No: 14) and/or allele C for SNP BO-0108746 (SEQ ID No:6), preferably allele C for SNP BO-0108746.
  • the invention is also directed to cells of B. oleracea cells, such that these cells comprise, in their genome, introgressed sequences conferring the phenotype of interest.
  • these cells are cells of B. oleracea var. Italica.
  • the introgressed sequences are those already defined in the frame of the present invention, they are characterized by the same features and preferred embodiments already disclosed with respect to the plants and seeds according to the preceding embodiments of the invention.
  • the presence of these introgressed sequences can be revealed by the techniques disclosed above and well known to the skilled reader. It can inter alia be determined whether the introgressed sequences are present homozygously or heterozygously in the genome of such a cell of the invention.
  • a plant, explant, scion, cutting, seed, root, rootstock, pollen, ovule, embryo, siliqua, protoplast, leaf, anther, stem, petiole, head and/or plant part as defined above preferably comprises at least one cell of the invention, preferably the majority of the cells thereof are cells according to the invention, more preferably all cells of the plant part as defined are cells of the invention.
  • Cells according to the invention can be any type of B. oleracea cell, preferably B. oleracea var. Italica, inter alia a cell capable of regenerating a whole B. oleracea plant, bearing the introgressed sequences.
  • the cell according to the invention can be a cell specifically not capable of regenerating a whole B. oleracea plant.
  • the cell according to the invention may be an isolated cell.
  • the present invention is also directed to a tissue culture of regenerable cells of the plant as defined above according to the present invention; preferably, the regenerable cells are derived from embryos, protoplasts, meristematic cells, callus, pollen, leaves, anthers, stems, petioles, roots, root tips, siliqua, seeds, flowers, cotyledons, and/or hypocotyls, and contain in their genome introgressed sequences on chromosome 4 conferring resistance to white rust caused by A.
  • Candida race 9 Australian variant are derived from embryos, protoplasts, meristematic cells, callus, pollen, leaves, anthers, stems, petioles, roots, root tips, siliqua, seeds, flowers, cotyledons, and/or hypocotyls
  • the tissue culture will preferably be capable of regenerating plants having the physiological and morphological characteristics of the foregoing broccoli plant, and of regenerating plants having substantially the same genotype as the foregoing broccoli plant.
  • the present invention also provides broccoli plants regenerated from the tissue cultures of the invention.
  • the invention also provides a protoplast of the plant defined above, or from the tissue culture defined above, said protoplast containing said introgressed sequences conferring resistance to A.
  • Candida race 9 Australian variant conferring resistance to A.
  • the present invention is also directed to the use of a B. oleracea plant as detailed according to the first aspect of the invention, i.e. resistant, especially a broccoli plant, as a breeding partner in a breeding program for obtaining B. oleracea plants resistant to white rust caused by A. Candida race 9 Australian variant.
  • a plant according to the first aspect harbors in its genome introgressed sequences conferring the phenotype of interest, i.e. resistance. By crossing this plant with susceptible or less resistant plants, it is thus possible to transfer these sequences, conferring the desired phenotype, to the progeny as the phenotype is a monogenic trait.
  • a plant to be used as a breeding partner is a plant homozygous with respect to the introgressed sequence conferring the resistance, such that all hybrid plants resulting from the crossing of this plant with another B. oleracea will also bear the introgressed sequence conferring the resistance phenotype.
  • a heterozygous plant according to the first aspect of the invention can also be used; in this case a selection step will advantageously be added, for example based on the presence of the SNP markers of the invention, in view of the segregation of the phenotype.
  • a plant according to the invention can thus be used as a breeding partner for introgressing sequences conferring the desired phenotype into a B. oleracea plant or germplasm.
  • the introgressed sequences of interest will advantageously be introduced into plant or varieties that contain other desirable genetic traits such as resistance to other diseases.
  • the introgressed sequences of interest will advantageously be introduced into plant or varieties that contain other white rust resistance genes such as the monogenic dominant gene on chromosome 1 as disclosed in WO2010135782; more preferably they comprise in their genome SEQ ID NO:1 and/or SEQ ID NO:2 as defined in WO2010/135782.
  • the invention is also directed to the same use with plants or seed of B. oleracea var. Italica - BROCCO-C4, deposited at the NCIMB under the accession number NCIMB 42433, or progeny thereof bearing the introgressed sequences of the invention conferring the resistance to white blister rust, especially progeny thereof having allele C of SNP BO-0108746.
  • Said plants are also suitable as introgression partners in a breeding program aiming at conferring the desired phenotype to B. oleracea plant or germplasm, although it is heterozygous for the introgression sequences of interest, i.e. for obtaining B. oleracea plants resistant to white blister rust caused by A. Candida race 9 Australian variant.
  • the selection of the progeny displaying the desired phenotype, or bearing sequences linked to the desired phenotype can advantageously be carried out on the basis of the alleles of the SNP markers.
  • the progeny is preferably selected on the presence of allele C of SNP BO-0108746 on chromosome 4.
  • the selection can alternatively be made on the basis of the simultaneous presence of allele T of SNP BN-0067786 and allele C of SNP BO-0108746.
  • SNP BO-0108436, SNP BO-0108747, SNP BO-0108748, SNP BO-0108749, SNP BO-0108750, SNP BO-0108751 , SNP BO- 0108752, SNP BO-0108753 and SNP BN-0067793 can also be used as detailed above.
  • the selection of the progeny having the desired phenotype can also be made on conditions of A.
  • Candida race 9 Australian variant infection as disclosed inter alia in example 1 (pathology test).
  • a plant according to the invention or grown from a seed as deposited under accession number NCIMB 42433, is thus particularly valuable in a marker assisted selection for obtaining commercial broccoli lines and varieties resistant to white rust caused by A.
  • Candida race 9 Australian variant, as well as progeny thereof bearing the introgressed sequences of the invention conferring the resistance to white blister rust, especially progeny thereof having allele C of SNP BO-0108746.
  • the invention is also directed to the use of said plants in a program aiming at identifying, sequencing and / or cloning the genes conferring the desired phenotype, i.e. resistance to white blister rust caused by the oomycete Albugo Candida race 9 Australian variant.
  • the invention also concerns methods or processes for the production of B. oleracea plants, preferably Brassica oleracea var. italica broccoli plants, having the desired phenotype, especially commercial plants.
  • the present invention is indeed also directed to transferring the introgressed sequences conferring the resistance, from the broccoli plant to other B. oleracea varieties and species, especially to other broccoli species or to cauliflower (B. oleracea convar. botrytis var. botrytis), Brussels sprouts ⁇ B. oleracea convar. oleracea var. gemnifera), white cabbage, oxheart cabbage (S. oleracea convar. capitata var. alba) and savoy cabbage (S. oleracea convar. capitata var. sabauda); the invention is useful for producing new types and varieties of A. Candida race 9 Australian variant resistant broccoli.
  • a method or process for the production of a plant having these features, i. e. resistant to A. Candida race 9 Australian variant, may comprise the following steps:
  • step c) Optionally self-pollinating one or several times the plant obtained at step b) and selecting a resistant plant in the progeny thus obtained;
  • SNPs markers are preferably used in steps b) and c), for selecting plants bearing sequences conferring resistance to white rust caused by A.
  • Candida race 9 Australian variant The SNP markers are preferably one or more of the 1 1 SNP markers of the invention, and preferably SNP BO-0108746. According to a preferred embodiment, the selection is at least partly carried out by detecting the alleles of SNP BN-0067786 and SNP BO-0108746.
  • the selection can be made on the detection of the allele of at least 2 SNPs chosen amongst SNP BO-0108436, SNP BO-0108747, SNP BO-0108748, SNP BO-0108749, SNP BO-0108750, SNP BO-0108751 , SNP BO-0108752, SNP BO-0108753 and SNP BN- 0067793, preferably at least 3 SNPs, for example at least 4, 5 or 6, one of them being SNP BO-0108746.
  • the selection can also be made on the detection of the alleles of all these 1 1 SNPs.
  • the plant, which is selected at the selection step disclosed above, is preferably selected on the presence of allele C of SNP BO-0108746.
  • the susceptible or less resistant B. oleracea plant of step a) is an elite line, used in order to introduce commercially desired traits or desired horticultural traits. It is preferably a broccoli plant.
  • a method or process for the production of a plant having these features may also comprise the following additional steps:
  • step c) Backcrossing the resistant plant selected in step c) with a susceptible B. oleracea plant; e) Selecting a plant in the progeny bearing the sequence conferring resistance to A.
  • the plant selected at step b), c) or g) of the preceding method may be a commercial plant.
  • Steps d), e) and / f) may be repeated twice or three times or more, not necessarily with the same susceptible B. oleracea plant.
  • Said susceptible B. oleracea plant is preferably a breeding line. This plant is preferably an elite line, used in order to introduce commercially desired traits or desired horticultural traits. It is preferably a broccoli plant.
  • the self-pollination/crossing and backcrossing steps may be carried out in any order and can be intercalated.
  • the methods of the invention are advantageously carried out by using SNP markers for one or more of the selection steps for selecting plants bearing the introgressed sequences linked to the resistance, or for selecting plants having the phenotype of interest.
  • a method of the invention for the production of resistant B. oleracea broccoli plants thus advantageously comprises the steps of:
  • step b) Optionally self-pollinating one or several times the resistant plant obtained at step b) and selecting a plant resistant to white blister rust in the progeny thus obtained;
  • step b) or c) Optionally backcrossing the resistant plant selected in step b) or c) with a susceptible B. oleracea broccoli plant and selecting a plant resistant to white blister rust,
  • SNPs markers are used in steps b), c) and/or d) for selecting plants resistant to white rust, as disclosed herein.
  • the SNP markers are preferably one or more of the 1 1 SNP markers of the invention, and preferably SNP BO-0108746. According to a preferred embodiment, the selection is at least partly made on the basis of the allele of SNP BO-0108746 on chromosome 4. The selection is for example carried out by detecting the alleles carrying/characterized by SNP BN-0067786 and SNP BO-0108746.
  • the plant selected at the selection step disclosed above is preferably selected on the presence of allele C of SNP BO-0108746.
  • the presence of allele C of SNP BO- 0108746 is detected in combination with the absence of allele A of SNP BO-0108746.
  • the other SNPs of the invention can also advantageously be used, namely SNP BO-0108436, SNP BO-0108747, SNP BO-0108748, SNP BO-0108749, SNP BO-0108750, SNP BO-0108751 , SNP BO-0108752, SNP BO-0108753, SNP BN-0067786 and SNP BN- 0067793, in place or advantageously in addition to SNP BO-0108746.
  • the selection of the progeny having the desired phenotype can also be made on conditions of A.
  • Candida race 9 Australian variant infection as disclosed inter alia in example 1.
  • the method used for allele detection can be based on any technique allowing the distinction between two different alleles of a SNP, on a specific chromosome locus.
  • the plant according to the first aspect of the invention used in step a of the methods is a plant obtained by germinating a deposited seed BROCCO-C4 NCIMB accession number 42433 or progeny thereof bearing the sequences conferring the resistance to white blister rust, especially progeny thereof having allele C of SNP BO-0108746.
  • the invention also provides a method for the production of B. oleracea plants, preferably broccoli, resistant to white rust caused by the oomycete Albugo Candida race 9 Australian variant, comprising the steps of:
  • step b) Optionally self-pollinating one or several times the resistant plant obtained at step b) and selecting a plant resistant to white rust in the progeny thus obtained;
  • step b) or c) Optionally backcrossing the resistant plant selected in step b) or c) with a susceptible B. oleracea plant, preferably broccoli, and selecting a plant resistant to white rust,
  • SNPs markers are used in steps b), c) and/or d) for selecting plants resistant to white rust, as disclosed herein.
  • the invention also provides a method for obtaining commercial broccoli plants, resistant to white blister rust caused by A. Candida race 9 Australian variant, comprising the steps of: a) Backcrossing a plant obtained by germinating a deposited seed BROCCO-C4 NCIMB accession number 42433 or a plant according the first aspect of the invention, with a B. oleracea broccoli plant susceptible to said white blister rust, b) Selecting a plant resistant to white blister rust caused by the oomycete Albugo Candida race 9 Australian variant.
  • the selection of a resistant plant is carried out by detection of at least one of the following alleles: allele G of BO- 0108436, allele C of BO-0108746, allele G of BO-0108747, allele A of BO-0108748, allele C of BO-0108749, allele A of BO-0108750, allele G of BO-0108751 , allele C of BO-0108752, allele C of BO-0108753, allele T of BN-0067786 and allele G of BN-0067793, preferably by detecting allele C of BO-0108746.
  • the plant according to the first aspect of the invention used in step a1 ) or a) of these methods is a plant obtained by germinating a deposited seed BROCCO-C4 NCIMB accession number 42433, or progeny thereof bearing the sequences conferring the resistance to white blister rust, especially progeny thereof having allele C of SNP BO-0108746.
  • the present invention also concerns a plant obtained or obtainable by one of the methods described above.
  • a plant is indeed a B. oleracea plant having the desired phenotype according to the first aspect of the invention, i.e. resistant to white rust caused by A.
  • Candida race 9 Australian variant Particularly preferred plants are broccoli plants ⁇ B. oleracea var. Italica ).
  • the invention is moreover directed to a method for detecting and/or selecting B. oleracea plants having introgressed sequences conferring resistance to white rust caused by A. Candida race 9 Australian variant, on the basis of the allele detection.
  • Such a method is based on the detection of the allele(s) of at least one of the 1 1 SNPs of the invention, especially based on the detection of the allele which is associated with the resistance, for at least one of the SNPs of the invention.
  • detection of the allele associated with the resistance is, on its own, indicative of the resistance phenotype, irrespective of whether the allele associated with the susceptibility is also detected, whereas the absence of detection of the allele associated with the resistance is indicative of susceptibility.
  • the detection of the "susceptible" allele is not informative on its own.
  • the method thus advantageously comprises the detection of whether at least one of the following alleles is present in the plant under test: allele G of BO-0108436, allele C of BO-0108746, allele G of BO-0108747, allele A of BO-0108748, allele C of BO-0108749, allele A of BO- 0108750, allele G of BO-0108751 , allele C of BO-0108752, allele C of BO-0108753, allele T of BN-0067786, and allele G of BN-0067793, the detection of at least one of these alleles allowing to conclude that the plant under test is resistant to white rust caused by A.
  • Candida race 9 Australian variant the detection of at least one of these alleles allowing to conclude that the plant under test is resistant to white rust caused by A.
  • the method comprises the detection of the alleles of at least one SNP chosen amongst SNP BN-0067786 and SNP BO-0108746 on chromosome 4, preferably SNP BO-0108746, whereas detection of allele C of BO-0108746 is indicative of resistance, and/or allele T of SNP BN-0067786.
  • the method can be carried out on B. oleracea plants resistant to white rust; the method thus can be used to confirm that such plants comprise in their genome the introgressed sequences according to this invention, and thus have been obtained according to the present invention.
  • plants bearing the introgressed sequences are selected if allele C of SNP BO- 0108746 is detected in a genetic material sample of the plant to be selected.
  • the allele of interest can be present homozygously or heterozygously in the selected plant.
  • the selection is thus made on the simultaneous presence of allele T of SNP BN-0067786 and allele C of SNP BO-0108746.
  • the selection is preferably made on the simultaneous detection of allele T of SNP BN-0067786 and allele C of SNP BO-0108746 in combination with no detection of any other allele for these SNPs, and especially no detection of allele C of SNP BN-0067786 or allele A of SNP BO-0108746.
  • the detection of both alleles of a SNP is indicative of a heterozygous plant with respect to the resistance sequences.
  • the method of the invention allows selection of plants bearing the resistance sequences homozygously, by detecting plants only displaying the allele associated with the resistance for a given SNP of the invention, and also of plants bearing these sequences heterozygously, by detecting plants displaying both alleles associated with the resistance and with the susceptibility.
  • the method also allows to make a distinction between these two types of resistant plants, those bearing the sequences heterozygously being characterized by the simultaneous presence of both the alleles associated with the resistance and with the susceptibility, for at least one of the SNPs of the invention.
  • the detection or selection may also comprise the identification of the alleles of at least one of SNP BO-0108436, SNP BO-0108747, SNP BO-0108748, SNP BO-0108749, SNP BO- 0108750, SNP BO-0108751 , SNP BO-0108752, SNP BO-0108753, SNP BN-0067786 and SNP BN-0067793, or at least 2, 3, or all 4 SNPs, or the identification of the alleles of at least one of SNP BO-0108436, SNP BO-0108747, SNP BO-0108748, SNP BO-0108749, SNP BO- 0108750, SNP BO-0108751 , preferably in addition to SNP BO-0108746.
  • the method of the invention is thus suitable for detecting and/or selecting B. oleracea, especially broccoli plants, having introgressed sequences conferring resistance to white blister rust caused by the oomycete A.
  • Candida race 9 Australian variant e.g. as found in the genome of a plant of BROCCO-C4 (NCIMB accession number 42433), comprising detection of at least one of the following alleles: allele G of BO-0108436, allele C of BO-0108746, allele G of BO- 0108747, allele A of BO-0108748, allele C of BO-0108749, allele A of BO-0108750, allele G of BO-0108751 , allele C of BO-0108752, allele C of BO-0108753, allele T of BN-0067786 and allele G of BN-0067793, in a genetic material sample of the plant to be selected and/or detected. Detection of allele C of BO-0108746 is highly preferred.
  • the SNPs markers of the invention can also be used to map the resistance locus, such that the smallest possible introgression conferring the phenotype can be identified and/or selected.
  • these sequences of the invention can also be introduced into B. oleracea background by genetic engineering in order to obtain a commercial B. oleracea plant resistant to white rust caused by A. Candida race 9 Australian variant.
  • the identification and cloning of the introgressed sequences conferring the desired phenotype, inter alia from the deposit NCIMB 42433, can be carried out by the skilled person, on the basis of the sequence information given in the present application and deposited material.
  • the invention also concerns the genetic manipulations aiming at cloning the introgressed sequences conferring the phenotype, and/or integrating them into a B. oleracea plant, as well as the plants thus obtained, preferably broccoli plants.
  • the present invention is also directed to hybrid plants of B. oleracea, obtainable by crossing a resistant plant according to the first aspect of the invention, or a resistant plant obtainable by the methods disclosed above, with a plant of B. oleracea, for example a plant susceptible to white rust caused by A.
  • Candida race 9 Australian variant or a plant with a different level of resistance to white rust caused by A.
  • Candida race 9 Australian variant for example a plant susceptible to white rust caused by A.
  • Candida race 9 Australian variant or a plant with a different level of resistance to white rust caused by A.
  • Candida race 9 Australian variant for example a plant susceptible to white rust caused by A.
  • Candida race 9 Australian variant or a plant with a different level of resistance to white rust
  • the resistant plant is preferably homozygous for the sequences conferring the resistance. If the resistant plant is heterozygous for the sequences conferring the resistance, only half of the progeny will be resistant; a selection step of the plants bearing the sequence conferring the resistance is thus preferably to be added.
  • a particularly preferred hybrid B. oleracea plant is a plant which displays male sterility, or any other trait or phenotype of agronomical interest.
  • the invention also provides a method of protecting a field of B. oleracea plants, especially broccoli plants, against infection by A. Candida race 9 Australian variant, said methd comprising planting seeds according to the invention, or growing plants according to the invention, exhibiting the resistance phenotype.
  • Example 1 Identification of a resistant plant.
  • the present inventors crossed the original romanesco B. oleracea plant with a broccoli inbred line to obtain a first generation hybrid, that was further backcrossed twice to the broccoli inbred line.
  • the plants obtained thereof have been screened through the pathology test described hereunder, with an European A. Candida race 9 strain and a symptomless plant was kept for the next steps backcross steps.
  • Next generation plants were again tested in pathology test, this time with an Australian A. Candida race 9 variant.
  • Candida race 9 variant This plant has been further crossed to a susceptible broccoli plant and the resulting hybrid progeny plants BROCCO-C4, harbouring the resistance in a heterozygous way are resistant to the Australian A.
  • Candida race 9 variant Seeds thereof were deposited at the NCIMB on 9 th July 2015 under accession number NCIMB 42433.
  • Candida strain has been collected in Templestowe, Australia and is kept in the freezer at -80°C. Every 2-3 months, it is periodically multiplied on susceptible varieties : the frozen cotyledons containing the pustules are washed with demineralized water to suspend the spores and the suspension is then vaporized on susceptible plants (cotyledon stage, 1 week after sowing) placed on growing chambers (16°C during the night, 15°C during the day, with 12 hours for each condition).
  • the cotyledon with the fresh, new pustules are collected into an Erienmeyer flask together with 500 ml of distilled water and the solution adjusted at 2.10 5 spores/ml in 2.5I of distilled water, thereby creating the inoculum.
  • the plant material is composed of 192 plants per genotype to be tested (i.e. 192 plants per F2 population), together with one susceptible and one resistant controls : seeds are sown and placed in greenhouses for about 3 weeks, up to the 1-2 leaves stage. Then, the leaves are gently rubbed to remove the leaf wax and the inoculum is sprayed on them. The reading is carried out 15 days after the spray, the plants being cultivated in growing chambers (16°C during the night, 15°C during the day, with 12 hours for each condition).
  • Candida Australian variant acts as a dominant one.
  • the population n°3 shows a slight deviation at 5%, but not at 1 % (significance assessed by a Chi-Square test).
  • Each F2 plant was sampled individually and DNA was isolated, using magnetic beads (NucleoMag® 96 Plant), according to the protocol of the manufacturer of the beads, Macherey-Nagel.
  • the Genotyping was done using KASPTM technology.
  • Phase 1 of the markers validation allowed refining the right boundary position of the resistance (i.e, downstream boundary of the interval according to coordinates along the chromosome), located on BN-0067793 at position C4: 8 081 104.
  • Phase 2 of the markers validation allowed refining the left boundary position of the resistance (i.e, upstream boundary of the interval according to coordinates along the chromosome), located on marker BN-0000253 at position C4:6 069 705.
  • phase 1 has been carried out on different populations
  • phase 2 has been carried out on a single population, namely F2 population n°1 .
  • it In order to determine the smallest introgression fragment, imparting the resistance, it must first be determined the highest -log p value, in a given population, and then to set the boundary of the introgression fragment to the nearest SNP showing a decrease in this value, preferably confirmed by results on another population.
  • the interval containing the resistance is thus spanning a 2 01 1 399 bp region between positions 6 069 705 and 8 081 104 on chromosome C4.
  • Genotyping was done using KASPTM technology.
  • Table 7 Thanks to the study of populations, and the overlap of confidence intervals, the resistance interval boundaries could be set up to: left boundary: C4: 7 427 499, corresponding to marker BO-0108436 and right boundary: C4: 8 081 104, corresponding to marker BN-0067793.
  • the interval containing the resistance is thus spanning a 653 605 bp region between positions 7 427 499 and 8 081 104 on chromosome C4.
  • Example 3 Identification of further markers linked to the resistance to Albugo Candida on chromosome C4.
  • the interval containing the resistance is spanning a 653 605 bp region between positions 7 427 499 and 8 081 104 on chromosome C4. Looking at the reference genome sequence mentioned herebefore, 73 genes were identified in this region. Polymorphisms within these genes were studied more closely, after amplification by PCR and sequencing the amplified region. The most promising amplified region was generated by using the following primers: Forward Primer CGCTCAAACGGTTAACATGA (SEQ ID No:41 )
  • PCR amplification was performed on a Applied Biosystems 2720 Thermal Cycler using the following program:
  • Step 1 3 min at 94°C; Step 2: 30 sec at 94°C; Step 3: 30 sec at 60°C; Step 4 :2 min at 72°C; Step 5 : 7 min at 72°C
  • Amplification was performed on parental lines of the 5 populations (including the resistance source) and one recombinant plant of population n°1 . This plant was scored 4 in the pathology test, has a susceptible parent profile upstream the resistance region and a heterozygous profile downstream the resistance region. As it is phenotypically susceptible, the plant is expected to carry the susceptible allele at the resistance gene location.
  • Genotyping was done using KASPTM technology. Some of the markers were genotyped in the F2 segregating populations n°1 and 3.
  • the interval containing the resistance is thus with a very high probability in a region between positions 6 069 705 and 7 463 248 on chromosome C4.
  • Example 4 Assessment of molecular makers in the breeding germplasm.
  • Genotyping was done using KASPTM technology. 488 different genotypes were sampled and DNA was isolated, using magnetic beads (NucleoMag® 96 Plant), according to the protocol of the manufacturer of the beads, Macherey-Nagel.
  • the 488 genotypes are constituted by:
  • Marker BO-0108746 was confirmed as the most predictive SNP for identifying and selecting broccoli plants resistant to A. Candida race 9 Australian variant.
  • a resistant plant obtained from an initial cross between a Romanesco B. oleracea plant and an inbred broccoli line was used in a dihaploid program to produce a resistant inbred line homozygous for the resistance to the Australian A.
  • Candida race 9 variant This plant has been further crossed to a susceptible broccoli plant and the resulting hybrid progeny plants BROCCO-C4, harbouring the resistance in a heterozygous way, are resistant to the Australian A.
  • Candida race 9 variant Seeds of BROCO-C4 plants, giving rise to hybrid plant bearing the introgressed sequences linked to the resistance were filed at the NCIMB on 9 th July 2015, under accession number NCIMB 42433.
  • Table 1 1 Marker sequences of all the SNP used in the examples, all on chromosome 4.
  • the allele associated to the susceptibility (S) phenotype is indicated first within brackets, followed by the allele associated with the resistance (R) phenotype.
  • S susceptibility
  • R resistance
  • GGGAGGCTTGTTAGCTAATAAAACCATGGTTGAAGAGTGGAA AAGAATATATGACGATATTCAAACTCA SEQ ID No :6
  • AAAG CAGTCGCG GG AATATG CACTGTAATCCAAACAAACACA AGTCTATGCTGCAAAACCCTTAAACA (SEQ ID No :27)
  • Example 6 Comparison of the resistance level of different plants.
  • Tyson Tyson, the variety referred to in Minchinton et al;
  • the resistance assay was repeated 4 times, with 6 plants for each genotype A-F and in each repetition. The results are reported in table 12 below.
  • Example 7 Field trials.
  • the 9 hybrids according to the invention are the sole resistant plants, with 100% of the tested plants being uninfected.
  • the tests have been reproduced in different localizations in Australia, for one given hybrid according to the invention: white rust has never been observed for this hybrid, confirming that the resistance to white rust caused by the oomycete Albugo Candida race 9 Australian variant is indeed a general resistance, which is not strain-dependent.
  • Table 12
  • Hybrid H1 containing the resistance of

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Abstract

La présente invention concerne des plantes de brocolis et d'autres plantes de l'espèce B. oleracea, résistantes à la rouille blanche provoquée par l'oomycète Albugo Candida race 9, variante Australienne, comportant dans son génome des séquences ayant subi une introgression conférant la résistance, lesdites séquences ayant subi une introgression étant situées sur le chromosome 4, dans la région chromosomique délimitée par SNP BO-0108436 (SEQ ID No:5) et SNP BN-0067793 (SEQ ID No:15), de préférence dans la région délimitée par SNP BO-0108436 (SEQ ID No:5) et SNP BO-0108751 (SEQ ID No:11), caractérisé entre autres par l'allèle C du SNP BO-0108746 (SEQ ID No:6). L'invention concerne également des procédés qui produisent ou identifient les plantes de l'espèce B. oleracea, en particulier des plantes de brocoli présentant une résistance à l'infection par la variante australienne de A. candida race 9, ainsi que des procédés de sélection. La présente invention concerne également des marqueurs génétiques moléculaires, notamment des SNP, liés au locus de résistance.
PCT/EP2016/069241 2015-08-12 2016-08-12 Résistance à la variante australienne de a. candida race 9 dans le broccoli WO2017025627A1 (fr)

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JP2018527016A JP6954903B2 (ja) 2015-08-12 2016-08-12 ブロッコリーにおけるａ．カンジダ レース９のオーストラリア変異体に対する抵抗性
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Publication number Priority date Publication date Assignee Title
JP2021533824A (ja) * 2018-08-10 2021-12-09 ヴィルモラン・エ・シ カリフラワーにおけるキサントモナス・カンペストリスｐｖ．カンペストリス（Ｘａｎｔｈｏｍｏｎａｓ ｃａｍｐｅｓｔｒｉｓ ｐｖ．ｃａｍｐｅｓｔｒｉｓ）（Ｘｃｃ）への抵抗性
JP7425062B2 (ja) 2018-08-10 2024-01-30 ヴィルモラン・エ・シ カリフラワーにおけるキサントモナス・カンペストリスｐｖ．カンペストリス（Ｘａｎｔｈｏｍｏｎａｓ ｃａｍｐｅｓｔｒｉｓ ｐｖ．ｃａｍｐｅｓｔｒｉｓ）（Ｘｃｃ）への抵抗性

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