Publications by authors named "Regine Delourme"

35 Publications

Large-scale transcriptomics to dissect 2 years of the life of a fungal phytopathogen interacting with its host plant.

BMC Biol 2021 03 23;19(1):55. Epub 2021 Mar 23.

Université Paris-Saclay, INRAE, AgroParisTech, UMR BIOGER, 78850, Thiverval-Grignon, France.

Background: The fungus Leptosphaeria maculans has an exceptionally long and complex relationship with its host plant, Brassica napus, during which it switches between different lifestyles, including asymptomatic, biotrophic, necrotrophic, and saprotrophic stages. The fungus is also exemplary of "two-speed" genome organisms in the genome of which gene-rich and repeat-rich regions alternate. Except for a few stages of plant infection under controlled conditions, nothing is known about the genes mobilized by the fungus throughout its life cycle, which may last several years in the field.

Results: We performed RNA-seq on samples corresponding to all stages of the interaction of L. maculans with its host plant, either alive or dead (stem residues after harvest) in controlled conditions or in field experiments under natural inoculum pressure, over periods of time ranging from a few days to months or years. A total of 102 biological samples corresponding to 37 sets of conditions were analyzed. We show here that about 9% of the genes of this fungus are highly expressed during its interactions with its host plant. These genes are distributed into eight well-defined expression clusters, corresponding to specific infection lifestyles or to tissue-specific genes. All expression clusters are enriched in effector genes, and one cluster is specific to the saprophytic lifestyle on plant residues. One cluster, including genes known to be involved in the first phase of asymptomatic fungal growth in leaves, is re-used at each asymptomatic growth stage, regardless of the type of organ infected. The expression of the genes of this cluster is repeatedly turned on and off during infection. Whatever their expression profile, the genes of these clusters are enriched in heterochromatin regions associated with H3K9me3 or H3K27me3 repressive marks. These findings provide support for the hypothesis that part of the fungal genes involved in niche adaptation is located in heterochromatic regions of the genome, conferring an extreme plasticity of expression.

Conclusion: This work opens up new avenues for plant disease control, by identifying stage-specific effectors that could be used as targets for the identification of novel durable disease resistance genes, or for the in-depth analysis of chromatin remodeling during plant infection, which could be manipulated to interfere with the global expression of effector genes at crucial stages of plant infection.
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http://dx.doi.org/10.1186/s12915-021-00989-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7986464PMC
March 2021

A gene-for-gene interaction involving a 'late' effector contributes to quantitative resistance to the stem canker disease in Brassica napus.

New Phytol 2021 08 2;231(4):1510-1524. Epub 2021 Apr 2.

INRAE, AgroParisTech, UMR BIOGER, Université Paris-Saclay, Avenue Lucien Brétignières, BP 01, Thiverval-Grignon, F-78850, France.

The control of stem canker disease of Brassica napus (rapeseed), caused by the fungus Leptosphaeria maculans is based largely on plant genetic resistance: single-gene specific resistance (Rlm genes) or quantitative, polygenic, adult-stage resistance. Our working hypothesis was that quantitative resistance partly obeys the gene-for-gene model, with resistance genes 'recognizing' fungal effectors expressed during late systemic colonization. Five LmSTEE (stem-expressed effector) genes were selected and placed under the control of the AvrLm4-7 promoter, an effector gene highly expressed at the cotyledon stage of infection, for miniaturized cotyledon inoculation test screening of a gene pool of 204 rapeseed genotypes. We identified a rapeseed genotype, 'Yudal', expressing hypersensitive response to LmSTEE98. The LmSTEE98-RlmSTEE98 interaction was further validated by inactivation of the LmSTEE98 gene with a CRISPR-Cas9 approach. Isolates with mutated versions of LmSTEE98 induced more severe stem symptoms than the wild-type isolate in 'Yudal'. This single-gene resistance was mapped in a 0.6 cM interval of the 'Darmor_bzh' × 'Yudal' genetic map. One typical gene-for-gene interaction contributes partly to quantitative resistance when L. maculans colonizes the stems of rapeseed. With numerous other effectors specific to stem colonization, our study provides a new route for resistance gene discovery, elucidation of quantitative resistance mechanisms and selection for durable resistance.
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http://dx.doi.org/10.1111/nph.17292DOI Listing
August 2021

Long-read assembly of the Brassica napus reference genome Darmor-bzh.

Gigascience 2020 12;9(12)

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, 2 rue Gaston Crémieux, 91057 Evry, France.

Background: The combination of long reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allows access to the gene catalogue of a given species but also reveals the architecture and organization of chromosomes, including complex regions such as telomeres and centromeres. The Brassica genus is not exempt, and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, was produced using short reads and its contiguity was extremely low compared with current assemblies of the Brassica genus.

Findings: Herein, we report the new long-read assembly of Darmor-bzh genome (Brassica napus) generated by combining long-read sequencing data and optical and genetic maps. Using the PromethION device and 6 flowcells, we generated ∼16 million long reads representing 93× coverage and, more importantly, 6× with reads longer than 100 kb. This ultralong-read dataset allows us to generate one of the most contiguous and complete assemblies of a Brassica genome to date (contig N50 > 10 Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes.

Conclusion: Using these cutting-edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable to the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.
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http://dx.doi.org/10.1093/gigascience/giaa137DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7736779PMC
December 2020

Identification and QTL mapping of resistance to Turnip yellows virus (TuYV) in oilseed rape, Brassica napus.

Theor Appl Genet 2020 Feb 5;133(2):383-393. Epub 2019 Nov 5.

School of Life Sciences, University of Warwick, Wellesbourne Campus, Warwick, CV35 9EF, UK.

Key Message: Partially dominant resistance to Turnip yellows virus associated with one major QTL was identified in the natural allotetraploid oilseed rape cultivar Yudal. Turnip yellows virus (TuYV) is transmitted by the peach-potato aphid (Myzus persicae) and causes severe yield losses in commercial oilseed rape crops (Brassica napus). There is currently only one genetic resource for resistance to TuYV available in brassica, which was identified in the re-synthesised B. napus line 'R54'. In our study, 27 mostly homozygous B. napus accessions, either doubled-haploid (DH) or inbred lines, representing a diverse subset of the B. napus genepool, were screened for TuYV resistance/susceptibility. Partial resistance to TuYV was identified in the Korean spring oilseed rape, B. napus variety Yudal, whilst the dwarf French winter oilseed rape line Darmor-bzh was susceptible. QTL mapping using the established Darmor-bzh × Yudal DH mapping population (DYDH) revealed one major QTL explaining 36% and 18% of the phenotypic variation in two independent experiments. A DYDH line was crossed to Yudal, and reciprocal backcross (BC) populations from the F with either the susceptible or resistant parent revealed the dominant inheritance of the TuYV resistance. The QTL on ChrA04 was verified in the segregating BC population. A second minor QTL on ChrC05 was identified in one of the two DYDH experiments, and it was not observed in the BC population. The TuYV resistance QTL in 'R54' is within the QTL interval on Chr A04 of Yudal; however, the markers co-segregating with the 'R54' resistance are not conserved in Yudal, suggesting an independent origin of the TuYV resistances. This is the first report of the QTL mapping of TuYV resistance in natural B. napus.
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http://dx.doi.org/10.1007/s00122-019-03469-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6985063PMC
February 2020

Oilseed rape (Brassica napus) resistance to growth of Leptosphaeria maculans in leaves of young plants contributes to quantitative resistance in stems of adult plants.

PLoS One 2019 12;14(9):e0222540. Epub 2019 Sep 12.

IGEPP, INRA, Agrocampus Ouest, Univ Rennes, BP, France.

Key message: One QTL for resistance against Leptosphaeria maculans growth in leaves of young plants in controlled environments overlapped with one QTL detected in adult plants in field experiments. The fungal pathogen Leptosphaeria maculans initially infects leaves of oilseed rape (Brassica napus) in autumn in Europe and then grows systemically from leaf lesions along the leaf petiole to the stem, where it causes damaging phoma stem canker (blackleg) in summer before harvest. Due to the difficulties of investigating resistance to L. maculans growth in leaves and petioles under field conditions, identification of quantitative resistance typically relies on end of season stem canker assessment on adult plants. To investigate whether quantitative resistance can be detected in young plants, we first selected nine representative DH (doubled haploid) lines from an oilseed rape DY ('Darmor-bzh' × 'Yudal') mapping population segregating for quantitative resistance against L. maculans for controlled environment experiment (CE). We observed a significant correlation between distance grown by L. maculans along the leaf petiole towards the stem (r = 0.91) in CE experiments and the severity of phoma stem canker in field experiments. To further investigate quantitative trait loci (QTL) related to resistance against growth of L. maculans in leaves of young plants in CE experiments, we selected 190 DH lines and compared the QTL detected in CE experiments with QTL related to stem canker severity in stems of adult plants in field experiments. Five QTL for resistance to L. maculans growth along the leaf petiole were detected; collectively they explained 35% of the variance. Two of these were also detected in leaf lesion area assessments and each explained 10-12% of the variance. One QTL on A02 co-localized with a QTL detected in stems of adult plants in field experiments. This suggests that resistance to the growth of L. maculans from leaves along the petioles towards the stems contributes to the quantitative resistance assessed in stems of adult plants in field experiments at the end of the growing season.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0222540PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6742359PMC
March 2020

Resolution of quantitative resistance to clubroot into QTL-specific metabolic modules.

J Exp Bot 2019 10;70(19):5375-5390

IGEPP, Agrocampus Ouest, INRA, Université de Rennes, Le Rheu, France.

Plant disease resistance is often under quantitative genetic control. Thus, in a given interaction, plant cellular responses to infection are influenced by resistance or susceptibility alleles at different loci. In this study, a genetic linkage analysis was used to address the complexity of the metabolic responses of Brassica napus roots to infection by Plasmodiophora brassicae. Metabolome profiling and pathogen quantification in a segregating progeny allowed a comparative mapping of quantitative trait loci (QTLs) involved in resistance and in metabolic adjustments. Distinct metabolic modules were associated with each resistance QTL, suggesting the involvement of different underlying cellular mechanisms. This approach highlighted the possible role of gluconasturtiin and two unknown metabolites in the resistance conferred by two QTLs on chromosomes C03 and C09, respectively. Only two susceptibility biomarkers (glycine and glutathione) were simultaneously linked to the three main resistance QTLs, suggesting the central role of these compounds in the interaction. By contrast, several genotype-specific metabolic responses to infection were genetically unconnected to resistance or susceptibility. Likewise, variations of root sugar profiles, which might have influenced pathogen nutrition, were not found to be related to resistance QTLs. This work illustrates how genetic metabolomics can help to understand plant stress responses and their possible links with disease.
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http://dx.doi.org/10.1093/jxb/erz265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6793449PMC
October 2019

Stable Quantitative Resistance Loci to Blackleg Disease in Canola ( L.) Over Continents.

Front Plant Sci 2018 23;9:1622. Epub 2018 Nov 23.

IGEPP, INRA, Agrocampus Ouest, Université Rennes, Le Rheu, France.

The hemibiotrophic fungus, is the most devastating pathogen, causing blackleg disease in canola ( L). To study the genomic regions involved in quantitative resistance (QR), 259-276 DH lines from Darmor-/Yudal (DYDH) population were assessed for resistance to blackleg under shade house and field conditions across 3 years. In different experiments, the broad sense heritability varied from 43 to 95%. A total of 27 significant quantitative trait loci (QTL) for QR were detected on 12 chromosomes and explained between 2.14 and 10.13% of the genotypic variance. Of the significant QTL, at least seven were repeatedly detected across different experiments on chromosomes A02, A07, A09, A10, C01, and C09. Resistance alleles were mainly contributed by 'Darmor-' but 'Yudal' also contributed few of them. Our results suggest that plant maturity and plant height may have a pleiotropic effect on QR in our conditions. We confirmed that which is present in 'Darmor-' is not effective to confer resistance in our Australian field conditions. Comparative mapping showed that several genes coding for nucleotide-binding leucine-rich repeat (LRR) receptors map in close proximity (within 200 Kb) of the significant trait-marker associations on the reference 'Darmor-' genome assembly. More importantly, eight significant QTL regions were detected across diverse growing environments: Australia, France, and United Kingdom. These stable QTL identified herein can be utilized for enhancing QR in elite canola germplasm via marker- assisted or genomic selection strategies.
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http://dx.doi.org/10.3389/fpls.2018.01622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6265502PMC
November 2018

Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps.

Nat Plants 2018 11 2;4(11):879-887. Epub 2018 Nov 2.

Genoscope, Institut de biologie François-Jacob, Commissariat à l'Energie Atomique (CEA), Université Paris-Saclay, Evry, France.

Plant genomes are often characterized by a high level of repetitiveness and polyploid nature. Consequently, creating genome assemblies for plant genomes is challenging. The introduction of short-read technologies 10 years ago substantially increased the number of available plant genomes. Generally, these assemblies are incomplete and fragmented, and only a few are at the chromosome scale. Recently, Pacific Biosciences and Oxford Nanopore sequencing technologies were commercialized that can sequence long DNA fragments (kilobases to megabase) and, using efficient algorithms, provide high-quality assemblies in terms of contiguity and completeness of repetitive regions. However, even though genome assemblies based on long reads exhibit high contig N50s (>1 Mb), these methods are still insufficient to decipher genome organization at the chromosome level. Here, we describe a strategy based on long reads (MinION or PromethION sequencers) and optical maps (Saphyr system) that can produce chromosome-level assemblies and demonstrate applicability by generating high-quality genome sequences for two new dicotyledon morphotypes, Brassica rapa Z1 (yellow sarson) and Brassica oleracea HDEM (broccoli), and one new monocotyledon, Musa schizocarpa (banana). All three assemblies show contig N50s of >5 Mb and contain scaffolds that represent entire chromosomes or chromosome arms.
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http://dx.doi.org/10.1038/s41477-018-0289-4DOI Listing
November 2018

Finding invisible quantitative trait loci with missing data.

Plant Biotechnol J 2018 12 28;16(12):2102-2112. Epub 2018 May 28.

Department of Plant Breeding, Justus Liebig University, Giessen, Germany.

Evolutionary processes during plant polyploidization and speciation have led to extensive presence-absence variation (PAV) in crop genomes, and there is increasing evidence that PAV associates with important traits. Today, high-resolution genetic analysis in major crops frequently implements simple, cost-effective, high-throughput genotyping from single nucleotide polymorphism (SNP) hybridization arrays; however, these are normally not designed to distinguish PAV from failed SNP calls caused by hybridization artefacts. Here, we describe a strategy to recover valuable information from single nucleotide absence polymorphisms (SNaPs) by population-based quality filtering of SNP hybridization data to distinguish patterns associated with genuine deletions from those caused by technical failures. We reveal that including SNaPs in genetic analyses elucidate segregation of small to large-scale structural variants in nested association mapping populations of oilseed rape (Brassica napus), a recent polyploid crop with widespread structural variation. Including SNaP markers in genomewide association studies identified numerous quantitative trait loci, invisible using SNP markers alone, for resistance to two major fungal diseases of oilseed rape, Sclerotinia stem rot and blackleg disease. Our results indicate that PAV has a strong influence on quantitative disease resistance in B. napus and that SNaP analysis using cost-effective SNP array data can provide extensive added value from 'missing data'. This strategy might also be applicable for improving the precision of genetic mapping in many important crop species.
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http://dx.doi.org/10.1111/pbi.12942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6230954PMC
December 2018

Multi-year linkage and association mapping confirm the high number of genomic regions involved in oilseed rape quantitative resistance to blackleg.

Theor Appl Genet 2018 Aug 4;131(8):1627-1643. Epub 2018 May 4.

IGEPP, AGROCAMPUS OUEST, INRA, Univ Rennes, 35650, Le Rheu, France.

Key Message: A repertoire of the genomic regions involved in quantitative resistance to Leptosphaeria maculans in winter oilseed rape was established from combined linkage-based QTL and genome-wide association (GWA) mapping. Linkage-based mapping of quantitative trait loci (QTL) and genome-wide association studies are complementary approaches for deciphering the genomic architecture of complex agronomical traits. In oilseed rape, quantitative resistance to blackleg disease, caused by L. maculans, is highly polygenic and is greatly influenced by the environment. In this study, we took advantage of multi-year data available on three segregating populations derived from the resistant cv Darmor and multi-year data available on oilseed rape panels to obtain a wide overview of the genomic regions involved in quantitative resistance to this pathogen in oilseed rape. Sixteen QTL regions were common to at least two biparental populations, of which nine were the same as previously detected regions in a multi-parental design derived from different resistant parents. Eight regions were significantly associated with quantitative resistance, of which five on A06, A08, A09, C01 and C04 were located within QTL support intervals. Homoeologous Brassica napus genes were found in eight homoeologous QTL regions, which corresponded to 657 pairs of homoeologous genes. Potential candidate genes underlying this quantitative resistance were identified. Genomic predictions and breeding are also discussed, taking into account the highly polygenic nature of this resistance.
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http://dx.doi.org/10.1007/s00122-018-3103-9DOI Listing
August 2018

A Major Locus for Manganese Tolerance Maps on Chromosome A09 in a Doubled Haploid Population of L.

Front Plant Sci 2017 12;8:1952. Epub 2017 Dec 12.

INRA, Agrocampus Ouest, Université de Rennes 1, UMR1349 Institut de Génétique, Environnement et de Protection des Plantes, Le Rheu, France.

Soil acidity poses a major threat to productivity of several crops; mainly due to the prevalence of toxic levels of Al and Mn. Crop productivity could be harnessed on acid soils via the development of plant varieties tolerant to phytotoxic levels of these cations. In this study, we investigated the extent of natural variation for Mn tolerance among ten parental lines of the Australian and International canola mapping populations. Response to Mn toxicity was measured on the bases of cotyledon chlorosis, shoot biomass, and leaf area in nutrient solution under control (9 μM of MnCl⋅4HO) and Mn treatment (125 μM of MnCl⋅4HO). Among parental lines, we selected Darmor- and Yudal that showed significant and contrasting variation in Mn tolerance to understand genetic control and identify the quantitative trait loci (QTL) underlying Mn tolerance. We evaluated parental lines and their doubled haploid (DH) progenies (196 lines) derived from an F cross, Darmor-/Yudal for Mn tolerance. Mn-tolerant genotypes had significantly higher shoot biomass and leaf area compared to Mn-sensitive genotypes. A genetic linkage map based on 7,805 DArTseq markers corresponding to 2,094 unique loci was constructed and further utilized for QTL identification. A major locus, . was further mapped with a SNP marker, Bn-A09-p29012402 (LOD score of 34.6) accounting for most of the variation in Mn tolerance on chromosome A09. This is the first report on the genomic localization of a Mn tolerance locus in . Additionally, an ortholog of encoding for cation efflux facilitator transporter was located within 3,991 bp from significant SNP marker associated with .. A suite of genome sequence based markers (DArTseq and Illumina Infinium SNPs) flanking the . locus would provide an invaluable tool for various molecular breeding applications to improve canola production and profitability on Mn toxic soils.
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http://dx.doi.org/10.3389/fpls.2017.01952DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5733045PMC
December 2017

Quantitative Resistance to Plant Pathogens in Pyramiding Strategies for Durable Crop Protection.

Front Plant Sci 2017 27;8:1838. Epub 2017 Oct 27.

Institute for Genetics, Environment and Plant Protection (INRA), UMR 1349, Leu Rheu, France.

Quantitative resistance has gained interest in plant breeding for pathogen control in low-input cropping systems. Although quantitative resistance frequently has only a partial effect and is difficult to select, it is considered more durable than major resistance (R) genes. With the exponential development of molecular markers over the past 20 years, resistance QTL have been more accurately detected and better integrated into breeding strategies for resistant varieties with increased potential for durability. This review summarizes current knowledge on the genetic inheritance, molecular basis, and durability of quantitative resistance. Based on this knowledge, we discuss how strategies that combine major R genes and QTL in crops can maintain the effectiveness of plant resistance to pathogens. Combining resistance QTL with complementary modes of action appears to be an interesting strategy for breeding effective and potentially durable resistance. Combining quantitative resistance with major R genes has proven to be a valuable approach for extending the effectiveness of major genes. In the plant genomics era, improved tools and methods are becoming available to better integrate quantitative resistance into breeding strategies. Nevertheless, optimal combinations of resistance loci will still have to be identified to preserve resistance effectiveness over time for durable crop protection.
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http://dx.doi.org/10.3389/fpls.2017.01838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5664368PMC
October 2017

Comparative genomic analysis of duplicated homoeologous regions involved in the resistance of Brassica napus to stem canker.

Front Plant Sci 2015 25;6:772. Epub 2015 Sep 25.

Institut National de la Recherche Agronomique, UMR1349 IGEPP Le Rheu, France.

All crop species are current or ancient polyploids. Following whole genome duplication, structural and functional modifications result in differential gene content or regulation in the duplicated regions, which can play a fundamental role in the diversification of genes underlying complex traits. We have investigated this issue in Brassica napus, a species with a highly duplicated genome, with the aim of studying the structural and functional organization of duplicated regions involved in quantitative resistance to stem canker, a disease caused by the fungal pathogen Leptosphaeria maculans. Genome-wide association analysis on two oilseed rape panels confirmed that duplicated regions of ancestral blocks E, J, R, U, and W were involved in resistance to stem canker. The structural analysis of the duplicated genomic regions showed a higher gene density on the A genome than on the C genome and a better collinearity between homoeologous regions than paralogous regions, as overall in the whole B. napus genome. The three ancestral sub-genomes were involved in the resistance to stem canker and the fractionation profile of the duplicated regions corresponded to what was expected from results on the B. napus progenitors. About 60% of the genes identified in these duplicated regions were single-copy genes while less than 5% were retained in all the duplicated copies of a given ancestral block. Genes retained in several copies were mainly involved in response to stress, signaling, or transcription regulation. Genes with resistance-associated markers were mainly retained in more than two copies. These results suggested that some genes underlying quantitative resistance to stem canker might be duplicated genes. Genes with a hydrolase activity that were retained in one copy or R-like genes might also account for resistance in some regions. Further analyses need to be conducted to indicate to what extent duplicated genes contribute to the expression of the resistance phenotype.
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http://dx.doi.org/10.3389/fpls.2015.00772DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4585320PMC
October 2015

Manipulating feeding stimulation to protect crops against insect pests?

J Chem Ecol 2014 Dec 30;40(11-12):1220-31. Epub 2014 Oct 30.

INRA, UMR1349 IGEPP, 35653, Le Rheu, France,

Enhancing natural mechanisms of plant defense against herbivores is one of the possible strategies to protect cultivated species against insect pests. Host plant feeding stimulation, which results from phagostimulant and phagodeterrent effects of both primary and secondary metabolites, could play a key role in levels of damage caused to crop plants. We tested this hypothesis by comparing the feeding intensity of the pollen beetle Meligethes aeneus on six oilseed rape (Brassica napus) genotypes in a feeding experiment, and by assessing the content of possible phagostimulant and phagodeterrent compounds in tissues targeted by the insect (flower buds). For this purpose, several dozens of primary and secondary metabolites were quantified by a set of chromatographic techniques. Intergenotypic variability was found both in the feeding experiment and in the metabolic profile of plant tissues. Biochemical composition of the perianth was in particular highly correlated with insect damage. Only a few compounds explained this correlation, among which was sucrose, known to be highly phagostimulating. Further testing is needed to validate the suggested impact of the specific compounds we have identified. Nevertheless, our results open the way for a crop protection strategy based on artificial selection of key determinants of insect feeding stimulation.
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http://dx.doi.org/10.1007/s10886-014-0517-yDOI Listing
December 2014

Plant genetics. Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome.

Science 2014 Aug 21;345(6199):950-3. Epub 2014 Aug 21.

Institut National de Recherche Agronomique (INRA)/Université d'Evry Val d'Essone, Unité de Recherche en Génomique Végétale, UMR1165, Organization and Evolution of Plant Genomes, 2 rue Gaston Crémieux, 91057 Evry, France.

Oilseed rape (Brassica napus L.) was formed ~7500 years ago by hybridization between B. rapa and B. oleracea, followed by chromosome doubling, a process known as allopolyploidy. Together with more ancient polyploidizations, this conferred an aggregate 72× genome multiplication since the origin of angiosperms and high gene content. We examined the B. napus genome and the consequences of its recent duplication. The constituent An and Cn subgenomes are engaged in subtle structural, functional, and epigenetic cross-talk, with abundant homeologous exchanges. Incipient gene loss and expression divergence have begun. Selection in B. napus oilseed types has accelerated the loss of glucosinolate genes, while preserving expansion of oil biosynthesis genes. These processes provide insights into allopolyploid evolution and its relationship with crop domestication and improvement.
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http://dx.doi.org/10.1126/science.1253435DOI Listing
August 2014

Homoeologous duplicated regions are involved in quantitative resistance of Brassica napus to stem canker.

BMC Genomics 2014 Jun 19;15:498. Epub 2014 Jun 19.

INRA, UMR1349 IGEPP, BP35327, 35653 Le Rheu, France.

Background: Several major crop species are current or ancient polyploids. To better describe the genetic factors controlling traits of agronomic interest (QTL), it is necessary to understand the structural and functional organisation of these QTL regions in relation to genome duplication. We investigated quantitative resistance to the fungal disease stem canker in Brassica napus, a highly duplicated amphidiploid species, to assess the proportion of resistance QTL located at duplicated positions.

Results: Genome-wide association analysis on a panel of 116 oilseed rape varieties genotyped with 3228 SNP indicated that 321 markers, corresponding to 64 genomic regions, are associated with resistance to stem canker. These genomic regions are relatively equally distributed on the A (53%) and C (47%) genomes of B. napus. Overall, 44% of these regions (28/64) are duplicated homoeologous regions. They are located in duplications of six (E, J, R, T, U and W) of the 24 ancestral blocks that constitute the B. napus genome. Overall, these six ancestral blocks have 34 duplicated copies in the B.napus genome. Almost all of the duplicated copies (82% of the 34 regions) harboured resistance associated markers for stem canker resistance, which suggests structural and functional conservation of genetic factors involved in this trait in B. napus.

Conclusions: Our study provides information on the involvement of duplicated loci in the control of stem canker resistance in B. napus. Further investigation of the similarity/divergence in sequence and gene content of these duplicated regions will provide insight into the conservation and allelic diversity of the underlying genes.
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http://dx.doi.org/10.1186/1471-2164-15-498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4082613PMC
June 2014

QTL meta-analysis provides a comprehensive view of loci controlling partial resistance to Aphanomyces euteiches in four sources of resistance in pea.

BMC Plant Biol 2013 Mar 16;13:45. Epub 2013 Mar 16.

INRA, UMR1349 IGEPP, Le Rheu F-35653, France.

Background: Development of durable plant genetic resistance to pathogens through strategies of QTL pyramiding and diversification requires in depth knowledge of polygenic resistance within the available germplasm. Polygenic partial resistance to Aphanomyces root rot, caused by Aphanomyces euteiches, one of the most damaging pathogens of pea worldwide, was previously dissected in individual mapping populations. However, there are no data available regarding the diversity of the resistance QTL across a broader collection of pea germplasm. In this study, we performed a meta-analysis of Aphanomyces root rot resistance QTL in the four main sources of resistance in pea and compared their genomic localization with genes/QTL controlling morphological or phenological traits and with putative candidate genes.

Results: Meta-analysis, conducted using 244 individual QTL reported previously in three mapping populations (Puget x 90-2079, Baccara x PI180693 and Baccara x 552) and in a fourth mapping population in this study (DSP x 90-2131), resulted in the identification of 27 meta-QTL for resistance to A. euteiches. Confidence intervals of meta-QTL were, on average, reduced four-fold compared to mean confidence intervals of individual QTL. Eleven consistent meta-QTL, which highlight seven highly consistent genomic regions, were identified. Few meta-QTL specificities were observed among mapping populations, suggesting that sources of resistance are not independent. Seven resistance meta-QTL, including six of the highly consistent genomic regions, co-localized with six of the meta-QTL identified in this study for earliness and plant height and with three morphological genes (Af, A, R). Alleles contributing to the resistance were often associated with undesirable alleles for dry pea breeding. Candidate genes underlying six main meta-QTL regions were identified using colinearity between the pea and Medicago truncatula genomes.

Conclusions: QTL meta-analysis provided an overview of the moderately low diversity of loci controlling partial resistance to A. euteiches in four main sources of resistance in pea. Seven highly consistent genomic regions with potential use in marker-assisted-selection were identified. Confidence intervals at several main QTL regions were reduced and co-segregation among resistance and morphological/phenological alleles was identified. Further work will be required to identify the best combinations of QTL for durably increasing partial resistance to A. euteiches.
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http://dx.doi.org/10.1186/1471-2229-13-45DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3680057PMC
March 2013

High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L.

BMC Genomics 2013 Feb 22;14:120. Epub 2013 Feb 22.

INRA, UMR1349 IGEPP, BP35327, 35653, Le Rheu cedex, France.

Background: High density genetic maps built with SNP markers that are polymorphic in various genetic backgrounds are very useful for studying the genetics of agronomical traits as well as genome organization and evolution. Simultaneous dense SNP genotyping of segregating populations and variety collections was applied to oilseed rape (Brassica napus L.) to obtain a high density genetic map for this species and to study the linkage disequilibrium pattern.

Results: We developed an integrated genetic map for oilseed rape by high throughput SNP genotyping of four segregating doubled haploid populations. A very high level of collinearity was observed between the four individual maps and a large number of markers (>59%) was common to more than two maps. The precise integrated map comprises 5764 SNP and 1603 PCR markers. With a total genetic length of 2250 cM, the integrated map contains a density of 3.27 markers (2.56 SNP) per cM. Genotyping of these mapped SNP markers in oilseed rape collections allowed polymorphism level and linkage disequilibrium (LD) to be studied across the different collections (winter vs spring, different seed quality types) and along the linkage groups. Overall, polymorphism level was higher and LD decayed faster in spring than in "00" winter oilseed rape types but this was shown to vary greatly along the linkage groups.

Conclusions: Our study provides a valuable resource for further genetic studies using linkage or association mapping, for marker assisted breeding and for Brassica napus sequence assembly and genome organization analyses.
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http://dx.doi.org/10.1186/1471-2164-14-120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600037PMC
February 2013

Partial resistance to clubroot in Arabidopsis is based on changes in the host primary metabolism and targeted cell division and expansion capacity.

Funct Integr Genomics 2013 Jun 19;13(2):191-205. Epub 2013 Feb 19.

Agrocampus Ouest, UMR1349 IGEPP, 35000 Rennes, France.

To date, studies of the molecular basis of disease resistance mainly focused on qualitative resistance. However, deciphering mechanisms underlying quantitative resistance could lead to insights into the relationship between qualitative and quantitative resistance and guide the utilization of these two types of resistance to produce durably resistant cultivars. A functional genomics approach, using the CATMA whole-genome microarray, was used to detect changes in gene expression associated with partial quantitative resistance in the Arabidopsis thaliana-Plasmodiophora brassicae pathosystem. The time course of transcript abundance during partial clubroot resistance response was monitored at the whole plant level, and direct comparisons between partial resistance and susceptibility responses were made using the same host genotype. An increasingly complex host response was revealed, as was the differential influence of P. brassicae infection on the transcription of Arabidopsis genes according to the isolate used. We observed, at the transcriptomic level, that metabolic diversion by the pathogen was reduced or delayed, classical plant defense responses were induced earlier and/or more strongly, and cell enlargement and proliferation were actively inhibited in the partial quantitative resistance response compared to the susceptible one.
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http://dx.doi.org/10.1007/s10142-013-0312-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3664179PMC
June 2013

A dominant point mutation in a RINGv E3 ubiquitin ligase homoeologous gene leads to cleistogamy in Brassica napus.

Plant Cell 2012 Dec 31;24(12):4875-91. Epub 2012 Dec 31.

Unité de Recherche en Génomique Végétale Institut National de la Recherche Agronomique, Centre National de la Recherche Scientifique, Université d'Evry Val d'Essones, Organization and Evolution of Plant Genomes, 91057 Evry cedex, France.

In the allopolyploid Brassica napus, we obtained a petal-closed flower mutation by ethyl methanesulfonate mutagenesis. Here, we report cloning and characterization of the Bn-CLG1A (CLG for cleistogamy) gene and the Bn-clg1A-1D mutant allele responsible for the cleistogamy phenotype. Bn-CLG1A encodes a RINGv E3 ubiquitin ligase that is highly conserved across eukaryotes. In the Bn-clg1A-1D mutant allele, a C-to-T transition converts a Pro at position 325 to a Leu (P325L), causing a dominant mutation leading to cleistogamy. B. napus and Arabidopsis thaliana plants transformed with a Bn-clg1A-1D allele show cleistogamous flowers, and characterization of these flowers suggests that the Bn-clg1A-1D mutation causes a pronounced negative regulation of cutin biosynthesis or loading and affects elongation or differentiation of petal and sepal cells. This results in an inhibition or a delay of petal development, leading to folded petals. A homoeologous gene (Bn-CLG1C), which shows 99.5% amino acid identity and is also constitutively and equally expressed to the wild-type Bn-CLG1A gene, was also identified. We showed that P325L is not a loss-of-function mutation and did not affect expression of Bn-clg1A-1D or Bn-CLG1C. Our findings suggest that P325L is a gain-of-function semidominant mutation, which led to either hyper- or neofunctionalization of a redundant homoeologous gene.
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http://dx.doi.org/10.1105/tpc.112.104315DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556963PMC
December 2012

Metabotyping: a new approach to investigate rapeseed (Brassica napus L.) genetic diversity in the metabolic response to clubroot infection.

Mol Plant Microbe Interact 2012 Nov;25(11):1478-91

AGROCAMPUS OUEST, Rennes, France.

Clubroot disease affects all Brassicaceae spp. and is caused by the obligate biotroph pathogen Plasmodiophora brassicae. The development of galls on the root system is associated with the establishment of a new carbon metabolic sink. Here, we aimed to deepen our knowledge of the involvement of primary metabolism in the Brassica napus response to clubroot infection. We studied the dynamics and the diversity of the metabolic responses to the infection. Root system metabotyping was carried out for 18 rapeseed genotypes displaying different degrees of symptom severity, under inoculated and noninoculated conditions at 42 days postinoculation (dpi). Clubroot susceptibility was positively correlated with clubroot-induced accumulation of several amino acids. Although glucose and fructose accumulated in some genotypes with minor symptoms, their levels were negatively correlated to the disease index across the whole set of genotypes. The dynamics of the metabolic response were studied for the susceptible genotype 'Yudal,' which allowed an "early" metabolic response (established from 14 to 28 dpi) to be differentiated from a "late" response (from 35 dpi). We discuss the early accumulation of amino acids in the context of the establishment of a nitrogen metabolic sink and the hypothetical biological role of the accumulation of glutathione and S-methylcysteine.
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http://dx.doi.org/10.1094/MPMI-02-12-0032-RDOI Listing
November 2012

Arginase induction represses gall development during clubroot infection in Arabidopsis.

Plant Cell Physiol 2012 May 19;53(5):901-11. Epub 2012 Mar 19.

Université Rennes 1, UMR1349 IGEPP, F-35000 Rennes, France.

Arginase induction can play a defensive role through the reduction of arginine availability for phytophageous insects. Arginase activity is also induced during gall growth caused by Plasmodiophora brassicae infection in roots of Arabidopsis thaliana; however, its possible role in this context has been unclear. We report here that the mutation of the arginase-encoding gene ARGAH2 abrogates clubroot-induced arginase activity and results in enhanced gall size in infected roots, suggesting that arginase plays a defensive role. Induction of arginase activity in infected roots was impaired in the jar1 mutant, highlighting a link between the arginase response to clubroot and jasmonate signaling. Clubroot-induced accumulation of the principal amino acids in galls was not affected by the argah2 mutation. Because ARGAH2 was previously reported to control auxin response, we investigated the role of ARGAH2 in callus induction. ARGAH2 was found to be highly induced in auxin/cytokinin-triggered aseptic plant calli, and callus development was enhanced in argah2 in the absence of the pathogen. We hypothesized that arginase contributes to a negative control over clubroot symptoms, by reducing hormone-triggered cellular proliferation.
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http://dx.doi.org/10.1093/pcp/pcs037DOI Listing
May 2012

Germination stimulants of Phelipanche ramosa in the rhizosphere of Brassica napus are derived from the glucosinolate pathway.

Mol Plant Microbe Interact 2012 Jul;25(7):993-1004

Phelipanche ramosa is a major parasitic weed of Brassica napus. The first step in a host-parasitic plant interaction is stimulation of parasite seed germination by compounds released from host roots. However, germination stimulants produced by B. napus have not been identified yet. In this study, we characterized the germination stimulants that accumulate in B. napus roots and are released into the rhizosphere. Eight glucosinolate-breakdown products were identified and quantified in B. napus roots by gas chromatography-mass spectrometry. Two (3-phenylpropanenitrile and 2-phenylethyl isothiocyanate [2-PEITC]) were identified in the B. napus rhizosphere. Among glucosinolate-breakdown products, P. ramosa germination was strongly and specifically triggered by isothiocyanates, indicating that 2-PEITC, in particular, plays a key role in the B. napus-P. ramosa interaction. Known strigolactones were not detected by ultraperformance liquid chromatography-tandem mass spectrometry, and seed of Phelipanche and Orobanche spp. that respond to strigolactones but not to isothiocyanates did not germinate in the rhizosphere of B. napus. Furthermore, both wild-type and strigolactone biosynthesis mutants of Arabidopsis thaliana Atccd7 and Atccd8 induced similar levels of P. ramosa seed germination, suggesting that compounds other than strigolactone function as germination stimulants for P. ramosa in other Brassicaceae spp. Our results open perspectives on the high adaptation potential of root-parasitic plants under host-driven selection pressures.
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http://dx.doi.org/10.1094/MPMI-01-12-0006-RDOI Listing
July 2012

Genetic and physiological analysis of the relationship between partial resistance to clubroot and tolerance to trehalose in Arabidopsis thaliana.

New Phytol 2011 Sep 20;191(4):1083-1094. Epub 2011 May 20.

Agrocampus Ouest, UMR 118, F-35042 Rennes, France.

In Arabidopsis thaliana the induction of plant trehalase during clubroot disease was proposed to act as a defense mechanism in the susceptible accession Col-0, which could thereby cope with the accumulation of pathogen-synthesized trehalose. In the present study, we assessed trehalose activity and tolerance to trehalose in the clubroot partially resistant accession Bur-0. We compared both accessions for several trehalose-related physiological traits during clubroot infection. A quantitative trait loci (QTLs) analysis of tolerance to exogenous trehalose was also conducted on a Bur-0xCol-0 RIL progeny. Trehalase activity was not induced by clubroot in Bur-0 and the inhibition of trehalase by validamycin treatments resulted in the enhancement of clubroot symptoms only in Col-0. In pathogen-free cultures, Bur-0 showed less trehalose-induced toxicity symptoms than Col-0. A QTL analysis identified one locus involved in tolerance to trehalose overlapping the confidence interval of a QTL for resistance to Plasmodiophora brassicae. This colocalization was confirmed using heterogeneous inbred family (HIF) lines. Although not based on trehalose catabolism capacity, partial resistance to clubroot is to some extent related to the tolerance to trehalose accumulation in Bur-0. These findings support an original model where contrasting primary metabolism-related regulations could contribute to the partial resistance to a plant pathogen.
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http://dx.doi.org/10.1111/j.1469-8137.2011.03751.xDOI Listing
September 2011

New consistent QTL in pea associated with partial resistance to Aphanomyces euteiches in multiple French and American environments.

Theor Appl Genet 2011 Jul 11;123(2):261-81. Epub 2011 Apr 11.

Université de Rennes 1, Amélioration des Plantes et Biotechnologies Végétales, Rennes, France.

Partial resistances, often controlled by quantitative trait loci (QTL), are considered to be more durable than monogenic resistances. Therefore, a precursor to developing efficient breeding programs for polygenic resistance to pathogens should be a greater understanding of genetic diversity and stability of resistance QTL in plants. In this study, we deciphered the diversity and stability of resistance QTL to Aphanomyces euteiches in pea towards pathogen variability, environments and scoring criteria, from two new sources of partial resistance (PI 180693 and 552), effective in French and USA infested fields. Two mapping populations of 178 recombinant inbred lines each, derived from crosses between 552 or PI 180693 (partially resistant) and Baccara (susceptible), were used to identify QTL for Aphanomyces root rot resistance in controlled and in multiple French and USA field conditions using several resistance criteria. We identified a total of 135 additive-effect QTL corresponding to 23 genomic regions and 13 significant epistatic interactions associated with partial resistance to A. euteiches in pea. Among the 23 additive-effect genomic regions identified, five were consistently detected, and showed highly stable effects towards A. euteiches strains, environments, resistance criteria, condition tests and RIL populations studied. These results confirm the complexity of inheritance of partial resistance to A. euteiches in pea and provide good bases for the choice of consistent QTL to use in marker-assisted selection schemes to increase current levels of resistance to A. euteiches in pea breeding programs.
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http://dx.doi.org/10.1007/s00122-011-1582-zDOI Listing
July 2011

Integration of linkage maps for the Amphidiploid Brassica napus and comparative mapping with Arabidopsis and Brassica rapa.

BMC Genomics 2011 Feb 9;12:101. Epub 2011 Feb 9.

Department of Plant Sciences, Rothamsted Research, Harpenden, AL5 2JQ, UK.

Background: The large number of genetic linkage maps representing Brassica chromosomes constitute a potential platform for studying crop traits and genome evolution within Brassicaceae. However, the alignment of existing maps remains a major challenge. The integration of these genetic maps will enhance genetic resolution, and provide a means to navigate between sequence-tagged loci, and with contiguous genome sequences as these become available.

Results: We report the first genome-wide integration of Brassica maps based on an automated pipeline which involved collation of genome-wide genotype data for sequence-tagged markers scored on three extensively used amphidiploid Brassica napus (2n = 38) populations. Representative markers were selected from consolidated maps for each population, and skeleton bin maps were generated. The skeleton maps for the three populations were then combined to generate an integrated map for each LG, comparing two different approaches, one encapsulated in JoinMap and the other in MergeMap. The BnaWAIT_01_2010a integrated genetic map was generated using JoinMap, and includes 5,162 genetic markers mapped onto 2,196 loci, with a total genetic length of 1,792 cM. The map density of one locus every 0.82 cM, corresponding to 515 Kbp, increases by at least three-fold the locus and marker density within the original maps. Within the B. napus integrated map we identified 103 conserved collinearity blocks relative to Arabidopsis, including five previously unreported blocks. The BnaWAIT_01_2010a map was used to investigate the integrity and conservation of order proposed for genome sequence scaffolds generated from the constituent A genome of Brassica rapa.

Conclusions: Our results provide a comprehensive genetic integration of the B. napus genome from a range of sources, which we anticipate will provide valuable information for rapeseed and Canola research.
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http://dx.doi.org/10.1186/1471-2164-12-101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3042011PMC
February 2011

A complex genetic network involving a broad-spectrum locus and strain-specific loci controls resistance to different pathotypes of Aphanomyces euteiches in Medicago truncatula.

Theor Appl Genet 2010 Mar 12;120(5):955-70. Epub 2009 Dec 12.

INRA, Agrocampus Ouest, Université de Rennes 1, UMR118, Amélioration des Plantes et Biotechnologies Végétales, 35653, Le Rheu Cedex, Rennes, France.

A higher understanding of genetic and genomic bases of partial resistance in plants and their diversity regarding pathogen variability is required for a more durable management of resistance genetic factors in sustainable cropping systems. In this study, we investigated the diversity of genetic factors involved in partial resistance to Aphanomyces euteiches, a very damaging pathogen on pea and alfalfa, in Medicago truncatula. A mapping population of 178 recombinant inbred lines, from the cross F83005.5 (susceptible) and DZA045.5 (resistant), was used to identify quantitative trait loci for resistance to four A. euteiches reference strains belonging to the four main pathotypes currently known on pea and alfalfa. A major broad-spectrum genomic region, previously named AER1, was localized to a reduced 440 kb interval on chromosome 3 and was involved in complete or partial resistance, depending on the A. euteiches strain. We also identified 21 additive and/or epistatic genomic regions specific to one or two strains, several of them being anchored to the M. truncatula physical map. These results show that, in M. truncatula, a complex network of genetic loci controls partial resistance to different pea and alfalfa pathotypes of A. euteiches, suggesting a diversity of molecular mechanisms underlying partial resistance.
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http://dx.doi.org/10.1007/s00122-009-1224-xDOI Listing
March 2010

Genetic and molecular approaches to improve nutritional value of Brassica napus L. seed.

C R Biol 2008 Oct 4;331(10):763-71. Epub 2008 Sep 4.

INRA-Agrocampus Rennes-University of Rennes1 Joint Laboratory, UMR118, Plant Genetics and Biotechnologies, BP 35327, 35653 Le Rheu cedex, France.

Oilseed rape (Brassica napus L.) is a major oil crop that also supplies proteins for the feed industry. In order to reduce total cost production, the objective is to increase oil yield while reducing crop inputs (especially nitrogen and pesticides). Concomitantly, it is necessary to anticipate specific uses (e.g., fatty acid composition) and to ensure the valorisation of the by-products (rapeseed meal). By the past, improvement of seed quality focused on fatty acid balance and low seed glucosinolate content. Current goals include the breeding of yellow-seeded rapeseed lines with high content of seed oil. The use of molecular tools and the exploitation of Arabidopsis knowledge will be presented and discussed.
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http://dx.doi.org/10.1016/j.crvi.2008.07.018DOI Listing
October 2008

Repetitive sequence-derived markers tag centromeres and telomeres and provide insights into chromosome evolution in Brassica napus.

Chromosome Res 2008 7;16(5):683-700. Epub 2008 Jun 7.

INRA, Agrocampus Rennes, Université Rennes 1, UMR 118 Amélioration des Plantes et Biotechnologies Végétales, Le Rheu Cedex, France.

Centromeres and telomeres are obvious markers on chromosomes but their location on genetic maps is difficult to determine, which hampers many basic and applied research programmes. In this study, we used the characteristic distribution of five Brassica repeated sequences to generate physically anchored molecular markers tentatively tagging Brassica centromeres (84 markers) and telomeres (31 markers). These markers were mapped to the existing oilseed rape genetic map. Clusters of centromere-related loci were observed on 14 linkage groups; in addition to previous reports, we could thus provide information about the most likely position of centromeres on 17 of the 19 B. napus linkage groups. The location of centromeres on linkage groups usually matches their position on chromosomes and coincides with sites of evolutionary breakage between chromosomes. Most telomere sequence-derived markers mapped interstitially or in the proximity of centromeres; this result echoes previous reports on many eukaryote genomes and may reflect different forms of chromosome evolution. Seven telomere sequence-derived markers were located at the outermost positions of seven linkage groups and therefore probably tagged telomeres.
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http://dx.doi.org/10.1007/s10577-008-1219-5DOI Listing
December 2008

Identification of quantitative trait loci controlling partial clubroot resistance in new mapping populations of Arabidopsis thaliana.

Theor Appl Genet 2008 Jul 22;117(2):191-202. Epub 2008 Apr 22.

Amélioration des Plantes et Biotechnologies Végétales, UMR118 INRA-Agrocampus Rennes-Université de Rennes 1, BP35327, 35653, Le Rheu Cedex, France.

To date, mechanisms of partial quantitative resistance, under polygenic control, remain poorly understood, studies of the molecular basis of disease resistance have mainly focused on qualitative variation under oligogenic control. However, oligogenic conferred resistance is rapidly overcome by the pathogen and knowledge of the relationship between qualitative and quantitative resistance is necessary to develop durably resistant cultivars. In this study, we exploited the Arabidopsis thaliana-Plasmodiophora brassicae pathosystem to decipher the genetic architecture determining partial resistance. This soil-borne pathogen causes clubroot, one of the economically most important diseases of Brassica crops in the world. A quantitative trait locus (QTL) approach was carried out using two segregating populations (F(2) and recombinant inbred lines) from crosses between the partially resistant accession Burren and the susceptible accession Columbia. Four additive QTLs (one moderate and three minor) controlling partial resistance to clubroot were identified, all the resistance alleles being derived from the partially resistant parent. In addition, four epistatic regions, which have no additive effect on resistance, were also found to be involved in partial resistance. An examination of candidate genes suggested that a potentially diverse array of mechanisms is related to the different QTLs. By fine-mapping and cloning these regions, the mechanisms involved in partial resistance will be identified.
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http://dx.doi.org/10.1007/s00122-008-0765-8DOI Listing
July 2008
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