CRG protéagineux à grosses graines, INRA dijon. Diversité biologique pour le maintien du patrimoine et la recherche de performances

National audienceLe centre de ressources génétiques des Protéagineux à grosses graines de l’INRA de Dijon gère des collections appartenant aux trois espèces : pisum (>10.000 accessions), Vicia faba (1400 accessions) et Lupinus albus (1600 accessions). Ces collections renferment aussi bien des génotypes « patrimoniaux » et historiques, que des génotypes issus de programmes de recherche et de sélection. Les ressources « naturelles » de pois (2000 accessions) renferment des formes cultivées ou sauvages ayant pour origine géographique plus d’une quarantaine de pays. La féverole, espèce allogame, ne comporte pas de formes sauvages, mais des formes cultivées (1200 accessions) provenant des 4 centres de diversification de l’espèce. Quant au lupin, la collection comporte essentiellement des formes naturelles et cultivées (1500 accessions), collectées dans les pays du pourtour méditerranéen. La grande diversité de ces collections permet, entre autres, des approches de génétique d’association et de génomique. Les marqueurs moléculaires, mis au point, par exemple, dans le programme ANR PeaMUST ou FP7 Legato, spécifiques de caractères agronomiques, peuvent être utilisés dans les programmes de sélection assistée par marqueurs, tel que dans le programme IVD INRA ou mis à disposition des membres du Groupement des Sélectionneurs de Protéagineux. Les nouveaux génotypes sélectionnés sont ensuite testés pour leur valeur agronomique et aptitude à la résistance aux stress biotiques et abiotiques, ainsi que pour leur valeur nutritionnelle, en collaboration avec Terres inovia. C’est l’intégration de toute cette filière de ces trois espèces, des formes ancestrales à l’application dans le secteur agroalimentaire, qui est pour le centre de ressources et ses partenaires, gage d’avancées stratégiques. Mots clés autres que dans le titre : pisum ; vicia faba , lupinus ; ressource

Partner choice in core collection of pea inoculated by a mix of five Rhizobium lecuminosarum sbv. viciae strains

BAPGEAPSIPea is the third most important grain legume worldwide. The crop natural ability to use, as main nitrogen resource, the atmospheric N2 symbiotically assimilated by Rhizobium leguminosarum sbv. viciae (Rlv) in the plant nodules is a major component of its attractiveness. However, the symbiosis may not be optimal because natural Rlv populations are quantitatively and qualitatively heterogeneous, with strains varying in competitiveness and efficiency of nitrogen fixation. The variability of pea-Rlv partner choice was investigated within a collection of 104 pea accessions co-inoculated with a mix of five diverse Rlv strains. Analyses of the genetic structure of the pea collection - genotyped using the GenoPea 13K SNP Array - uncovered different genetic groups representative of the pea geographic origin or history of selection. Proportions of nodules formed with each strain were estimated in each pea accession. Differences in the Rlv choice were observed between the different pea genetic groups, revealing changes in partner choice during domestication and breeding selection. Additional experiments performed on a subset of pea accessions showed that in most cases competiveness for nodulation of a given pea-Rlv symbiotic association could not be related to its nitrogen fixation efficiency. Further studies involving larger pea panel and mix of Rlv strains together with a higher density SNP genotyping will be carried out to identify specific loci underlying the partner choice trait

Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

BAPGEAPSIINRASUPDATAPea (Pisum sativum, L.) is a major pulse crop used both for animal and human alimentation. Owing to its association with nitrogen-fixing bacteria, it is also a valuable component for low-input cropping systems. To evaluate the genetic diversity and the scale of linkage disequilibrium (LD) decay in pea, we genotyped a collection of 917 accessions gathering elite cultivars, landraces and wild relatives using an array of ~13,000 single nucleotide polymorphisms (SNP). Genetic diversity is broadly distributed across three groups corresponding to wild/landraces peas, winter types and spring types. At a finer subdivision level, genetic groups relate to local breeding programs and type usage. Linkage disequilibrium is steeply decreasing as genetic distance increase. When considering subsets of the data, LD values can be higher, even if the steep decay remains. We looked for genomic regions exhibiting high level of differentiation between wild/landraces, winter and spring pea respectively. Two regions on linkage groups 5 and 6 containing 33 SNPs exhibit stronger differentiation between winter and spring peas than would be expected under neutrality. Interestingly QTLs for resistance to cold acclimation and frost resistance have been identified previously in the same regions

Genomic Prediction in Pea: Effect of Marker Density and Training Population Size and Composition on Prediction Accuracy

International audiencePea is an important food and feed crop and a valuable component of low input farming systems. Improving resistance to biotic and abiotic stresses is a major breeding target to enhance yield potential and regularity. Genomic selection (GS) has lately emerged as a promising technique to increase the accuracy and gain of marker-based selection. It uses genome-wide molecular marker data to predict the breeding values of candidate lines to selection. A collection of 339 genetic resource accessions (CRB339) was subjected to high-density genotyping using the GenoPea 13.2K SNP Array. Genomic prediction accuracy was evaluated for thousand seed weight (TSW), the number of seeds per plant (NSeed), and the date of flowering (BegFlo). Mean cross environment prediction accuracies reached 0.83 for TSW, 0.68 for NSeed, and 0.65 for BegFlo. For each trait, the statistical method, the marker density, and/or the training population size and composition used for prediction were varied to investigate their effects on prediction accuracy: the effect was large for the size and composition of the training population but limited for the statistical method and marker density. Maximizing the relatedness between individuals in the training and test sets, through the CDmean-based method, significantly improved prediction accuracies. A cross-population cross-validation experiment was further conducted using the CRB339 collection as a training population set and nine recombinant inbred lines populations as test set. Prediction quality was high with mean Q(2) of 0.44 for TSW and 0.59 for BegFlo. Results are discussed in the light of current efforts to develop GS strategies in pea

Co-inoculation of a Pea Core-Collection with Diverse Rhizobial Strains Shows Competitiveness for Nodulation and Efficiency of Nitrogen Fixation Are Distinct traits in the Interaction

Pea forms symbiotic nodules with Rhizobium leguminosarum sv. viciae (Rlv). In the field, pea roots can be exposed to multiple compatible Rlv strains. Little is known about the mechanisms underlying the competitiveness for nodulation of Rlv strains and the ability of pea to choose between diverse compatible Rlv strains. The variability of pea-Rlv partner choice was investigated by co-inoculation with a mixture of five diverse Rlv strains of a 104-pea collection representative of the variability encountered in the genus Pisum. The nitrogen fixation efficiency conferred by each strain was determined in additional mono-inoculation experiments on a subset of 18 pea lines displaying contrasted Rlv choice. Differences in Rlv choice were observed within the pea collection according to their genetic or geographical diversities. The competitiveness for nodulation of a given pea-Rlv association evaluated in the multi-inoculated experiment was poorly correlated with its nitrogen fixation efficiency determined in mono-inoculation. Both plant and bacterial genetic determinants contribute to pea-Rlv partner choice. No evidence was found for co-selection of competitiveness for nodulation and nitrogen fixation efficiency. Plant and inoculant for an improved symbiotic association in the field must be selected not only on nitrogen fixation efficiency but also for competitiveness for nodulation

Diversité du choix de partenaires symbiotiques parmi une collection de pois inoculée par un mélange de souches de<em> rhizobium</em>

National audienceLes légumineuses sont des cultures de grand intérêt pour répondre aux enjeux de sécurité alimentaire et de développement durable. Dans un contexte de forte croissance démographique, ce sont des sources de protéines pour les alimentations humaine et animale. Un autre atout des légumineuses est qu’elles peuvent s’affranchir d’un apport d’engrais azoté grâce à leur capacité à former des associations symbiotiques au sein de nodosités racinaires avec des bactéries du sol (les rhizobia) qui fixent l’azote de l’air. Cependant, la fixation symbiotique n’est pas toujours optimale ; elle est très sensible aux stress abiotiques et dépend directement de l’efficacité symbiotique du partenaire bactérien. Les populations naturelles de rhizobia sont quantitativement et qualitativement hétérogènes et peuvent aboutir à des symbioses inefficaces. Une approche pluridisciplinaire a été menée afin d’évaluer l’impact du génotype de pois et des rhizobia qui nodulent cette espèce sur l’établissement et l’efficacité de la symbiose fixatrice d’azote. Des essais ont été réalisés en serre sur une collection de 104 accessions de pois avec des historiques de sélection et des origines géographiques diverses. Ces 104 accessions ont été inoculées par un mélange de cinq souches de Rhizobium leguminosarum sv. viciae (Rlv) choisies pour leur diversité. Une forte variation du choix entre les partenaires symbiotiques a été observée. Ceci a permis de mettre en évidence des liens entre la diversité génétique des accessions de pois et l’établissement préférentiel de la symbiose avec certaines souches de Rlv. Une expérimentation complémentaire sur un sous-ensemble de 18 génotypes de pois, inoculés chacun séparément avec chacune des cinq souches de Rlv, a révélé que la plante ne s’associe pas toujours préférentiellement avec la souche de rhizobium qui permet la fixation symbiotique la plus efficace. Des effets d’interaction pois x rhizobium ont été mis en évidence. Cette expérimentation a montré la grande variabilité de l’interaction symbiotique entre pois et Rlv et son importance pour l’établissement d’un rendement optimal. Des expérimentations supplémentaires permettront de préciser les déterminants génétiques de la plante et de la bactérie qui pilotent les capacités d’association des partenaires symbiotiques et/ou leurs efficacités. Des stratégies d’inoculation des semences de pois par des bactéries rhizobiacées, qui sont actuellement très peu pratiquées en Europe, combinées à une meilleure prise en compte de l’interaction symbiotique dans les processus de création de variétés sont des leviers à travailler pour accroître les performances des légumineuses dans des systèmes de cultures à bas intrants

Genetic diversity and trait genomic prediction in a pea diversity panel

Background: Pea (Pisum sativum L.), a major pulse crop grown for its protein-rich seeds, is an important component of agroecological cropping systems in diverse regions of the world. New breeding challenges imposed by global climate change and new regulations urge pea breeders to undertake more efficient methods of selection and better take advantage of the large genetic diversity present in the Pisum sativum genepool. Diversity studies conducted so far in pea used Simple Sequence Repeat (SSR) and Retrotransposon Based Insertion Polymorphism (RBIP) markers. Recently, SNP marker panels have been developed that will be useful for genetic diversity assessment and marker-assisted selection. Results: A collection of diverse pea accessions, including landraces and cultivars of garden, field or fodder peas as well as wild peas was characterised at the molecular level using newly developed SNP markers, as well as SSR markers and RBIP markers. The three types of markers were used to describe the structure of the collection and revealed different pictures of the genetic diversity among the collection. SSR showed the fastest rate of evolution and RBIP the slowest rate of evolution, pointing to their contrasted mode of evolution. SNP markers were then used to predict phenotypes - the date of flowering (BegFlo), the number of seeds per plant (Nseed) and thousand seed weight (TSW)-that were recorded for the collection. Different statistical methods were tested including the LASSO (Least Absolute Shrinkage ans Selection Operator), PLS (Partial Least Squares), SPLS (Sparse Partial Least Squares), Bayes A, Bayes B and GBLUP (Genomic Best Linear Unbiased Prediction) methods and the structure of the collection was taken into account in the prediction. Despite a limited number of 331 markers used for prediction, TSW was reliably predicted. Conclusion: The development of marker assisted selection has not reached its full potential in pea until now. This paper shows that the high-throughput SNP arrays that are being developed will most probably allow for a more efficient selection in this species

High-density genotyping of pea and faba bean diversity panels using exome capture

International audienceGenome-wide association studies (GWAS) represent a powerful tool to decipher the geneticdeterminism of complex traits in crop plants and to identify responsible genes. As GWAS require large diversitypanels segregating for the traits of interest, one faba bean and three pea collections were constituted toaddress different questions in the PeaMUST project. The faba bean panel comprises 248 accessions comingfrom five continents and displaying the phenotypic diversity of the species. The first pea collection includes239 accessions that represent the species diversity for aerial and root architecture and for biotic and abioticstress responses. The second and third pea panels were constituted with 300 accessions of cultivated springtype, 396 accessions of winter type, accessions (376 conventional, hr, 20 Hr) respectively. To generate a largenumber of unbiased genetic markers, exome capture [1] was performed by taking advantage of (i)transcriptome sequence resources available for pea [2,3], and (ii) newly developed transcriptome for fababean. The designed probes allowed capturing over 33,000 transcripts in faba bean and 50,000 transcripts inpea. In total, 1.7 and 2.3 million high-quality SNPs have been identified for faba bean and pea, respectively.These markers have been used to assess the genetic structure of the different panels, to perform GWAS fortraits of agricultural interest and to design genotyping by capture experiments to undertake genomic selection[4]. These SNP resources will serve to design genotyping arrays in both crops for further experiments

High-density genotyping of pea and faba bean diversity panels using exome capture

International audienceGenome-wide association studies (GWAS) represent a powerful tool to decipher the geneticdeterminism of complex traits in crop plants and to identify responsible genes. As GWAS require large diversitypanels segregating for the traits of interest, one faba bean and three pea collections were constituted toaddress different questions in the PeaMUST project. The faba bean panel comprises 248 accessions comingfrom five continents and displaying the phenotypic diversity of the species. The first pea collection includes239 accessions that represent the species diversity for aerial and root architecture and for biotic and abioticstress responses. The second and third pea panels were constituted with 300 accessions of cultivated springtype, 396 accessions of winter type, accessions (376 conventional, hr, 20 Hr) respectively. To generate a largenumber of unbiased genetic markers, exome capture [1] was performed by taking advantage of (i)transcriptome sequence resources available for pea [2,3], and (ii) newly developed transcriptome for fababean. The designed probes allowed capturing over 33,000 transcripts in faba bean and 50,000 transcripts inpea. In total, 1.7 and 2.3 million high-quality SNPs have been identified for faba bean and pea, respectively.These markers have been used to assess the genetic structure of the different panels, to perform GWAS fortraits of agricultural interest and to design genotyping by capture experiments to undertake genomic selection[4]. These SNP resources will serve to design genotyping arrays in both crops for further experiments