Use of translational genomics to identify genes important for legume seed filling

International audience; Translational genomics, i.e., the transfer of genetic information from model species to cultivated crops, is on the brink of revolutionizing plant breeding. The recent publication of genomic sequences for several cultivated legumes is also accelerating this process. For pea, recent highthroughput RNA sequencing, and the prospect of a genome sequencing project, will further accelerate the transfer of information from the Medicago truncatula model to the cultivated crop. We have been using genomics approaches with Medicago as a tool to identify key genes determining seed yield and composition in closely related legumes. Analyses of the proteome and transcriptome of the…

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

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 pan…

A workflow to assemble plant mitochondrial genomes using long-reads: case study in Pisum sativum and Phaseolus vulgaris

Plant mitochondrial genomes are generally not used to study evolution within and between species. They are larger than animal mitochondrial genomes and evolve by accumulating rearrangements rather than mutations [1]. These characteristics make it difficult to obtain complete assemblies using short-reads like in mammals. To address this problem, we developed and tested a plant-based assembly workflow using Nanopore and Pacbio long-reads from Pisum sativum and Phaseolus vulgaris, respectively. Nanopore long-reads from Pisum sativum whole genome sequencing and Pacbio long-reads from Phaseolus vulgaris whole genome sequencing were mapped on all mitochondrial genomes available for legumes at NCB…

Beyond the sequencing of the pea genome: opportunities for genomics-based breeding and translational approaches

International audience; 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 th…

The pan-transcriptome of Vicia faba

Vicia faba (faba bean) is a nitrogen-fixing protein crop that, in contrast to soya bean, yields well in temperate climates. It is diploid but has a very large genome of ~13 Gb, and genomic resources are currently limited. To provide a high-quality reference gene set and expression atlas, we have carried out RNA-seq of multiple tissues from five faba bean accessions. For each tissue, an assembly was produced using the Trinity software package using both Illumina and PacBio reads. For each accession, the assemblies were then merged to create a more complete reference gene set. The assemblies were of high quality, with more than 95% complete BUSCOs [1] and read mapping rates of ~90%. The assem…

Pea in the genomic era

Analysis of eIF4E gene sconfering resistance to Pea seed-borne mosaic virus (PSbMV) and other potyviruses in pea

Pea seed-borne mosaic virus (PSbMV) belongs among the most frequent viral pathogens causing severe losses in field pea and other legumes. These losses might be prevented by growth of resistant varieties. Resistance to the common P1 strain of PSbMV isconferred by a single recessive gene (eIF4E), localized on LG VI (sbm-1 locus), while to lentil L1 strainis localized on LGII atsbm-2locus. Gene-specific single nucleotide polymorphism and co-dominant amplicon length polymorphism markers were developed. From the comparison of genotype verses phenotype for selection of resistance/susceptibility in F2 plants, there was a 26% discrepancy between the PCR and ELISA-based assays with potentially susce…

Plant resistance and architecture for protection of pulses against pathogens

Prod 2019-213c BAP GEAPSI INRA; National audience

Key Note speaker Plant resistance and architecture for protection of pulses against biotic stresses

Prod 2019-88l BAP GEAPSI INRA DOCT; National audience; Major diseases and pests, such as root rots, ascochyta blights and aphids, are limiting factors to cool season pulse production in many countries worldwide, especially in Europe. In the context of pesticide reduction, plant genetic resistance and architecture are main traits that can be mobilised in breeding for disease and pest management. Knowledge of quantitative resistance to major diseases and pests of pea and faba bean in France has benefited from the development of sequenced genomes and massive SNP markers [1], which have recently been highly valuable to identify candidate genes controlling resistance. Fine mapping and sequencing…

Comparative genome-wide-association mapping identifies common loci controlling root system architecture and resistance to Aphanomyces euteiches in pea

BAP GEAPSI INRA; International audience; Plant architecture can contribute to decrease plant susceptibility to pathogens by favoring mechanisms leading to infection escape or increased tolerance. Combining genetic resistance with architectural traits that can negatively impact disease development is thus a strategy of great interest to reduce epidemics. Until now, most strategies exploiting plant architecture have focused on the aerial parts of plants. Few studies have been done on the identification of root system architecture (RSA) traits limiting root disease development and even less on their use in breeding. Aphanomyces euteiches, a soil-borne pathogen infecting roots, is a major limit…

Use of translational genomics to identify genes important for legume seed development

BAP Pôle GEAPSI; International audience; We have exploited the extensive synteny between the model legume Medicago truncatula and the cultivated garden pea, Pisumsativum, to identify loci controlling seed filling and seedcomposition in the crop species. QTLs for these traits are mapped by analyzing variation with in collections of recombinant inbred lines. Candidate genes with in the QTL intervals are identified by reference to the M.truncatula genomic sequence. This approach was used to uncover an endosperm subtilase that is associated with syntenic seed weight QTLs in Medicago and pea, and we discuss the possible role played by this enzyme in contributing to final seed weight.

The Pea genome and after...

The Pea genome and after …

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 ab…

The role of sulfur in the control of seed quality traits in legumes: from model to crop species

National audience; voir pdf

Pea Genomics : What Else ?

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 expr…

Towards bruchid resistance in pulses

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 sativ…

Regulation of legume seed size by an endosperm-expressed transcription factor

BAP Pôle GEAPSI; International audience; There are numerous reports of transcription factors (TFs) which are implicated in the control of seed size and seed composition. We have identified, using a platform of TF sequences derived from the Medicago truncatula genome sequence, a class of TFs specifically expressed during the seed filling stage. One such TF, DASH, was shown to be confined to the developing endosperm. We investigated the role played by DASH through analysis of mutant alleles. These give rise to seed-lethal or near-lethal phenotypes, with degeneration of the endosperm and arrested embryo development. The relation of this phenotype to seed auxin action was investigated.

RésiLens: A research project aiming at identifying bruchid and root rot resistance sources in lentil (Lens culinaris)

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 …

Development of new plant resources (genetic resources and ril populations) in [i]Vicia faba[/i] L. for genetic studies

BAP GEAPSIBAPGEAPSI; absent

GRaSP project Genetics of Rhizobia Selection by Pea

Prod 2019-88aa; National audience; Because of their ability to fix nitrogen in symbiosis with soil bacteria, legumes such as peas have an important role to play in the development of a sustainable agriculture. However, in the field, biological nitrogen fixation (BNF) could be suboptimal as natural Rhizobium leguminosarum viciae (Rlv) populations are quantitatively and qualitatively heterogeneous, with strains varying in their competitiveness and efficiency of BNF [1,2]. There is a general agreement concerning the interest of Rlv inoculation for improving BNF and thus pea yield [3]. However, even when pea seeds are inoculated by efficient Rlv strains these can be outcompeted by indigenous rh…

Bruchid resistance in pulses

Prod 2019-213a BAP GEAPSI INRA; National audience

Co-concepdes variétés de féveroles à valeur nutritionnelle améliorée pour l'homme et l'animal : cible de la sélection réaliste, permise par la variabilité génétique disponible et par les outils moléculaires développés en appui à la selection variétale

National audience

Genetic diversity of nodulated root structure and nitrogen nutrition in a core collection of pea

Pea (Pisum sativum) is the third most important grain legume worldwide, and the increasing demand for protein-rich raw material for animal feed or human nutrition has led to a greater interest in this crop as a protein source. Moreover, legumes do not need nitrogen (N) fertilizers, thanks to their natural ability to use, as main N resource, the atmospheric N2 from symbiosis in nodules with Rhizobiaceae spp. However, N nutrition can still be a limiting factor of yield and seed quality in legumes because nodules are very sensitive to their local environment, in particular to nitrate, and root systems of N2 fixing legumes are poorly developed, which makes them unable to explore a large soil vo…

Taking cool-season grain legume breeding to the next level: the key role of the pea genome sequence

International audience; 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 h…

The roles of the embryo-surrounding tissues in regulating Medicago truncatula seed filling

National audience

Association of SNP markers with pea grain protein and grain yield traits in Italy : preliminary results

Grain yield and quality are the main economically important traits in breeding of field pea (Pisum sativum L.). The objective of our work was investigating trait-marker associations in elite pea germplasm, with the final aim to develop marker-assisted selection procedures for these traits. The genetic base for this study was represented by three connected recombinant inbred line (RIL) populations obtained from paired crosses between three genotypes (the varieties Attika, Isard and Kaspa) which featured different geographical origin and outstanding adaptation to Italian cropping environments. At least 86 F7 lines per RIL generated by single-seed descent were evaluated for grain yield, plant …

Phylogeny and gene expression analyses of ammonium transporters (AMT) induced by mycorrhization and nodule symbiosis among Papilionoideae subfamily

The study of plant-microbe associations through nutrient exchanges has significantly improved our understanding of plant microbiome. Legume plants establish mutualistic associations with both rhizobial bacteria and arbuscular mycorrhizal fungi [1]. These symbioses improve mineral plant nutrition and increase plant resistance against biotic and abiotic stresses. Plant-microbe associations provide key features for the current agricultural and environmental challenges [2]. Translocation mechanisms of nitrogen from the fungal and rhizobial symbiotic interfaces to the plant are not well-defined yet. In Poaceae plant, inductions of specific ammonium transporters (AMT) genes [3, 4] and nitrogen/pe…

Complementary approaches towards the discovery of genes controlling yield in pea

International audience; Pea is one of the most important grain legumes in the world. Improving pea yield is a critical breedingtarget in the current context of consumers’ increasing demand for plant proteins for food and feed. Becauseof its polygenic nature and the impact of the environment, breeding for higher yield is challenging. Weinvestigated the genetic determinism of yield (SW), seed number (SN) and thousand seed weight (TSW) usingboth linkage and linkage-disequilibrium approaches.Nine interconnected mapping populations, representing a total of 1,213 recombinant inbred lineswere phenotyped for SW, SN and TSW in six different field environments. These lines were genotyped usingthe Gen…

The pea genome and beyond

International audience; The recently generated pea genome sequence is a significant step for the pea research community towards unravelling functional diversity and establishing genome-enabled breeding. Re-sequencing data reveal the considerable diversity present in the Pisum genus. High-throughput genotyping is now available to explore large collections using the exome capture technology in genome-wide association studies (GWAS) or tackle map-based QTL cloning. Furthermore, genomic selection strategies have been developed in order to tackle complex traits such as yield regularity and improve selection efficiency. We will present snapshots of these results and discuss potential transfer of …

Le système racinaire nodulé du pois : un rôle pivot pour sa stabilité sous contraintes hydriques fluctuantes

National audience; Dans le contexte du changement climatique, des épisodes de stress hydrique plus fréquents sont attendus, entraînant des modifications de nutrition, de croissance des plantes, et donc des pertes de rendements. Chez les plantes légumineuses, telles que le pois protéagineux, un stress hydrique du sol diminue drastiquement l’acquisition de l’azote (N) par la fixation symbiotique du N2 atmosphérique, conduisant à une carence azotée de la plante et pouvant diminuer le rendement de 30 à 60% suivant les variétés. Il apparait donc nécessaire de sélectionner des génotypes de pois mieux adaptés à la sécheresse. Dans cette étude, les réponses architecturales, physiologiques et transc…

Genetic diversity of nodulated root structure in a very diverse pea collection

National audience; The root system is responsible for nitrogen (N) acquisition, which in legumes, combines mineral acquisition and symbiotic fixation in nodules. Despite these two complementary pathways, N nutrition may be a limiting factor of legumes yield because nodules are very sensitive to their local environment and N fixing legume root system is poorly developed which may limit soil exploration [1]. Pea establishes in root nodules a symbiotic association with Rhizobium leguminosarum sv viciae bacteria (Rlv) [2]. This study assessed the potential of naturally occurring genetic variability of nodulated root structure and functioning traits to improve yield pea performance. Two successi…

Identifications des gènes sous-jacents à un QTL de tolérance au gel chez le pois

Prod 2018-220o BAP GEAPSI INRA; National audience

Pea in the genomic era

Pea in the genomic era. Séminaire IFR AIB (Agrobiosciences, Interactions & Biodiversité)

Identification of genes underlying frost tolerance within a pea QTL

Prod 2019-88dd BAP GEAPSI INRA; National audience; Seeding legumes in autumn would allow increasing and regulating yield, but requires to improve the level of frost tolerance in varieties, which motivates the interest in deciphering the genetic determinism of this trait. In pea (Pisum sativum L.), this character is controlled by a few quantitative trait loci (QTL) that were identified by the analysis of RIL populations derived from contrasted genotypes, such as Champagne (Ch, tolerant) x Térèse (Té, sensitive), or by association analysis [1,2,3]. We study a QTL located on the pea linkage group 6 (WFD6.1), which accounts for a large part of frost tolerance variability, making it a choice tar…