Search

Legumes, and especially pulses, are an important source of protein for food and feed, and are appreciated for their positive impact on the “one health”. However, their unstable yields and their susceptibility to biotic and abiotic stresses highlight the need for varietal improvement in order to increase the cultivated areas and productivity. With the advent of sequencing technologies, a large pool of genetic and -omics resources, heterogeneous at the inter- and intra-species scale, is emerging. Thus, it is important to capitalize on these scattered heterogeneous data to develop translational research to boost breeding projects and crop diversification. To meet this need, we undertook the development of the Orthology-driven knowledge base framework for translational research (Ortho_KB). For a set of species of interest, it infers orthologous relationships between genes, proposes associated syntenic blocks between chromosomes and creates a graph database linking genetic and RNA-seq data. To explore the possibilities of this framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. This database includes four cultivated crops, namely Pisum sativum, Vicia faba, Lens culinaris and Vigna radiata, and the model legume Medicago truncatula. Available information on quantitative trait loci (QTL) for multiple traits are being integrated as well as expression data. The proposed database model was evaluated by studying the conservation of a flowering-promoting gene

National audience

Legumes, and especially pulses, are an important source of protein for food and feed, and areappreciated for their positive impact on the “one health”. However, their unstable yields andtheir susceptibility to biotic and abiotic stresses highlight the need for varietal improvement inorder to increase the cultivated areas and productivity. With the advent of sequencingtechnologies, a large pool of genetic and -omic resources, heterogeneous at the inter- and intraspecies scale, is emerging. Thus, it is important to capitalize on these scattered heterogeneousdata to develop translational research and boost breeding projects and crop diversification.To meet this need, we undertook the development of NeoLeg, a NoSQL graph-based databaseusing Neo4j, dedicated for translational research in pulses. Starting from genome sequencesand annotation files, we inferred orthologous relationships between genes, and proposedassociated syntenic blocks between the chromosomes of four cultivated crops, namely Pisumsativum, Vicia faba, Lens culinaris and Vigna radiata, and model legume Medicago truncatula.Available information on quantitative trait loci (QTL) for multiple traits are being included aswell as expression data. The proposed modeling was evaluated in studying the conservation ofa flowering-promoting gene. The main achievements as well as remaining challenges andperspectives will be discussed

Les légumineuses sont capables d’accumuler des quantités importantes de protéines dans leurs graines même en l’absence d’engrais azoté, ce qui fait d’elles des espèces à haut potentiel pour relever les défis alimentaires et accompagner la transition agroécologique. Des avancées génétiques ont permis de réduire la présence de certains facteurs « anti-nutritionnels » dans les graines de pois et de féverole (exemple des variétés pauvres en tanins, en inhibiteurs trypsiques, ou en vicine et convicine). Afin de promouvoir l’utilisation de ces graines en alimentation humaine, il est nécessaire d’aller plus loin dans l’amélioration de leur valeur nutritionnelle, en termes de teneur et composition en protéines, d’équilibre en acides aminés, de goût, mais aussi de résistance vis-à-vis des insectes, notamment les bruches qui se nourrissent des cotylédons. A cet effet, le levier de la sélection peut s’appuyer sur une diversité génétique naturelle et/ou induite pour ces caractères, révélée dans des travaux récents. Cette variabilité sera présentée, ainsi que les outils mobilisables pour mieux adapter les graines de légumineuses aux usages alimentaires. Parmi ces outils, est le déploiement des approches translationnelles pour l’étude de la conservation des déterminants génétiques et le transfert d’acquis entre espèces légumineuses (Medicago truncatula, pois, féverole, lentille).

National audience; Présentation de l'Atelier :Les protéines sont des macronutriments majeurs dans l’alimentation des hommes et des animaux. Or la production de protéines végétales est toujours déficitaire en France qui a recours à des importations pour couvrir ses besoins.Les légumineuses contiennent plus de protéines que les céréales. En outre, leur culture contribue à la mise en œuvre de systèmes moins demandeurs en intrants qui peuvent ainsi, seuls, en rotation ou en mélange, contribuer efficacement à la démarche one health, vers une meilleure santé globale des hommes, des animaux, des cultures et de l’environnement. Améliorer la qualité des protéines végétales, tout en maintenant voire en augmentant le rendement est un objectif à poursuivre.Dans ce contexte, l’atelier a pour but de rapprocher les communautés de recherche en alimentation, en biologie végétale et en amélioration des plantes, des secteurs public et privé, afin de dégager les priorités communes interdisciplinaires.Cet atelier se tiendra soit sous forme de webinaire, soit en présentiel, en fonction de l'évolution de la situation sanitaire.

Le protéome des graines en développement de lignées recombinantes issues du croisement entre desgénotypes de féverole résistants et sensibles aux bruches a été étudié par l’approche shotgun. Cetravail a permis d’identifier 749 protéines au début du remplissage des graines, dont 80 sontdifférentiellement accumulées entre les lignées sensibles et résistantes aux bruches. En plus de fournirun premier aperçu des protéines présentes à ce stade clé du développement des graines chez laféverole, ces données ont fait émerger des protéines candidates pour améliorer la résistance desgraines aux bruches. Parmi les protéines préférentiellement accumulée dans les lignées résistantes estune glycoprotéine pariétale inhibitrice des polygalacturonases d’origine pathogène qui dégradent lesparois cellulaires végétales. Cette glycoprotéine est donc susceptible de jouer un rôle clé dans lesmécanismes de défense lors du développement des graines. Ces résultats et les perspectives visant àmieux comprendre les mécanismes de résistance des graines de légumineuses aux bruches serontprésentés.

Legumes, and especially pulses, are an important source of protein for food and feed, and are appreciated or their positive impact on the “one health”. However their yields are sometimes unstable and their tolerance to some biotic and abiotic stresses highlight the need for varietal improvement to increase the cultivated area and stabilize the production.With the advent of sequencing technologies, a large pool of genetic and genomic resources, heterogeneous at the inter- and intra-species scale, is emerging. Thus, it is now time to capitalize on these scattered heterogeneous data to develop translationnal research and boost breeding projects.To meet this need, we undertook the development of NeoLeg, a graph-based database using Neo4j and dedicated for translational research between legumes. Starting from genome sequences and annotation files, we inferred orthologous relationships between genes, and proposed associated syntenic blocks between the chromosomes of four pulse species, namely Pisum sativum, Vicia faba, Lens culinaris and Vigna radiata, and model legume Medicago truncatula. Available information on quantitative trait loci (QTL) for multiple traits are being included. The proposed modeling was tested in basic case studies and for other scenarios related to the identification of the genetic determinants of resistance to an insect pest. The main achievements as well as remaining challenges and perspectives will be discussed.

National audience

Pea (Pisum sativum L.) is the second most important grain legume in the world after common bean and Gregor Mendel’s original genetic model. With a genome size of 4.3Gb and a large amount of transposable element, Pisum sativum was lagging behind other important legume crops for genomics development. We reported the first annotated chromosome-level reference genome assembly for pea (J. Kreplak et al 2019). Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from it’s sister tribes. Other species like Vicia faba, with genome larger than pea, are still not sequenced and the sequence of pea is a valuable resources to have insight on gene conservation and tackle translational genomics approaches.

The tribe Fabeae comprises more than 300 legume species, including some of the most ancient and important crops like Pisum sativum (pea), Lens culinaris (lentil), and Vicia faba (faba bean) used for food and feed. The genome sequence of pea, released in 2019, is an important milestone for the community working on legumes and especially on Fabeae. It brings into light evidences related to the genome expansion that occurred after the divergence of Fabeae from their sister tribes and highlights different chromosomal rearrangement events specific or not to the Pisum lineage. The pea genome sequence also represents a valuable resource to accelerate our understanding of the molecular basis of agronomically important traits and support breeding efforts. Great opportunities to address current agriculture challenges through genomics-based breeding and translational research projects are currently available. They are crucial for improving legume production and maintaining agricultural sustainability in the context of current and future agricultural challenges.

The transition from a standalone phenotypic selection to a marker-assisted selection has been seen as a great step forward to improve the breeding process and reach the expected goals. More recently, the genomic revolution has also had its great impact on breeding. -omics are now part of the required toolkit for a successful, cost and time-efficient breeding. The genome sequence of pea (Pisum sativum) has been made available in 2019 through a collaborative international effort. This is a great tool for the pea community in general and the Fabeae community in particular. Current challenges facing pea and other Fabeae production are numerous. A large number of traits has also to be tackled in order to adapt the products to the various intended markets while guaranteeing their quality and quantity. This talk will highlight ongoing efforts to take pea breeding to the next step with genomics-assisted breeding. Examples will be given to illustrate how the pea resource is also important for lentil and faba bean programs.

International audience

International audience; Having a genome sequence available is a critical step towards unravelling functional diversity andestablishing genome-enabled breeding. The recently generated pea genome sequence represents a great toolfor genomicists, geneticists and breeders not only for the pea community but also for legume research. In thegenome project, re-sequencing data revealed the considerable diversity present in the Pisum genus. In thePeaMUST project, an unprecedented effort was made to genotype large pea collections using the exomecapture technology. This high-density SNP data was exploited in genome-wide association studies (GWAS) ona large number of traits related to yield, as well as response to biotic and abiotic stresses. Comparative GWASand meta-QTL analysis identified important putative loci involved in the control of yield and its components inpea. Furthermore, genomic selection strategies have been developed in order to tackle complex traits such asyield regularity and improve selection efficiency. We will present snapshots of these results and discusspotential transfer of knowledge from pea to related crops.

National audience

International audience; Genome-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.

National audience; Introducing legumes in modern cropping systems increases crop diversity and reduces the use of external inputs. It thus contributes to achieving sustainable food and feed production. Lentil (Lens culinaris Medik.) is an environmentally friendly, nutritious, protein-rich legume food crop. It is grown in a wide range of climatic conditions and fixes atmospheric nitrogen through bacterial symbiosis. In France, lentil cultivated areas are continuously increasing but are still largely inferior to the areas cultivated with cereals or other legumes such as pea and faba bean. One of the most serious problems for lentil cultivation is due to the insect pests known as seed beetles (Coleoptera, Bruchinae). Their larvae feed on developing seeds provoking severe yield losses. Lentil is also susceptible to root rot. Various fungal and fungus-like organisms including Aphanomyces and Pythium make up a disease complex and provoke poor root development and stunting/yellowing of aerial parts. The French research project called RésiLens (2019-2021), funded by the special allocation account for agriculture and rural development (CasDAR), aims at addressing these urgent questions. Seven public and private partners will be working together to characterize the diversity of a lentil collection comprising 300 accessions at the phenotypic and molecular levels. Phenotyping trials under different environments will allow generating knowledge about lentil response to main stresses and identifying resistant genitors for breeding.

National audience

Prod 2019-213a BAP GEAPSI INRA; National audience

National audience; The INRA Plant Biology and Breeding division works together with the breeding company Agri Obtentions under the LAGoPEDE project to develop performant grain legume varieties for tomorrow’s agriculture. Grain legumes represent an important source of proteins for food and feed. One of the main targets of LAGoPEDE is to increase the area of cultivation and improve the seed quality of faba bean (Vicia faba) in France, by developing performant winter varieties well adapted to the North-East of the country. A frost tolerance screening of a diverse germplasm collection of 1,500 faba bean accessions available at INRA, Dijon was first conducted. Eleven frost-tolerant accessions were selected as genitors in LAGoPEDE. Considering the objective of producing FEVITA varieties, i.e. seeds with zero tannin and low vicine-convicine content, crosses between frost genitors and Mandoline, a FEVITA spring cultivar were performed. Additional crosses were made with genotypes exhibiting partial levels of tolerance to seed beetles (Coleoptera, Bruchinae) [1], an increasing problem for faba bean production. Phenotypic genealogical selection has essentially been undertaken for frost tolerance. Marker-assisted selection has been used to select low vicine-convicine genotypes [2]. LAGoPEDE will soon benefit of the outcomes of the PeaMUST project to include the SNP markers linked to quantitative trait loci responsible for bruchid and frost tolerance in the selection process.

Prod 2019-88ff BAP GEAPSI INRA; National audience; Seed weevils (Bruchus spp.) are major pests of pulses, causing yield losses and affecting marketability 1,2 . Available insecticides have low efficiency and important negative impacts on the environment, humans and non-target organisms. Therefore, breeding resistant varieties represent the most promising strategy to overcome seed weevils. The pyramiding of several resistance genes in cultivars is an important objective because this will make the resistance more durable and suitable for sustainable agriculture. The PeaMUST project (ANR-11-BTBR0002) aims at discovering the mechanisms of tolerance and resistance to bruchids in pea (Pisum sativum L.) and faba bean (Vicia faba L.) crops and identifying the functional candidate genes for future implementation in Genomics-Assisted Breeding (GAB). A multidisciplinary approach that includes Genome- Wide Association Studies (GWAS), Quantitative trait locus (QTLs) mapping, RNA sequencing (RNA-Seq), shotgun proteomics and Volatile Organic Compounds (VOCs) analysis has been used to identify potential candidate genes for resistance to bruchids. The results will provide (i) original basic knowledge about resistance strategies in pea and faba bean, the candidate genes underlying quantitative resistance to bruchids and its conservation in other legume species, as well as, (ii) innovative applied knowledge and tools for breeding pea and faba bean varieties resistant to bruchids, which will be useful in future strategies of durable resistance management.

National audience; Comme source de protéines, tant pour l’alimentation humaine qu’animale, les variétés de légumineuses àgraines et fourragères qui ont la capacité d’utiliser la ressource azotée de l’air, constituent des leviersimportants pour la construction d’une agriculture durable. Que ce soit en Europe ou en Afrique du Nord, uneforte demande variétale se développe pour les légumineuses, afin de répondre au besoin d’une diversitéd’espèces et de systèmes de culture pourvoyeurs de services alimentaires, environnementaux etécologiques. Un progrès génétique a été fait au courant des dernières décennies mais reste limité à cause deverrous biotechniques, financiers et parfois organisationnels au sein des filières.Le marché des semences de légumineuses se caractérise par une forte proportion de semences de ferme(souvent > 50%). Ceci affaiblit la filière semencière, les investissements en sélection et recherche, et parconséquence le renouvellement variétal. Nous décrirons plus en détail cette situation par des données dumarché des semences et des variétés illustrant des différences entre les espèces de légumineuses et desdivergences-convergences entre les contextes France-Afrique du Nord. La dynamique insufflée par leCatalogue des Espèces et variétés constitue un pilier fondamental du secteur semencier formelprépondérant en France alors qu’en Afrique du Nord, un secteur informel peu régulé prédomine.Une grande diversité de légumineuses est conservée en ex-situ dans d’importantes collections nationales etinternationales qui seront présentées. En Afrique du Nord, les dispositifs de gestion à la ferme desressources génétiques sont aussi une composante déterminante de la gestion de la diversité. Les actions depréservation et de caractérisation phénotypique des ressources génétiques ont un coût important, mais sontessentielles pour la construction et l’adaptation d’une diversité variétale composée de formes améliorées,traditionnelles ou de mélanges, comme facteur de résilience.Pour les systèmes agricoles marginaux mobilisant peu d’intrants dans les conduites agricoles, le leviervariétal est une composante clé du progrès agronomique. Des actions d’amélioration génétique participativesont souvent mises en place pour permettre l’exploitation des spécificités des variétés locales tout endiversifiant les objectifs d’utilisation (qualité nutritionnelle, résistance aux stress biotiques et abiotiques …).Nous évoquerons quelques exemples.La mobilisation des avancées scientifiques pour des fins de sélection, notamment par l’utilisation des outilsmoléculaires, est divergente entre la France et l’Afrique du Nord. Le programme collaboratif français sur lespois d’hiver à semis précoce (pois Hr) est un exemple d’une action très intégrée filière-sélectionneurrecherche.D’autres programmes de recherche nationaux et internationaux ont permis aussi un gain detemps et d’efficacité par l’introduction d’une sélection multi-caractérielle, assistée par marqueurs et ledéploiement d’une approche translationnelle qui vise à transférer les connaissances acquises sur une espèce vers une autre. L’utilisation des résultats de recherche est plus modeste en Afrique du Nord où la sélectionreste essentiellement phénotypique.Les 50 dernières années de recherche et de sélection ont apporté un progrès génétique certain mais encoreinsuffisant. Si l’amélioration des rendements reste un objectif important, des attentes plus précises sontexprimées et font l'objet de travaux de génétique et d'amélioration. On enregistre, à titre d’exemple, desattentes montantes sur les résistances aux stress hydriques et thermiques et aux bio-agresseurs dans uncontexte de changement climatique, de réduction de l’usage des pesticides et de développement del’agroécologie. De multiples questions sont transversales entre les espèces et sont communes à la France età l’Afrique du Nord. Nous en parlerons.

National audience

BAP GEAPSIBAPGEAPSI; Legume use in arable rotations provides several significant ecological services that can help to meet the challenge of delivering high quality food in an environmentally sustainable manner. Among legumes, pea has long been a model species for geneticists. But despite its major role in the discovery of the laws of genetics by Mendel, the keys to decipher the impressive phenotypic diversity of the species have been lacking until recently. Under the impetus of large national and international programs, and driven by innovations in informatics and biotechnology, useful genomic resources are now available in pea. High precision mapping of the pea genome, an atlas of the expression of its genes in many tissues, and the ongoing sequencing of its genome are valuable tools for dissecting the genetic determinism of traits of interest and ultimately select new varieties more effectively for these traits. In order to develop novel pea varieties and optimize seed yield and quality regularity in the context of pesticide reduction and climate change, different complementary approaches are used: (i) develop genomic selection programs based on naturally occurring variability, (ii) enhance gene discovery through comparative mapping, and (iii) create innovative plant architecture ideotypes by screening mutations and symbiotic biological regulations. Thanks to the high conservation of synteny, that is to say, the order of genes on the genome, between peas and other legumes species, knowledge gained on peas will be useful to accelerate progress in the species’ close relatives such as fava beans.

BAP GEAPSI BAP GEAPSIBAPGEAPSI; Pea (Pisum sativum L.) was the original model organism for Mendel´s discovery of the laws of inheritance and kept this model status until the advent of molecular biology at the end of the 20th century. Pea is also one of the world’s oldest domesticated crops. It is currently the third most widely grown pulse crop, as its seeds serve as a protein-rich food for humans and livestock alike. While several legume species genome's draft sequences have been produced, progress in pea genomics has lagged behind largely as a consequence of its complex and large genome size. The pea genome is large (ca 4.45 Gb), probably resulting from recent expansion of retrotransposons followed by sequence diversification. The Pea Genome International Project has undertaken several complementary strategies in order to produce a high-quality draft sequence of the species. We will present how this draft sequence opens the way to renew strategies in pea breeding.

Linkage disequilibrium (LD) decay in the pea-Aphanomyces collection. Coloured curves represent the estimated LD decay for each linkage group (LG). Dashed horizontal lines represent half of the maximum LD value (LD threshold=0.5). Arrows represent the LD decay rate, as the estimated genetic distance (cM) to drop to the LD threshold on each LG. (PDF 157 kb)

Clustered heatmap of correlation coefficients between disease resistance, earliness and height variables data. Variables are coded as described in Additional file 4. Only correlations with a p-value < 0.05 are shown. Colours represent level of correlation, coded as follow: dark red: r < −0.8; medium red: −0.8 < r < −0.5; light red: −0.5 < r < −0.2; white: −0.2 < r < 0.2 or p-value > 0.05; light green: 0.2 < r < 0.5; medium green: 0.5 < r < 0.8; dark green: r > 0.8. Clustering is based on the UPGMA method. (PDF 48 kb)

Frequency distribution of least square means obtained for Aphanomyces resistance, earliness and plant height in the pea-Aphanomyces collection. Least square means were obtained from analysis of variance for three Aphanomyces resistance traits (Root Rot Index, first and second Aerial Decline Indexes, coded RRI, ADI1 and ADI2, respectively), three earliness traits (dates to 50 % bloom, 100 % bloom and 100 % dried plants, coded FLO1, FLO2 and RIPE, respectively) and plant height (HT). Aphanomyces resistance traits were assessed over nine infested field environments and against two reference strains of A. euteiches (RB84 and Ae109) in controlled conditions. Earliness and height were assessed in two healthy environments. n: total number of pea lines assessed; m: mean ± standard deviation of the pea-Aphanomyces collection; h2: mean-based heritability. (PDF 38 kb)

Clustered heatmap of the Kinship matrix. Kinship matrix from the GAPIT R package [75] based on 2937 SNP markers. Clustering is based on the UPGMA method. Colours represent the degree of relationship between two given lines. Pea line information is described as in Additional file 1. Lines sharing same pedigree or end use or sowing type are well clustered thus the Kinship matrix efficiently represents the relationships between individuals. (PDF 1253 kb)

Example of MLMM R package plot outputs for analysis of the MFA.Dim.1 variable. (A): Bonferroni correction of the highest marker p-value for each step of the forward and backward analysis. Optimal step (dashed blue vertical line) is determined as the largest stepwise mixed model regression in which all cofactors have –log10(p-value) above the mBonf threshold (dashed black horizontal line). (B): QQ-plot at the optimal step. (C): Partition of variance for each forward and backward step. Variance explained by population structure (PCA; grey); all markers used as cofactors (blue); Kinship matrix (green) and unexplained variance (= missing heritability; red). The dashed blue vertical line represents the optimal step according to mBonf threshold. (D) Genome-wide Manhattan plot without marker cofactors. The dotted line represents the multiple-Bonferroni threshold above which markers are considered as significant. (E): Genome-wide Manhattan plot at the optimal step with marker cofactors (4 red dots). The dotted line represents the multiple-Bonferroni threshold above which markers are considered as significant. (PDF 148 kb)