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1. Identification of QTLs associated with seed protein concentration in two diverse recombinant inbred line populations of pea

Author

Krishna Kishore Gali, Ambuj Jha, Bunyamain Tar’an, Judith Burstin, Gregoire Aubert, Dengjin Bing, Gene Arganosa, and Thomas D Warkentin

Subjects
marker-assisted selection, Pisum sativum, SNP genotyping, vegetable protein, QTL, Plant culture, SB1-1110
Abstract

Improving the seed protein concentration (SPC) of pea (Pisum sativum L.) has turned into an important breeding objective because of the consumer demand for plant-based protein and demand from protein fractionation industries. To support the marker-assisted selection (MAS) of SPC towards accelerated breeding of improved cultivars, we have explored two diverse recombinant inbred line (RIL) populations to identify the quantitative trait loci (QTLs) associated with SPC. The two RIL populations, MP 1918 × P0540-91 (PR-30) and Ballet × Cameor (PR-31), were derived from crosses between moderate SPC × high SPC accessions. A total of 166 and 159 RILs of PR-30 and PR-31, respectively, were genotyped using an Axiom® 90K SNP array and 13.2K SNP arrays, respectively. The RILs were phenotyped in replicated trials in two and three locations of Saskatchewan, Canada in 2020 and 2021, respectively, for agronomic assessment and SPC. Using composite interval mapping, we identified three QTLs associated with SPC in PR-30 and five QTLs in PR-31, with the LOD value ranging from 3.0 to 11.0. A majority of these QTLs were unique to these populations compared to the previously known QTLs for SPC. The QTL SPC-Ps-5.1 overlapped with the earlier reported SPC associated QTL PC-QTL-3. Three QTLs, SPC-Ps-4.2, SPC-Ps-5.1, and SPC-Ps-7.2 with LOD scores of 7.2, 7.9, and 11.3, and which explained 14.5%, 11.6%, and 11.3% of the phenotypic variance, respectively, can be used for marker-assisted breeding to increase SPC in peas. Eight QTLs associated with the grain yield were identified with LOD scores ranging from 3.1 to 8.2. Two sets of QTLs, SPC-Ps-2.1 and GY-Ps-2.1, and SPC-Ps-5.1 and GY-Ps-5.3, shared the QTL/peak regions. Each set of QTLs contributed to either SPC or grain yield depending on which parent the QTL region is derived from, thus confirming that breeding for SPC should take into consideration the effects on grain yield.

Published
2024
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2. The Taxonomic Status of Genera within the Fabeae (Vicieae), with a Special Focus on Pisum

Author

T. H. Noel Ellis, Petr Smýkal, Nigel Maxted, Clarice J. Coyne, Claire Domoney, Judith Burstin, Yanis Bouchenak-Khelladi, and Noam Chayut

Subjects
Leguminosae, systematics, phylogenetics, Pisum sativum, Lathyrus oleraceus, nomenclature, Biology (General), QH301-705.5
Abstract

The taxonomy of the tribe Fabeae (Vicieae) has long been problematic, but an analysis by Schaefer et al. in 2012 gave an exceptionally clear view of the tribe and noted the possibility that some nomenclatural adjustments may be required at some future date. These authors suggested several options, expressing some preferences. However, there has been a recent change to formally accepted names, implementing one of these possibilities, but without any additional relevant information. This change seems unjustified and unhelpful. We therefore present an argument for the retention, or re-instatement, of the genera Pisum, Vavilovia, and Lens until such time as new data support this requirement and there is no nomenclatural solution that is both accurate and convenient.

Published
2024
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3. Development of a knowledge graph framework to ease and empower translational approaches in plant research: a use-case on grain legumes

Author

Baptiste Imbert, Jonathan Kreplak, Raphaël-Gauthier Flores, Grégoire Aubert, Judith Burstin, and Nadim Tayeh

Subjects
graph database, orthology, ontology, quantitative genetics, gene expression, comparative omics, Electronic computers. Computer science, QA75.5-76.95
Abstract

While the continuing decline in genotyping and sequencing costs has largely benefited plant research, some key species for meeting the challenges of agriculture remain mostly understudied. As a result, heterogeneous datasets for different traits are available for a significant number of these species. As gene structures and functions are to some extent conserved through evolution, comparative genomics can be used to transfer available knowledge from one species to another. However, such a translational research approach is complex due to the multiplicity of data sources and the non-harmonized description of the data. Here, we provide two pipelines, referred to as structural and functional pipelines, to create a framework for a NoSQL graph-database (Neo4j) to integrate and query heterogeneous data from multiple species. We call this framework Orthology-driven knowledge base framework for translational research (Ortho_KB). The structural pipeline builds bridges across species based on orthology. The functional pipeline integrates biological information, including QTL, and RNA-sequencing datasets, and uses the backbone from the structural pipeline to connect orthologs in the database. Queries can be written using the Neo4j Cypher language and can, for instance, lead to identify genes controlling a common trait across species. To explore the possibilities offered by such a framework, we populated Ortho_KB to obtain OrthoLegKB, an instance dedicated to legumes. The proposed model was evaluated by studying the conservation of a flowering-promoting gene. Through a series of queries, we have demonstrated that our knowledge graph base provides an intuitive and powerful platform to support research and development programmes.

Published
2023
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4. Assembly of the 81.6 Mb centromere of pea chromosome 6 elucidates the structure and evolution of metapolycentric chromosomes.

Author

Jiří Macas, Laura Ávila Robledillo, Jonathan Kreplak, Petr Novák, Andrea Koblížková, Iva Vrbová, Judith Burstin, and Pavel Neumann

Subjects
Genetics, QH426-470
Abstract

Centromeres in the legume genera Pisum and Lathyrus exhibit unique morphological characteristics, including extended primary constrictions and multiple separate domains of centromeric chromatin. These so-called metapolycentromeres resemble an intermediate form between monocentric and holocentric types, and therefore provide a great opportunity for studying the transitions between different types of centromere organizations. However, because of the exceedingly large and highly repetitive nature of metapolycentromeres, highly contiguous assemblies needed for these studies are lacking. Here, we report on the assembly and analysis of a 177.6 Mb region of pea (Pisum sativum) chromosome 6, including the 81.6 Mb centromere region (CEN6) and adjacent chromosome arms. Genes, DNA methylation profiles, and most of the repeats were uniformly distributed within the centromere, and their densities in CEN6 and chromosome arms were similar. The exception was an accumulation of satellite DNA in CEN6, where it formed multiple arrays up to 2 Mb in length. Centromeric chromatin, characterized by the presence of the CENH3 protein, was predominantly associated with arrays of three different satellite repeats; however, five other satellites present in CEN6 lacked CENH3. The presence of CENH3 chromatin was found to determine the spatial distribution of the respective satellites during the cell cycle. Finally, oligo-FISH painting experiments, performed using probes specifically designed to label the genomic regions corresponding to CEN6 in Pisum, Lathyrus, and Vicia species, revealed that metapolycentromeres evolved via the expansion of centromeric chromatin into neighboring chromosomal regions and the accumulation of novel satellite repeats. However, in some of these species, centromere evolution also involved chromosomal translocations and centromere repositioning.

Published
2023
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5. A QTL approach in faba bean highlights the conservation of genetic control of frost tolerance among legume species

Author

Estefanía Carrillo-Perdomo, Jean-Bernard Magnin-Robert, Blandine Raffiot, Chrystel Deulvot, Matthieu Floriot, Isabelle Lejeune-Hénaut, Pascal Marget, Judith Burstin, Nadim Tayeh, and Grégoire Aubert

Subjects
Frost tolerance, faba bean (Vicia faba L.), genetic linkage mapping, recombinant inbred line (RIL) population, quantitative trait loci (QTL), synteny, Plant culture, SB1-1110
Abstract

Frost is a major abiotic stress of winter type faba beans (Vica faba L.) and has adverse effects on crop yield. Climate change, far from reducing the incidence of frost events, is making these phenomena more and more common, severe, and prolonged. Despite the important interaction that the environment has in the tolerance of faba bean to frost, this trait seems to have good levels of heritability. Several QTLs for frost tolerance have already been reported, however, a more robust identification is needed to more precisely identify the genomic regions involved in faba bean tolerance to sub-zero temperatures. Several pea (Pisum sativum L.) and barrel medic (Medicago truncatula L.) frost tolerance QTLs appear to be conserved between these two species, furthering the hypothesis that the genetic control of frost tolerance in legume species might be more generally conserved. In this work, the QTL mapping in two faba bean recombinant inbred line (RIL) populations connected by a common winter-type parent has led to the identification of five genomic regions involved in the control of frost tolerance on linkage groups I, III, IV, and V. Among them, a major and robust QTL of great interest for marker-assisted selection was identified on the lower part of the long-arm of LGI. The synteny between the faba bean frost tolerance QTLs and those previously identified in other legume species such as barrel medic, pea or soybean highlighted at least partial conservation of the genetic control of frost tolerance among different faba bean genetic pools and legume species. Four novel RILs showing high and stable levels of tolerance and the ability to recover from freezing temperatures by accumulating frost tolerance QTLs are now available for breeding programs.

Published
2022
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6. Genome-wide association study identifies favorable SNP alleles and candidate genes for frost tolerance in pea

Author

Sana Beji, Véronique Fontaine, Rosemonde Devaux, Martine Thomas, Sandra Silvia Negro, Nasser Bahrman, Mathieu Siol, Grégoire Aubert, Judith Burstin, Jean-Louis Hilbert, Bruno Delbreil, and Isabelle Lejeune-Hénaut

Subjects
Frost damages, Frost tolerance, Genome wide association study (GWAS), Pea (Pisum sativum L.), Quantitative trait loci (QTL), Haplotypes of markers, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which allowed to collect data for 11,366 single nucleotide polymorphism (SNP) markers. Results GWAS identified 62 SNPs significantly associated with frost tolerance and distributed over six of the seven pea linkage groups (LGs). These results confirmed 3 QTLs that were already mapped in multiple environments on LG III, V and VI with bi-parental populations. They also allowed to identify one locus, on LG II, which has not been detected yet and two loci, on LGs I and VII, which have formerly been detected in only one environment. Fifty candidate genes corresponding to annotated significant SNPs, or SNPs in strong linkage disequilibrium with the formers, were found to underlie the frost damage (FD)-related loci detected by GWAS. Additionally, the analyses allowed to define favorable haplotypes of markers for the FD-related loci and their corresponding accessions within the association mapping collection. Conclusions This study led to identify FD-related loci as well as corresponding favorable haplotypes of markers and representative pea accessions that might to be used in winter pea breeding programs. Among the candidate genes highlighted at the identified FD-related loci, the results also encourage further attention to the presence of C-repeat Binding Factors (CBF) as potential genetic determinants of the frost tolerance locus on LG VI.

Published
2020
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7. PeaMUST (Pea MultiStress Tolerance), a multidisciplinary French project uniting researchers, plant breeders, and the food industry

Author

Judith Burstin, Komlan Avia, Estefania Carillo‐Perdomo, Christophe Lecomte, Sana Beji, Eric Hanocq, Gregoire Aubert, Nadim Tayeh, Anthony Klein, Valérie Geffroy, Christine Le Signor, Stéphanie Pflieger, Marion Dalmais, Aurore Desgroux, Clément Lavaud, Anne Quillévéré‐Hamard, Jonathan Kreplak, Isabelle Lejeune‐Hénaut, Virginie Bourion, Marie‐Laure Pilet‐Nayel, Magalie Leveugle, Xavier Pinochet, Richard Thompson, and the PeaMUST Consortium

Subjects
abiotic, biotic, faba bean, genome, legume, pea, Plant culture, SB1-1110
Abstract

Abstract The French government has supported as part of its “Investments for the Future” program a 9‐year research project, PeaMUST, devoted to pea and to a lesser extent, faba bean improvement. Focusing on the main causes of yield irregularity that limit pea and faba bean cultivation, an integrated approach, including molecular exploitation of the pea genome sequence, was applied to identify and incorporate favorable alleles and allele combinations in prebreeding material.

Published
2021
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8. Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping

Author

Barbara Pivato, Amélie Semblat, Thibault Guégan, Samuel Jacquiod, Juliette Martin, Florence Deau, Nathalie Moutier, Christophe Lecomte, Judith Burstin, and Philippe Lemanceau

Subjects
bacterial community, biodiversity, intercropping, networks, pea, rhizosphere, Microbiology, QR1-502
Abstract

Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.

Published
2021
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9. Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)

Author

Krishna Kishore Gali, Alison Sackville, Endale G. Tafesse, V.B. Reddy Lachagari, Kevin McPhee, Mick Hybl, Alexander Mikić, Petr Smýkal, Rebecca McGee, Judith Burstin, Claire Domoney, T.H. Noel Ellis, Bunyamin Tar'an, and Thomas D. Warkentin

Subjects
field pea, genetic diversity, genome-wide association study, genotyping-by-sequencing, single nucleotide polymorphisms, Plant culture, SB1-1110
Abstract

Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.

Published
2019
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10. Patterns of Genetic Structure and Linkage Disequilibrium in a Large Collection of Pea Germplasm

Author

Mathieu Siol, Françoise Jacquin, Marianne Chabert-Martinello, Petr Smýkal, Marie-Christine Le Paslier, Grégoire Aubert, and Judith Burstin

Subjects
genetic diversity, linkage disequilibrium, FST, Pisum sativum, Genetics, QH426-470
Abstract

Pea (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. LD decreases steeply as genetic distance increases. 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, QTL for resistance to cold acclimation and frost resistance have been identified previously in the same regions.

Published
2017
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11. Transcriptional Reprogramming of Pea Leaves at Early Reproductive Stages

Author

Karine Gallardo, Alicia Besson, Anthony Klein, Christine Le Signor, Grégoire Aubert, Charlotte Henriet, Morgane Térézol, Stéphanie Pateyron, Myriam Sanchez, Jacques Trouverie, Jean-Christophe Avice, Annabelle Larmure, Christophe Salon, Sandrine Balzergue, and Judith Burstin

Subjects
legumes, leaves, reproductive period, nitrogen remobilization, transcriptomics, co-expression, Plant culture, SB1-1110
Abstract

Pea (Pisum sativum L.) is an important source of dietary proteins. Nutrient recycling from leaves contributes to the accumulation of seed proteins and is a pivotal determinant of protein yields in this grain legume. The aim of this study was to unveil the transcriptional regulations occurring in pea leaves before the sharp decrease in chlorophyll breakdown. As a prelude to this study, a time-series analysis of 15N translocation at the whole plant level was performed, which indicated that nitrogen recycling among organs was highly dynamic during this period and varied depending on nitrate availability. Leaves collected on vegetative and reproductive nodes were further analyzed by transcriptomics. The data revealed extensive transcriptome changes in leaves of reproductive nodes during early seed development (from flowering to 14 days after flowering), including an up-regulation of genes encoding transporters, and particularly of sulfate that might sustain sulfur metabolism in leaves of the reproductive part. This developmental period was also characterized by a down-regulation of cell wall-associated genes in leaves of both reproductive and vegetative nodes, reflecting a shift in cell wall structure. Later on, 27 days after flowering, genes potentially switching the metabolism of leaves toward senescence were pinpointed, some of which are related to ribosomal RNA processing, autophagy, or transport systems. Transcription factors differentially regulated in leaves between stages were identified and a gene co-expression network pointed out some of them as potential regulators of the above-mentioned biological processes. The same approach was conducted in Medicago truncatula to identify shared regulations with this wild legume species. Altogether the results give a global view of transcriptional events in leaves of legumes at early reproductive stages and provide a valuable resource of candidate genes that could be targeted by reverse genetics to improve nutrient remobilization and/or delay catabolic processes leading to senescence.

Published
2019
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12. Development of a Sequence-Based Reference Physical Map of Pea (Pisum sativum L.)

Author

Krishna Kishore Gali, Bunyamin Tar’an, Mohammed-Amin Madoui, Edwin van der Vossen, Jan van Oeveren, Karine Labadie, Helene Berges, Abdelhafid Bendahmane, Reddy V. B. Lachagari, Judith Burstin, and Tom Warkentin

Subjects
bacterial artificial chromosome, fingerprinted contigs, Pisum sativum, sequence-based physical map, whole genome profiling, Plant culture, SB1-1110
Abstract

Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (∼4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

Published
2019
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13. Association of SNP markers with agronomic and quality traits of field pea in Italy

Author

Barbara Ferrari, Massimo Romani, Gregoire Aubert, Karen Boucherot, Judith Burstin, Luciano Pecetti, Myriam Huart-Naudet, Anthony Klein, and Paolo Annicchiarico

Subjects
grain yield, marker-assisted selection, pisum sativum, protein content, qtl, Plant culture, SB1-1110
Abstract

Only a few studies on pea (Pisum sativum) investigated the association of single nucleotide polymorphisms (SNP) markers with key agronomic traits. This study aimed to explore the association of a standard set of 384 SNP with grain yield, seed protein content, seed weight, onset of flowering, plant height and lodging susceptibility, in three connected bi-parental recombinant inbred line (RIL) populations including 90 lines each. These RIL originated from crosses between three cultivars that displayed high and stable grain yield across Italian environments, namely, Attika (A), Isard (I), and Kaspa (K). The 270 lines were phenotyped in a spring-sown environment of Lodi (northern Italy; 45°19'N, 9°30'E). Variation among lines within the populations was significant (P < 0.01) in all cases except lodging susceptibility in one cross and, when expressed in terms of the genetic coefficient of variation, proved moderately large for most traits (including grain yield and seed protein content). Overall, we detected six quantitative trait loci (QTL) in the A × I linkage map, eight QTL in K × A, and nine QTL in K × I. Among them, there were three QTL in K × A and two QTL in K × I for grain yield, and one QTL in A × I and two QTL in both K × A and K × I for seed protein content. The consensus map, which included 130 markers (covering about 1094 cM), retained one QTL for grain yield and one for flowering time that co-located on LGII, and three for seed weight on LGIII, LGVI and LGVII. The QTL co-locating for yield and flowering time explained 8% and 31% of the overall phenotypic variation, respectively, for the two traits, and could be exploited in marker-assisted selection for adaptation to the target region.

Published
2016
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14. 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

Author

Virginie Bourion, Karine Heulin-Gotty, Véronique Aubert, Pierre Tisseyre, Marianne Chabert-Martinello, Marjorie Pervent, Catherine Delaitre, Denis Vile, Mathieu Siol, Gérard Duc, Brigitte Brunel, Judith Burstin, and Marc Lepetit

Subjects
partner choice, competitiveness for nodulation, pea-rhizobium symbiosis, nitrogen fixation efficiency, genetic diversity, plant breeding, Plant culture, SB1-1110
Abstract

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.

Published
2018
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15. Comparative Genome-Wide-Association Mapping Identifies Common Loci Controlling Root System Architecture and Resistance to Aphanomyces euteiches in Pea

Author

Aurore Desgroux, Valentin N. Baudais, Véronique Aubert, Gwenola Le Roy, Henri de Larambergue, Henri Miteul, Grégoire Aubert, Gilles Boutet, Gérard Duc, Alain Baranger, Judith Burstin, Maria Manzanares-Dauleux, Marie-Laure Pilet-Nayel, and Virginie Bourion

Subjects
root system architecture, disease resistance, Pisum sativum, GWAS, root rot, Plant culture, SB1-1110
Abstract

Combining plant genetic resistance with architectural traits that are unfavorable to disease development is a promising strategy for reducing epidemics. However, few studies have identified root system architecture (RSA) traits with the potential to limit root disease development. Pea is a major cultivated legume worldwide and has a wide level of natural genetic variability for plant architecture. The root pathogen Aphanomyces euteiches is a major limiting factor of pea crop yield. This study aimed to increase the knowledge on the diversity of loci and candidate genes controlling RSA traits in pea and identify RSA genetic loci associated with resistance to A. euteiches which could be combined with resistance QTL in breeding. A comparative genome wide association (GWA) study of plant architecture and resistance to A. euteiches was conducted at the young plant stage in a collection of 266 pea lines contrasted for both traits. The collection was genotyped using 14,157 SNP markers from recent pea genomic resources. It was phenotyped for ten root, shoot and overall plant architecture traits, as well as three disease resistance traits in controlled conditions, using image analysis. We identified a total of 75 short-size genomic intervals significantly associated with plant architecture and overlapping with 46 previously detected QTL. The major consistent intervals included plant shoot architecture or flowering genes (PsLE, PsTFL1) with putative pleiotropic effects on root architecture. A total of 11 genomic intervals were significantly associated with resistance to A. euteiches confirming several consistent previously identified major QTL. One significant SNP, mapped to the major QTL Ae-Ps7.6, was associated with both resistance and RSA traits. At this marker, the resistance-enhancing allele was associated with an increased total root projected area, in accordance with the correlation observed between resistance and larger root systems in the collection. Seven additional intervals associated with plant architecture overlapped with GWA intervals previously identified for resistance to A. euteiches. This study provides innovative results about genetic interdependency of root disease resistance and RSA inheritance. It identifies pea lines, QTL, closely-linked markers and candidate genes for marker-assisted-selection of RSA loci to reduce Aphanomyces root rot severity in future pea varieties.

Published
2018
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16. Pea (Pisum sativum L.) in the Genomic Era

Author

Robert J. Redden, Diego Rubiales, Kevin E. McPhee, Pavel Neumann, Jiří Macas, Miroslav Hýbl, Rebecca Ford, Andrew J. Flavell, Noel T. H. Ellis, Clarice J. Coyne, Judith Burstin, Gregoire Aubert, Petr Smýkal, Jim L. Weller, and Tom D. Warkentin

Subjects
breeding, germplasm, genetic diversity, marker-assisted breeding, legumes, pea, Agriculture
Abstract

Pea (Pisum sativum L.) was the original model organism used in Mendel’s discovery (1866) of the laws of inheritance, making it the foundation of modern plant genetics. However, subsequent progress in pea genomics has lagged behind many other plant species. Although the size and repetitive nature of the pea genome has so far restricted its sequencing, comprehensive genomic and post genomic resources already exist. These include BAC libraries, several types of molecular marker sets, both transcriptome and proteome datasets and mutant populations for reverse genetics. The availability of the full genome sequences of three legume species has offered significant opportunities for genome wide comparison revealing synteny and co-linearity to pea. A combination of a candidate gene and colinearity approach has successfully led to the identification of genes underlying agronomically important traits including virus resistances and plant architecture. Some of this knowledge has already been applied to marker assisted selection (MAS) programs, increasing precision and shortening the breeding cycle. Yet, complete translation of marker discovery to pea breeding is still to be achieved. Molecular analysis of pea collections has shown that although substantial variation is present within the cultivated genepool, wild material offers the possibility to incorporate novel traits that may have been inadvertently eliminated. Association mapping analysis of diverse pea germplasm promises to identify genetic variation related to desirable agronomic traits, which are historically difficult to breed for in a traditional manner. The availability of high throughput ‘omics’ methodologies offers great promise for the development of novel, highly accurate selective breeding tools for improved pea genotypes that are sustainable under current and future climates and farming systems.

Published
2012
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17. MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development

Author

Marie-Françoise Jardinaud, Justine Fromentin, Marie-Christine Auriac, Sandra Moreau, Yann Pecrix, Ludivine Taconnat, Ludovic Cottret, Grégoire Aubert, Sandrine Balzergue, Judith Burstin, Sébastien Carrere, Pascal Gamas, Laboratoire des Interactions Plantes Microbes Environnement (LIPME), Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de La Réunion (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université d'Évry-Val-d'Essonne (UEVE)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Université Paris Cité (UPCité)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Unité expérimentale du GEVES, Institut National de la Recherche Agronomique (INRA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), INRAE (CJS fellowship for J.F., SPE grant 'EFFOR'), ANR-09-GENM-0026,GENOPEA,Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées(2009), ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010), ANR-10-LABX-0040,SPS,Saclay Plant Sciences(2010), and Université de Bourgogne (UB)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Dijon

Subjects
[SDV.BIO]Life Sciences [q-bio]/Biotechnology, Nitrogen, CNRS, Physiology, food and beverages, Plant Science, Ethylenes, [SDV.BV.BOT]Life Sciences [q-bio]/Vegetal Biology/Botanics, [SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology, Gene Expression Regulation, Plant, Nitrogen Fixation, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Medicago truncatula, Genetics, Root Nodules, Plant, Symbiosis, LIPME, Research Articles, Université de Toulouse, [SDV.MP.MYC]Life Sciences [q-bio]/Microbiology and Parasitology/Mycology, Plant Proteins, Transcription Factors, INRAE
Abstract

Rhizobium–legume nitrogen-fixing symbiosis involves the formation of a specific organ, the root nodule, which provides bacteria with the proper cellular environment for atmospheric nitrogen fixation. Coordinated differentiation of plant and bacterial cells is an essential step of nodule development, for which few transcriptional regulators have been characterized. Medicago truncatula ETHYLENE RESPONSE FACTOR REQUIRED FOR NODULE DIFFERENTIATION (MtEFD) encodes an APETALA2/ETHYLENE RESPONSIVE FACTOR (ERF) transcription factor, the mutation of which leads to both hypernodulation and severe defects in nodule development. MtEFD positively controls a negative regulator of cytokinin signaling, the RESPONSE REGULATOR 4 (MtRR4) gene. Here we showed that that the Mtefd-1 mutation affects both plant and bacterial endoreduplication in nodules, as well as the expression of hundreds of genes in young and mature nodules, upstream of known regulators of symbiotic differentiation. MtRR4 expressed with the MtEFD promoter complemented Mtefd-1 hypernodulation but not the nodule differentiation phenotype. Unexpectedly, a nonlegume homolog of MtEFD, AtERF003 in Arabidopsis (Arabidopsis thaliana), could efficiently complement both phenotypes of Mtefd-1, in contrast to the MtEFD paralog MtEFD2 expressed in the root and nodule meristematic zone. A domain swap experiment showed that MtEFD2 differs from MtEFD by its C-terminal fraction outside the DNA binding domain. Furthermore, clustered regularly interspaced short palindromic repeats-CRISPR associated protein 9 (CRISPR-Cas9) mutagenesis of MtEFD2 led to a reduction in the number of nodules formed in Mtefd-1, with downregulation of a set of genes, including notably NUCLEAR FACTOR-YA1 (MtNF-YA1) and MtNF-YB16, which are essential for nodule meristem establishment. We, therefore, conclude that nitrogen-fixing symbiosis recruited two proteins originally expressed in roots, MtEFD and MtEFD2, with distinct functions and neofunctionalization processes for each of them.

Published
2022

18. A major-effect genetic locus, ApRVII, controlling resistance against both adapted and non-adapted aphid biotypes in pea

Author

Rémi Ollivier, Isabelle Glory, Romuald Cloteau, Jean-François Le Gallic, Gaëtan Denis, Stéphanie Morlière, Henri Miteul, Jean-Philippe Rivière, Angélique Lesné, Anthony Klein, Grégoire Aubert, Jonathan Kreplak, Judith Burstin, Marie-Laure Pilet-Nayel, Jean-Christophe Simon, Akiko Sugio, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut Agro Rennes Angers, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Direction de l'évaluation, de la prospective et de la performance (DEPP), Ministère de l'Education nationale, de l’Enseignement supérieur et de la Recherche (M.E.N.E.S.R.), Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Different parts of the presented work were funded byPlant2Pro-2018-CharaP, ANR-P-Aphid (ANR-18-CE20-0021–01),ANR-Mecadapt (ANR-18-CE02-0012) and ANR-PeaMUST (ANR-11-BTBR-0002). RO is supported by INRAE-SPE, INRAE-BAP andRegion Bretagne PhD grants., ANR-18-CE02-0012,Mecadapt,Mécanismes d'adaptation et de diversification chez un ravageur des cultures(2018), and ANR-18-CE20-0021,P-Aphid,Identification et caractérisation des facteurs de compatibilité et d'incompatibilité chez les plantes et chez les pucerons(2018)

Subjects
[SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, fungi, Peas, food and beverages, General Medicine, Plant Breeding, Aphids, Genetics, Animals, Agronomy and Crop Science, Biotechnology, Genome-Wide Association Study
Abstract

A genome-wide association study for pea resistance against a pea-adapted biotype and a non-adapted biotype of the aphid, Acyrthosiphon pisum, identified a genomic region conferring resistance to both biotypes. In a context of reduced insecticide use, the development of cultivars resistant to insect pests is crucial for an integrated pest management. Pea (Pisum sativum) is a crop of major importance among cultivated legumes, for the supply of dietary proteins and nitrogen in low-input cropping systems. However, yields of the pea crop have become unstable due to plant parasites. The pea aphid (Acyrthosiphon pisum) is an insect pest species forming a complex of biotypes, each one adapted to feed on one or a few related legume species. This study aimed to identify resistance to A. pisum and the underlying genetic determinism by examining a collection of 240 pea genotypes. The collection was screened against a pea-adapted biotype and a non-adapted biotype of A. pisum to characterize their resistant phenotype. Partial resistance was observed in some pea genotypes exposed to the pea-adapted biotype. Many pea genotypes were completely resistant to non-adapted biotype, but some exhibited partial susceptibility. A genome-wide association study, using pea exome-capture sequencing data, enabled the identification of the major-effect quantitative trait locus ApRVII on the chromosome 7. ApRVII includes linkage disequilibrium blocks significantly associated with resistance to one or both of the two aphid biotypes studied. Finally, we identified candidate genes underlying ApRVII that are potentially involved in plant-aphid interactions and marker haplotypes linked with aphid resistance. This study sets the ground for the functional characterization of molecular pathways involved in pea defence to the aphids but also is a step forward for breeding aphid-resistant cultivars.

Published
2022

19. Meta-analysis of QTL reveals the genetic control of yield-related traits and seed protein content in pea

Author

Pascal Marget, Hervé Houtin, Myriam Naudet-Huart, Michael Touratier, Judith Burstin, Anthony Klein, Céline Rond-Coissieux, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Domaine expérimental d'Époisses - UE0115 U2E (DIJ EPOISSES), and Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, 0301 basic medicine, Candidate gene, Plant genetics, Genotype, Genetic Linkage, Population, Quantitative Trait Loci, lcsh:Medicine, Quantitative trait locus, Biology, 01 natural sciences, Polymorphism, Single Nucleotide, Article, Plant breeding, 03 medical and health sciences, Genetic linkage, education, lcsh:Science, Gene, Plant Proteins, 2. Zero hunger, Genetics, education.field_of_study, Multidisciplinary, lcsh:R, Peas, Chromosome Mapping, 030104 developmental biology, Phenotype, [SDE]Environmental Sciences, Seeds, Trait, lcsh:Q, 010606 plant biology & botany, SNP array
Abstract

Pea is one of the most important grain legume crops in temperate regions worldwide. Improving pea yield is a critical breeding target. Nine inter-connected pea recombinant inbred line populations were evaluated in nine environments at INRAE Dijon, France and genotyped using the GenoPea 13.2 K SNP array. Each population has been evaluated in two to four environments. A multi-population Quantitative Trait Loci (QTL) analysis for seed weight per plant (SW), seed number per plant (SN), thousand seed weight (TSW) and seed protein content (SPC) was done. QTL were then projected on the multi-population consensus map and a meta-analysis of QTL was performed. This analysis identified 17 QTL for SW, 16 QTL for SN, 35 QTL for TSW and 21 QTL for SPC, shedding light on trait relationships. These QTL were resolved into 27 metaQTL. Some of them showed small confidence intervals of less than 2 cM encompassing less than one hundred underlying candidate genes. The precision of metaQTL and the potential candidate genes reported in this study enable their use for marker-assisted selection and provide a foundation towards map-based identification of causal polymorphisms.

Published
2020

20. Development of new genetic resources for faba bean (Vicia faba L.) breeding through the discovery of gene-based SNP markers and the construction of a high-density consensus map

Author

Pascal Marget, H. Duborjal, Estefanía Carrillo-Perdomo, Jorge Duarte, Magalie Leveugle, Blandine Raffiot, Jonathan Kreplak, Olivier C. Martin, C. Desmetz, Judith Burstin, Matthieu Falque, Jean-Philippe Pichon, Nadim Tayeh, Grégoire Aubert, Chrystel Deulvot, A. Vidal, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), AgroParisTech-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), BIOGEMMA [Chappes, France], Centre de Recherche de Chappes, and Terres Inovia, Thiverval-Grignon, France

Subjects
Agricultural genetics, Genetic Markers, 0106 biological sciences, 0301 basic medicine, Conservation of Natural Resources, Candidate gene, Plant genetics, lcsh:Medicine, Computational biology, Biology, Polymorphism, Single Nucleotide, Synteny, 01 natural sciences, Genome, Article, Plant breeding, Chromosomes, Plant, 03 medical and health sciences, Genetics, Sequencing, Association mapping, lcsh:Science, 2. Zero hunger, Comparative genomics, Genetic diversity, Multidisciplinary, Phylogenetic tree, Gene Expression Profiling, lcsh:R, Chromosome Mapping, food and beverages, Agriculture, Fabaceae, Genomics, 15. Life on land, Vicia faba, Genetic linkage study, 030104 developmental biology, [SDE]Environmental Sciences, lcsh:Q, 010606 plant biology & botany
Abstract

Faba bean (Vicia faba L.) is a pulse crop of high nutritional value and high importance for sustainable agriculture and soil protection. With the objective of identifying gene-based SNPs, transcriptome sequencing was performed in order to reduce faba bean genome complexity. A set of 1,819 gene-based SNP markers polymorphic in three recombinant line populations was selected to enable the construction of a high-density consensus genetic map encompassing 1,728 markers well distributed in six linkage groups and spanning 1,547.71 cM with an average inter-marker distance of 0.89 cM. Orthology-based comparison of the faba bean consensus map with legume genome assemblies highlighted synteny patterns that partly reflected the phylogenetic relationships among species. Solid blocks of macrosynteny were observed between faba bean and the most closely-related sequenced legume species such as pea, barrel medic or chickpea. Numerous blocks could also be identified in more divergent species such as common bean or cowpea. The genetic tools developed in this work can be used in association mapping, genetic diversity, linkage disequilibrium or comparative genomics and provide a backbone for map-based cloning. This will make the identification of candidate genes of interest more efficient and will accelerate marker-assisted selection (MAS) and genomic-assisted breeding (GAB) in faba bean.

Published
2020

21. Rhizosphere Bacterial Networks, but Not Diversity, Are Impacted by Pea-Wheat Intercropping

Author

Judith Burstin, Barbara Pivato, Samuel Jacquiod, Nathalie Moutier, Amélie Semblat, Florence Deau, Thibault Guégan, Philippe Lemanceau, Juliette Martin, Christophe Lecomte, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Domaine expérimental d'Époisses - UE0115 U2E (DIJ EPOISSES), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), FEDER-Bourgogne 'Qualit'Asso' project [BG0019912], 'Varietal Innovation and Diversification' program - INRAE and AgriObtentions - 'CereLAG' project, Agroecologie - INRAE internal fund, Plant2Pro-Carnot Institute 'POSiTiF' project, Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)

Subjects
0106 biological sciences, Microbiology (medical), pea, Biodiversity, 01 natural sciences, Microbiology, bacterial community, Crop, 03 medical and health sciences, wheat, Gammaproteobacteria, Original Research, 030304 developmental biology, biodiversity, 2. Zero hunger, 0303 health sciences, Rhizosphere, biology, Alphaproteobacteria, Bacteroidetes, food and beverages, Intercropping, 15. Life on land, biology.organism_classification, QR1-502, Agronomy, networks, [SDE]Environmental Sciences, rhizosphere, intercropping, 010606 plant biology & botany, Acidobacteria
Abstract

International audience; Plant-plant associations, notably cereal-legume intercropping, have been proposed in agroecology to better value resources and thus reduce the use of chemical inputs in agriculture. Wheat-pea intercropping allows to decreasing the use of nitrogen fertilization through ecological processes such as niche complementarity and facilitation. Rhizosphere microbial communities may account for these processes, since they play a major role in biogeochemical cycles and impact plant nutrition. Still, knowledge on the effect of intecropping on the rhizosphere microbiota remains scarce. Especially, it is an open question whether rhizosphere microbial communities in cereal-legume intercropping are the sum or not of the microbiota of each plant species cultivated in sole cropping. In the present study, we assessed the impact of wheat and pea in IC on the diversity and structure of their respective rhizosphere microbiota. For this purpose, several cultivars of wheat and pea were cultivated in sole and intercropping. Roots of wheat and pea were collected separately in intercropping for microbiota analyses to allow deciphering the effect of IC on the bacterial community of each plant species/cultivar tested. Our data confirmed the well-known specificity of the rhizosphere effect and further stress the differentiation of bacterial communities between pea genotypes (Hr and hr). As regards the intercropping effect, diversity and structure of the rhizosphere microbiota were comparable to sole cropping. However, a specific co-occurrence pattern in each crop rhizosphere due to intercropping was revealed through network analysis. Bacterial co-occurrence network of wheat rhizosphere in IC was dominated by OTUs belonging to Alphaproteobacteria, Bacteroidetes and Gammaproteobacteria. We also evidenced a common network found in both rhizosphere under IC, indicating the interaction between the plant species; this common network was dominated by Acidobacteria, Alphaproteobacteria, and Bacteroidetes, with three OTUs belonging to Acidobacteria, Betaproteobacteria and Chloroflexi that were identified as keystone taxa. These findings indicate more complex rhizosphere bacterial networks in intercropping. Possible implications of these conclusions are discussed in relation with the functioning of rhizosphere microbiota in intercropping accounting for its beneficial effects.

Published
2021

22. Identification des déterminants génétiques impliqués dans les défenses du pois contre le puceron Acyrthosiphon pisum

Author

Rémi Ollivier, Glory, I., Le Gallic, J. F., Denis, G., Morliere, S., Miteul, H., Buchard, C., Duval F, Hudaverdian, S., Mahéo, F., Prunier-Leterme, N., Tanguy, S., Cloteau, R., Toussaint, G., Jean-Philippe Rivière, Angélique Lesné, Leveugle, M., J-P, Pichon, Duborjal, H., Klein, A., Aubert, G., Kreplak, J., Judith Burstin, Jean-Christophe Simon, M-L, Pilet-Nayel, Sugio, A., EL Mjiyad, Noureddine, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biogemma, 63720, Chappes, France, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], GWAS, interaction hôte/non-hôte, résistance génétique, biotype, Pisum sativum
Abstract

National audience; Le pois (Pisum sativum) constitue une culture d’importance majeure parmi les légumineuses pour ses qualités de plante protéagineuse, notamment en Europe en réduisant la part de protéines végétales importées ainsi que pour son rôle dans la rotation des cultures en fixant l’azote atmosphérique dans le sol. Cependant, ces dernières années, les rendements ont été rendus instables dus aux contraintes biotiques et abiotiques. Pour lutter contre certains ravageurs, les producteurs ont recours à de grandes quantités de pesticides qui sont coûteuses et dangereuses pour l’environnement et la santé humaine. Pour ces raisons, des alternatives sont mises en œuvre tels que le développement de stratégies d’utilisation et de gestion des résistances génétiques. Le puceron vert du pois (Acyrthosiphon pisum) est un ravageur important des cultures de légumineuses et créée des dommages directement en se nourrissant de la sève phloémienne au cours des périodes d’infestations et indirectement en étant vecteur de virus pathogènes. Cette espèce de puceron forme un complexe d'au moins 15 biotypes, chacun est adapté pour se nourrir sur une ou quelques espèces de légumineuses et révèle des performances réduites sur d'autres espèces. Nos travaux de recherche portent sur la compréhension des mécanismes génétiques et moléculaires des interactions plante-puceron conduisant à la résistance hôte et non-hôte des légumineuses face à A. pisum. Un phénotypage par test de fécondité de puceron sur plante a été réalisé pour déterminer les profils de résistance de 240 génotypes de pois face à deux biotypes d’A. pisum, l’un adapté et l’autre non-adapté au pois. Aucune résistante complète au biotype adapté d’A. pisum n’a été observée dans les accessions de pois , alors que de nombreuses accessions ont montré une résistance complète au biotype non-adapté. De plus, de grandes variations de niveaux de résistance quantitative ont été observées parmi les génotypes de pois face aux deux biotypes d'A. pisum. A partir de données de séquençage exome capture obtenues sur les 240 génotypes dans le cadre du projet PeaMUST, une approche de génétique d’association sur le génome entier (GWAS), a été réalisée afin d’identifier les déterminants génétiques de la résistance du pois aux deux biotypes d’A. pisum. Les résultats ont permis de mettre en évidence des loci significativement associés à la résistance du pois sur le chromosome 7, incluant des loci spécifiques de chacun des deux biotypes d’A. pisum, dont l’un présentant un effet majeur, et deux loci communs aux deux biotypes. Une analyse d’haplotypes dans les intervalles sous-jacents à ces loci a confirmé des différences significatives de phénotypes entre groupes de lignées partageant les mêmes haplotypes. Cette approche a permis d’identifier une liste de génotypes de pois dont les comportements de résistance seront confirmés au champ. Elle a permis d’identifier des loci et gènes candidats sous-jacents à valider expérimentalement pour leur implication dans la compatibilité et incompatibilité du pois aux différents biotypes d’A. pisum.

Published
2021

23. Quel impact de la génomique végétale sur l’innovation variétale : l’exemple du projet PeaMUST. Le génome du pois: vers de nouvelles strategies de sélection

Author

Judith Burstin, Nadim Tayeh, Klein, Anthony, Komlan Avia, Marie-Laure Pilet-Nayel, Virginie Bourion, Estefania Carrillo Perdomo, Christophe Lecomte, Grégoire Aubert, Jonathan Kreplak, Duborjal, H., Pichon, J. P., Leveugle, M., Marie-Christine Le Paslier, Herbommez, J. F., Declerck, P., Mathieu Floriot, Hanocq, E., Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Université de Rennes (UR)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and EL Mjiyad, Noureddine

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio]
Abstract

International audience; L’avancée des technologies « nouvelle génération » de séquençage de l’ADN permettent une connaissance de plus en plus poussée des génomes et de leur expression. Ces connaissances permettent d’approcher plus finement les déterminants moléculaires des traits phénotypiques et ouvrent des perspectives d’augmentation du progrès génétique dans le cadre de la sélection variétale. Le pois est une espèce modèle depuis les travaux de G. Mendel conduisant à la découverte des lois de l’hérédité. La séquence du génome de cette espèce longtemps délaissée des approches de génomique a récemment été obtenue par un consortium international piloté par l’INRAE (1,2). Dans le cadre du projet de recherche français PeaMUST regroupant un large partenariat entre secteurs public et privé, différentes stratégies tirant partie de ces connaissances ont été mises en oeuvre pour améliorer le pois (3). Ces stratégies varient en fonction des caractères ciblés : pour améliorer la régularité du rendement, un trait hautement multifactoriel qui résulte de la capacité des plantes à s'adapter et à répondre à l'environnement, une approche de sélection à l’échelle du génome entier a été testée ; pour la résistance durable aux pathogènes, une stratégie prometteuse est de pyramider plusieurs gènes de résistance correspondant à des mécanismes divers ; enfin, des mutations à effet majeur contrôlant l’architecture aérienne et racinaire des plantes ont été testées pour leur effet sur la tolérance aux stress. L'amélioration des cultures doit en effet plusieurs réussites remarquables à la manipulation de l'architecture végétale, comme l'utilisation des caractères afila et de nanisme chez le pois.PeaMust is an international program on pea breeding goals and techniques and pea genomics. Two convergent achievements testify to its pertinence. It associates the complete sequencing and deciphering of the DNA on one hand with efficient genetic approaches to phenotype analysis and methods dealing with quantitative and adaptative traits on the other. Examples of PeaMust successbear on regularity of production, on the confrontation with pathogens or environmental stress, on the architecture of the plant. In each case PeaMust offers innovative opportunities.

Published
2020

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

Author

Nadim Tayeh, Jonathan Kreplak, Anthony Klein, Komlan Avia, Estefania Carrillo Perdomo, Hervé Houtin, Céline Rond, Chrystel Deulvot, Marianne Chabert-Martinello, Florence Naudé, Jean-Bernard Magnin-Robert, Karen Boucherot, Emilie Vieille, Chantal Martin, Damien Ollivier, Virginie Quantin Bourion, Gregoire Aubert, Judith Burstin, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and EL Mjiyad, Noureddine

Subjects
[SDE] Environmental Sciences, [SDE]Environmental Sciences
Abstract

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 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.

Published
2020

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

Author

Nadim Tayeh, Jonathan Kreplak, Anthony Klein, Komlan Avia, Estefania Carrillo Perdomo, Hervé Houtin, Céline Rond, Chrystel Deulvot, Marianne Chabert-Martinello, Florence Naudé, Jean-Bernard Magnin-Robert, Karen Boucherot, Emilie Vieille, Chantal Martin, Damien Ollivier, Virginie Quantin Bourion, Gregoire Aubert, Judith Burstin, Agroécologie [Dijon], Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and EL Mjiyad, Noureddine

Subjects
[SDE] Environmental Sciences, [SDE]Environmental Sciences
Abstract

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 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.

Published
2020

26. Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.)

Author

Petr Smýkal, Judith Burstin, Alison Sackville, T. H. Noel Ellis, Endale G. Tafesse, Claire Domoney, Thomas D. Warkentin, V. B. Reddy Lachagari, Bunyamin Tar’an, Alexander Mikić, Kevin McPhee, Krishna K. Gali, Rebecca J. McGee, Mick Hybl, Crop Development Centre, University of Saskatchewan, AgriGenome Labs Pvt Ltd, Partenaires INRAE, Dep Plant Sci, North Dakota State University (NDSU), Centre of the Region Haná for Biotechnological and Agricultural Research - Department of Genetic Resources for Vegetables - Medicinal and Special Plants, Crop Research Institute, Forage Crops Department, Institute of Field and Vegetable Crops [Novi Sad], Department of Botany, Faculty of Sciences, Palacky University Olomouc, Grain Legume Genetics Physiology Research, USDA-ARS : Agricultural Research Service, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Department of Metabolic Biology, John Innes Centre [Norwich], School of Biological Sciences [Auckland], University of Auckland [Auckland], and Saskatchewan Ministry of Agriculture and Saskatchewan Pulse Growers

Subjects
0106 biological sciences, 0301 basic medicine, [SDV]Life Sciences [q-bio], Single-nucleotide polymorphism, Genome-wide association study, Plant Science, lcsh:Plant culture, Biology, 01 natural sciences, Pisum, 03 medical and health sciences, Field pea, single nucleotide polymorphisms, Sativum, genotyping-by-sequencing, lcsh:SB1-1110, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Cultivar, Original Research, 2. Zero hunger, Genetic diversity, genome-wide association study, food and beverages, genetic diversity, biology.organism_classification, Minor allele frequency, 030104 developmental biology, Agronomy, field pea, 010606 plant biology & botany
Abstract

Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.

Published
2019

27. Transcriptional Reprogramming of Pea Leaves at Early Reproductive Stages

Author

Judith Burstin, Alicia Besson, Charlotte Henriet, Sandrine Balzergue, Christophe Salon, Grégoire Aubert, Myriam Sanchez, Karine Gallardo, Christine Le Signor, Stéphanie Pateyron, Jean-Christophe Avice, Jacques Trouverie, Morgane Terezol, Annabelle Larmure, Anthony Klein, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA), Ecophysiologie Végétale, Agronomie et Nutritions (EVA), Université de Caen Normandie (UNICAEN), Normandie Université (NU)-Normandie Université (NU)-Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR) ANR-09-GENM-026, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Institut National de la Recherche Agronomique (INRA)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)-Université Paris Diderot - Paris 7 (UPD7)-Université Paris-Saclay-Université Paris-Sud - Paris 11 (UP11), and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, 0301 basic medicine, legumes, reproductive period, Chromosomal translocation, Plant Science, lcsh:Plant culture, 01 natural sciences, Pisum, Transcriptome, 03 medical and health sciences, transcriptomics, Nutrient, Sativum, Botany, Transcription factors, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Transcription factor, Gene, Original Research, biology, food and beverages, nitrogen remobilization, biology.organism_classification, Medicago truncatula, co-expression, Transporters, 030104 developmental biology, leaves, 010606 plant biology & botany
Abstract

International audience; Pea (Pisum sativum L.) is an important source of dietary proteins. Nutrient recycling from leaves contributes to the accumulation of seed proteins and is a pivotal determinant of protein yields in this grain legume. The aim of this study was to unveil the transcriptional regulations occurring in pea leaves before the sharp decrease in chlorophyll breakdown. As a prelude to this study, a time-series analysis of N-15 translocation at the whole plant level was performed, which indicated that nitrogen recycling among organs was highly dynamic during this period and varied depending on nitrate availability. Leaves collected on vegetative and reproductive nodes were further analyzed by transcriptomics. The data revealed extensive transcriptome changes in leaves of reproductive nodes during early seed development (from flowering to 14 days after flowering), including an up-regulation of genes encoding transporters, and particularly of sulfate that might sustain sulfur metabolism in leaves of the reproductive part. This developmental period was also characterized by a down-regulation of cell wall-associated genes in leaves of both reproductive and vegetative nodes, reflecting a shift in cell wall structure. Later on, 27 days after flowering, genes potentially switching the metabolism of leaves toward senescence were pinpointed, some of which are related to ribosomal RNA processing, autophagy, or transport systems. Transcription factors differentially regulated in leaves between stages were identified and a gene co-expression network pointed out some of them as potential regulators of the above-mentioned biological processes. The same approach was conducted in Medicago truncatula to identify shared regulations with this wild legume species. Altogether the results give a global view of transcriptional events in leaves of legumes at early reproductive stages and provide a valuable resource of candidate genes that could be targeted by reverse genetics to improve nutrient remobilization and/or delay catabolic processes leading to senescence.

Published
2019

28. Development of a sequence-based reference physical map of pea (Pisum sativum L.)

Author

Abdelhafid Bendahmane, Reddy V. B. Lachagari, Jan van Oeveren, Mohammed-Amin Madoui, Bunyamin Tar’an, Edwin A. G. van der Vossen, Thomas D. Warkentin, Karine Labadie, Krishna K. Gali, Judith Burstin, Hélène Bergès, Crop Development Centre, University of Saskatchewan, Genomics Institute, Clemson University, Keygene N.V., Centre National de Ressources Génomiques Végétales (CNRGV), Institut National de la Recherche Agronomique (INRA), Institut des Sciences des Plantes de Paris-Saclay (IPS2 (UMR_9213 / UMR_1403)), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Université d'Évry-Val-d'Essonne (UEVE)-Centre National de la Recherche Scientifique (CNRS), AgriGenome Labs Pvt Ltd, Partenaires INRAE, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Saskatchewan Pulse Growers (SPG), University of Saskatchewan [Saskatoon] (U of S), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Université Paris-Sud - Paris 11 (UP11)-Université Paris Diderot - Paris 7 (UPD7)-Centre National de la Recherche Scientifique (CNRS)-Université d'Évry-Val-d'Essonne (UEVE)-Institut National de la Recherche Agronomique (INRA)

Subjects
0106 biological sciences, 0301 basic medicine, Positional cloning, Plant Science, Computational biology, lcsh:Plant culture, 01 natural sciences, Genome, DNA sequencing, Restriction fragment, analyse de génome, 03 medical and health sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, sequence-based physical map, Pisum sativum, Original Research, 030304 developmental biology, Whole genome sequencing, 0303 health sciences, Bacterial artificial chromosome, Vegetal Biology, biology, Contig, food and beverages, bacterial artificial chromosome, fingerprinted contigs, whole genome profiling, 030104 developmental biology, biology.protein, cartographie, Restriction digest, Biologie végétale, 010606 plant biology & botany
Abstract

Whole genome profiling (WGP) is a sequence-based physical mapping technology and uses sequence tags generated by next generation sequencing for construction of bacterial artificial chromosome (BAC) contigs of complex genomes. The physical map provides a framework for assembly of genome sequence and information for localization of genes that are difficult to find through positional cloning. To address the challenges of accurate assembly of the pea genome (~4.2 GB of which approximately 85% is repetitive sequences), we have adopted the WGP technology for assembly of a pea BAC library. Multi-dimensional pooling of 295,680 BAC clones and sequencing the ends of restriction fragments of pooled DNA generated 1,814 million high quality reads, of which 825 million were deconvolutable to 1.11 million unique WGP sequence tags. These WGP tags were used to assemble 220,013 BACs into contigs. Assembly of the BAC clones using the modified Fingerprinted Contigs (FPC) program has resulted in 13,040 contigs, consisting of 213,719 BACs, and 6,294 singleton BACs. The average contig size is 0.33 Mbp and the N50 contig size is 0.62 Mbp. WGPTM technology has proved to provide a robust physical map of the pea genome, which would have been difficult to assemble using traditional restriction digestion based methods. This sequence-based physical map will be useful to assemble the genome sequence of pea. Additionally, the 1.1 million WGP tags will support efficient assignment of sequence scaffolds to the BAC clones, and thus an efficient sequencing of BAC pools with targeted genome regions of interest.

Published
2019
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29. Key Note speaker Plant resistance and architecture for protection of pulses against biotic stresses

Author

Marie-Laure Nayel, A-A, Josselin, Gilles Boutet, Angélique Lesne, Fabrice Legeai, Rémi Ollivier, Jonathan Kreplak, Gregoire Aubert, Arnaud Bellec, Aurore Desgroux, Kévin Cartelier, Clément Lavaud, Anne Quillevere Hamard, Anthony Klein, Leveugle, M., Olivier Bouchez, Porter, L. D., Christophe Le May, Amandine Rémy, Pascal Marget, Jean-Claude Simon, Virginie Bourion, Coyne, C. J., Akiko Sugio, Catherine Rameau, Judith Burstin, Alain Baranger, ProdInra, Migration, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Centre National de Ressources Génomiques Végétales (CNRGV), BIOGEMMA, Génome et Transcriptome - Plateforme Génomique (GeT-PlaGe), Institut National de la Recherche Agronomique (INRA)-Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), USDA-ARS : Agricultural Research Service, Domaine expérimental d'Époisses - UE0115 U2E (DIJ EPOISSES), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)

Subjects
[SDE] Environmental Sciences, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], fungi, food and beverages, [SDV.GEN] Life Sciences [q-bio]/Genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.IDA] Life Sciences [q-bio]/Food engineering, [SDV] Life Sciences [q-bio], [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDE]Environmental Sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

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 of major resistance QTL [2], as well as Linkage Analysis (LA) [3] and Genome-Wide Association Studies (GWAS) coupled with Genotyping By Sequencing (GBS) technologies, have been developed to identify, compare and study synteny of loci and candidate genes for resistance. Plant and canopy architectures have been studied in pea for their effect on limiting disease severity and epidemics. Alleles at genes controlling aerial or root plant architectural traits were found to cosegregate with resistance alleles at QTL controlling aerial or root diseases [4]. Combining plant resistance and architecture traits unfavourable to diseases and pests will be a key strategy for durable crop protection. Future research will combine other plant traits with resistance and architecture, such as plant ability to select useful micro-organisms or to produce compounds that are beneficial to plant protection, as well as agricultural practices.

Published
2019

30. 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

Author

Catherine Delaitre, Marianne Chabert-Martinello, Brigitte Brunel, Marc Lepetit, Mathieu Siol, Denis Vile, Pierre Tisseyre, Gérard Duc, Véronique Aubert, Marjorie Pervent, Judith Burstin, Virginie Bourion, Karine Heulin-Gotty, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Écophysiologie des Plantes sous Stress environnementaux (LEPSE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), French ANR GENOPEA program, 'INRA-BAP projet scientifique' SYMBIOPEA program, ANR-09-GENM-0026,GENOPEA,Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées(2009), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
0301 basic medicine, competitiveness for nodulation, Plant Science, lcsh:Plant culture, Biology, medicine.disease_cause, Genetic diversity, Plant breeding, Rhizobium leguminosarum, Pisum, 03 medical and health sciences, plant breeding, medicine, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, nodulation, lcsh:SB1-1110, Partner choice, Competitiveness for nodulation, Pea-rhizobium symbiosis, Nitrogen fixation efficiency, Pisum sativum, Rhizobium leguminosarum sv. viciae, rhizobium leguminosarum, Microbial inoculant, pea-rhizobium symbiosis, Original Research, 2. Zero hunger, Vegetal Biology, Strain (biology), food and beverages, genetic diversity, biology.organism_classification, nitrogen fixation efficiency, 030104 developmental biology, Agronomy, fixation de l'azote, diversité génétique, partner choice, Nitrogen fixation, Co inoculation, Biologie végétale, amélioration des plantes
Abstract

International audience; 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.

Published
2018

31. Variability within a pea core collection of LEAM and HSP22, two mitochondrial seed proteins involved in stress tolerance

Author

Judith Burstin, David Macherel, Marie-Hélène Avelange-Macherel, Dimitri Tolleter, Martine Neveu, Nicole Payet, and David Lalanne

Subjects
2. Zero hunger, Genetics, Gene isoform, Molecular mass, Physiology, food and beverages, Plant Science, Biology, biology.organism_classification, Pisum, Desiccation tolerance, Heat shock protein, Coding region, Indel, Gene
Abstract

LEAM, a late embryogenesis abundant protein, and HSP22, a small heat shock protein, were shown to accumulate in the mitochondria during pea (Pisum sativum L.) seed development, where they are expected to contribute to desiccation tolerance. Here, their expression was examined in seeds of 89 pea genotypes by Western blot analysis. All genotypes expressed LEAM and HSP22 in similar amounts. In contrast with HSP22, LEAM displayed different isoforms according to apparent molecular mass. Each of the 89 genotypes harboured a single LEAM isoform. Genomic and RT-PCR analysis revealed four LEAM genes differing by a small variable indel in the coding region. These variations were consistent with the apparent molecular mass of each isoform. Indels, which occurred in repeated domains, did not alter the main properties of LEAM. Structural modelling indicated that the class A α-helix structure, which allows interactions with the mitochondrial inner membrane in the dry state, was preserved in all isoforms, suggesting functionality is maintained. The overall results point out the essential character of LEAM and HSP22 in pea seeds. LEAM variability is discussed in terms of pea breeding history as well as LEA gene evolution mechanisms.

Published
2014

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

Author

Aurore Desgroux, Valentin Baudais, Véronique Aubert, Gwenola Le Roy, Henri de Larambergue, Henri Miteul, Gregoire Aubert, Gilles Boutet, Alain Baranger, Judith Burstin, Maria J. Manzanares-Dauleux, Marie-Laure Pilet-Nayel, Virginie Bourion, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), PISOM, Institut National de la Recherche Agronomique (INRA), Noble Research Institute., ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
[SDV] Life Sciences [q-bio], [SDE] Environmental Sciences, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, food and beverages, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SDV.BV] Life Sciences [q-bio]/Vegetal Biology
Abstract

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 limiting factor of pea crop yield. Consistent quantitative trait loci controlling partial resistance were identified in this species [1,2], and other studies reported its RSA as highly variable and under polygenic control [3]. However, the contribution of RSA to resistance to A. euteiches has not yet been explored in pea. To identify common loci controlling RSA and resistance to A. euteiches, we performed a genome wide association (GWA) study using a collection of 266 pea lines contrasted for root architecture or Aphanomyces root rot resistance. The study used recent 14,157 Single Nucleotide Polymorphism resources developed in pea [4,5]. The collection was phenotyped in controlled conditions and using image analysis. The GWA study identified precise genomic regions controlling RSA and common loci associated with resistance to A. euteiches, opening prospects in mining RSA loci in breeding to limit Aphanomyces root rot severity on pea.

Published
2017

33. Genome-wide association studies with proteomics data reveal genes important for synthesis, transport and packaging of globulins in legume seeds

Author

Christine Le Signor, Julia Buitink, Valérie Labas, Jean Marie Prosperi, Delphine Aime, Jérôme Gouzy, Judith Burstin, Olivier Leprince, Karine Gallardo, Richard D. Thompson, Nevin D. Young, Amandine Bordat, Maya Belghazi, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Centre de recherche en neurobiologie - neurophysiologie de Marseille (CRN2M), Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Centre National de la Recherche Scientifique (CNRS)-Université de Tours-Institut Français du Cheval et de l'Equitation [Saumur]-Institut National de la Recherche Agronomique (INRA), Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Department of Plant Pathology, Cornell University, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, French National Research Agency : ANR-06-GPLA-0008, ANR-09-GENM-026, Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Biologie du fruit et pathologie ( BFP ), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique ( INRA ) -Université Sciences et Technologies - Bordeaux 1, Centre de recherche en neurobiologie - neurophysiologie de Marseille ( CRN2M ), Aix Marseille Université ( AMU ) -Institut National de la Santé et de la Recherche Médicale ( INSERM ) -Centre National de la Recherche Scientifique ( CNRS ), Physiologie de la reproduction et des comportements [Nouzilly] ( PRC ), Institut National de la Recherche Agronomique ( INRA ) -Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique ( CNRS ), Interactions plantes-microorganismes et santé végétale, Institut National de la Recherche Agronomique ( INRA ) -Université Nice Sophia Antipolis ( UNS ), Université Côte d'Azur ( UCA ) -Université Côte d'Azur ( UCA ) -Centre National de la Recherche Scientifique ( CNRS ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur] (IFCE)-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Cornell University [New York], Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
0301 basic medicine, Proteomics, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Candidate gene, [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, protein quantity loci (PQL), Globulin, Physiology, legumes, Plant Science, Chromatin remodeling, 03 medical and health sciences, Gene Expression Regulation, Plant, Botany, Medicago truncatula, genome-wide association studies (GWAS), vegetable, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Electrophoresis, Gel, Two-Dimensional, Gene Regulatory Networks, Gene, Transcription factor, [ SDV.SA ] Life Sciences [q-bio]/Agricultural sciences, Plant Proteins, 2. Zero hunger, Genetics, seed proteome, amélioration génétique, biology, Pisum sativum (pea), Seed Storage Proteins, Peas, food and beverages, légume, biology.organism_classification, Protein Transport, 030104 developmental biology, Vicilin, Mutation, Seeds, biology.protein, qualité des semences, semence, globulins, Genome-Wide Association Study, Transcription Factors
Abstract

AGAP : équipe GE2pop; Improving nutritional seed quality is an important challenge in grain legume breeding. However, the genes controlling the differential accumulation of globulins, which are major contributors to seed nutritional value in legumes, remain largely unknown. We combined a search for protein quantity loci with genome-wide association studies on the abundance of 7S and 11S globulins in seeds of the model legume species Medicago truncatula. Identified genomic regions and genes carrying polymorphisms linked to globulin variations were then cross-compared with pea (Pisum sativum), leading to the identification of candidate genes for the regulation of globulin abundance in this crop. Key candidates identified include genes involved in transcription, chromatin remodeling, post-translational modifications, transport and targeting of proteins to storage vacuoles. Inference of a gene coexpression network of 12 candidate transcription factors and globulin genes revealed the transcription factor ABA-insensitive 5 (ABI5) as a highly connected hub. Characterization of loss-of-function abi5 mutants in pea uncovered a role for ABI5 in controlling the relative abundance of vicilin, a sulfur-poor 7S globulin, in pea seeds. This demonstrates the feasibility of using genome-wide association studies in M. truncatula to reveal genes that can be modulated to improve seed nutritional value.

Published
2017

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

Author

Christine Le Signor, Charlotte Henriet, Julia Buitink, Young, Nevin D., Jean-Marie Prosperi, Vanessa Vernoud, Gregoire Aubert, Olivier Leprince, Richard Thompson, Judith Burstin, Karine Gallardo-Guerrero, ProdInra, Migration, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of plant pathology, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), and Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)

Subjects
[SDV.SA]Life Sciences [q-bio]/Agricultural sciences, [SDV.SA] Life Sciences [q-bio]/Agricultural sciences
Abstract

National audience; voir pdf

Published
2017

35. D’un répertoire de gènes contrôlant la composition protéique des graines des légumineuses vers de nouveaux profils protéiques

Author

Christine Le Signor, Delphine Aime, Myriam Sanchez, Julia Buitink, Young, Nevin D., Jean-Marie Prosperi, Olivier Leprince, Charlotte Henriet, Gregoire Aubert, Vanessa Vernoud, Richard Thompson, Judith Burstin, Karine Gallardo, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Recherche en Horticulture et Semences (IRHS), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Department of plant pathology, University of Minnesota [Twin Cities] (UMN), University of Minnesota System-University of Minnesota System, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut National de la Recherche Agronomique (INRA). FRA.

Subjects
[SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2017

36. QTL analysis of frost damage in pea suggests different mechanisms involved in frost tolerance

Author

Judith Burstin, Céline Rond, Hervé Houtin, Pascal Marget, Karen Boucherot, Françoise Jacquin, Anthony Klein, Nathalie Rivière, Isabelle Lejeune-Hénaut, Gilles Boutet, Myriam Huart, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, BIOGEMMA, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), Institut National de la Recherche Agronomique (INRA)-Université de Lille, Sciences et Technologies, Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Stress Abiotiques et Différenciation des Végétaux Cultivés ( SADV ), Institut National de la Recherche Agronomique ( INRA ) -Université de Lille, Sciences et Technologies, AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), and Université de Lille, Sciences et Technologies-Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV]Life Sciences [q-bio], Quantitative Trait Loci, Population, Context (language use), Biology, Field pea, Inbred strain, Stress, Physiological, Freezing, Genetics, Temperate climate, Cultivar, education, 2. Zero hunger, Principal Component Analysis, education.field_of_study, [ SDV ] Life Sciences [q-bio], Peas, food and beverages, General Medicine, biology.organism_classification, eye diseases, Phenotype, Agronomy, Plant protein, Frost, Agronomy and Crop Science, Biotechnology
Abstract

International audience; Avoidance mechanisms and intrinsic resistance are complementary strategies to improve winter frost tolerance and yield potential in field pea. The development of the winter pea crop represents a major challenge to expand plant protein production in temperate areas. Breeding winter cultivars requires the combination of freezing tolerance as well as high seed productivity and quality. In this context, we investigated the genetic determinism of winter frost tolerance and assessed its genetic relationship with yield and developmental traits. Using a newly identified source of frost resistance, we developed a population of recombinant inbred lines and evaluated it in six environments in Dijon and Clermont-Ferrand between 2005 and 2010. We developed a genetic map comprising 679 markers distributed over seven linkage groups and covering 947.1 cM. One hundred sixty-one quantitative trait loci (QTL) explaining 9-71 % of the phenotypic variation were detected across the six environments for all traits measured. Two clusters of QTL mapped on the linkage groups III and one cluster on LGVI reveal the genetic links between phenology, morphology, yield-related traits and frost tolerance in winter pea. QTL clusters on LGIII highlighted major developmental gene loci (Hr and Le) and the QTL cluster on LGVI explained up to 71 % of the winter frost damage variation. This suggests that a specific architecture and flowering ideotype defines frost tolerance in winter pea. However, two consistent frost tolerance QTL on LGV were independent of phenology and morphology traits, showing that different protective mechanisms are involved in frost tolerance. Finally, these results suggest that frost tolerance can be bred independently to seed productivity and quality.

Published
2014

37. A protein quantity loci approach combined with a genome-wide association study revealed regulators of protein accumulation in legume seeds

Author

Christine Le Signor, Delphine Aime, Young, N. D., Jean-Marie Prosperi, Richard Thompson, Julia Buitink, Judith Burstin, Karine Gallardo-Guerrero, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), Department of Plant Biology, The Royal Veterinary and Agricultural University, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC ), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales ( UMR AGAP ), Institut national de la recherche agronomique [Montpellier] ( INRA Montpellier ) -Centre international d'études supérieures en sciences agronomiques ( Montpellier SupAgro ) -Centre de Coopération Internationale en Recherche Agronomique pour le Développement ( CIRAD ) -Institut national d’études supérieures agronomiques de Montpellier ( Montpellier SupAgro ), Institut de Recherche en Horticulture et Semences ( IRHS ), Université d'Angers ( UA ) -Institut National de la Recherche Agronomique ( INRA ) -AGROCAMPUS OUEST, Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Royal Veterinary and Agricultural University = Kongelige Veterinær- og Landbohøjskole (KVL ), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université d'Angers (UA)-Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, and Legume Society.

Subjects
[ SDV ] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], food and beverages
Abstract

BAPGEAPSI; The seeds of grain legumes provide proteins (20-40% protein content depending on species) for human nutrition and animal feed. The nutritional and technological quality of legume seeds is mainly determined by the composition and functional properties of the seed protein fractions. By accounting for up to 70% of total proteins in mature seeds, the globulins are major determinants of seed quality. In pea, which is one of the grain legumes most cultivated in Europe, the variability in the abundance of globulin polypeptides across lines is significant, which might enable a wide range of food application. To provide knowledge about the molecular determinants underlying differences in seed protein composition, we have used the model legume species M. truncatula for which extensive genetics and genomics resources were available (Young and Bharti, 2012), along with comprehensive transcriptomics data related to seed development (Benedito et al., 2008; Thompson et al., 2009). A PQL approach identified the genomic regions controlling variations in seed protein composition, and a translational approach exploiting the resources developed for M. truncatula and pea provided a set of candidate genes underlying PQLs conserved between the two species. The candidate gene selection was then refined by genome-wide association studies (GWAS), which enabled the identification of nucleotide variations associated with variations in globulin synthesis and/or maturation.

Published
2016

38. The PeaMUST project: defining ideotypes for the pea crop development

Author

Nadim Tayeh, Judith Burstin, Virginie Bourion, Catherine Rameau, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Université Paris Saclay (COmUE)

Subjects
0106 biological sciences, 0301 basic medicine, durable resistance, [SDV]Life Sciences [q-bio], pea, lcsh:TP670-699, Biology, 01 natural sciences, Biochemistry, genomic selection, Crop, Fight-or-flight response, 03 medical and health sciences, [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, aerial and root architecture, Selection (genetic algorithm), 2. Zero hunger, business.industry, Crop yield, food and beverages, Ideotype, ideotype, Biotechnology, 030104 developmental biology, [SDE]Environmental Sciences, lcsh:Oils, fats, and waxes, business, Agronomy and Crop Science, Genomic selection, 010606 plant biology & botany, Food Science
Abstract

Pea is the most widely cultivated grain legume crop in Europe. In the French research project PeaMUST, a large public and private sector partnership has been set up to undertake complementary strategies towards the development of high and stable yielding cultivars. These different strategies will contribute to the definition of a pea ideotype based on both a priori and a posteriori approaches. On the one hand, genomic selection will identify interesting genotypes which may display new phenotypic ideotypes. On the other hand, marker-assisted selection will enable cumulating resistance for a given or different stresses to reach more durably stable phenotypes. Moreover, mutations identified in candidate genes controlling aerial and root architecture will be tested for their effects on stress tolerance.

Published
2018

39. Identification of LATE BLOOMER2 as a CYCLING DOF FACTOR Homolog Reveals Conserved and Divergent Features of the Flowering Response to Photoperiod in Pea

Author

Jacqueline K. Vander Schoor, Valérie Hecht, Judith Burstin, Richard C. Macknight, Grégoire Aubert, James L. Weller, Stephen Ridge, Frances C. Sussmilch, Robyn Lee, Department of Plant Sciences, University of California, School of Biological Sciences [Hobart], University of Tasmania [Hobart, Australia] (UTAS), Department of Biochemistry, Hôpital Lapeyronie, Agroécologie [Dijon], Université de Bourgogne (UB)-Institut National de la Recherche Agronomique (INRA)-Université Bourgogne Franche-Comté [COMUE] (UBFC)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, University of Tasmania (UTAS), Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté [COMUE] (UBFC), University of Tasmania, and Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Université Bourgogne Franche-Comté ( UBFC )

Subjects
0106 biological sciences, 0301 basic medicine, endocrine system, Photoperiod, [SDV]Life Sciences [q-bio], Circadian clock, Mutant, pea, Arabidopsis, Locus (genetics), Plant Science, Flowers, Biology, 01 natural sciences, 03 medical and health sciences, Transcription (biology), Gene Expression Regulation, Plant, LATE2, Gene, Research Articles, gene identification, Genetics, photoperiodism, Regulation of gene expression, flowering, [ SDV ] Life Sciences [q-bio], Arabidopsis Proteins, Peas, food and beverages, Cell Biology, biology.organism_classification, 030104 developmental biology, photoperiod response, 010606 plant biology & botany
Abstract

BAPGEAPSISUPDAT; The molecular pathways responsible for the flowering response to photoperiod have been extensively studied in Arabidopsis thaliana and cereals but remain poorly understood in other major plant groups. Here, we describe a dominant mutant at the LATE BLOOMER2 (LATE2) locus in pea (Pisum sativum) that is late-flowering with a reduced response to photoperiod. LATE2 acts downstream of light signaling and the circadian clock to control expression of the main photoperiod-regulated FT gene, FTb2, implying that it plays a primary role in photoperiod measurement. Mapping identified the CYCLING DOF FACTOR gene CDFc1 as a strong candidate for LATE2, and the late2-1D mutant was found to carry a missense mutation in CDFc1 that impairs its capacity to bind to the blue-light photoreceptor FKF1 in yeast two-hybrid assays and delays flowering in Arabidopsis when overexpressed. Arabidopsis CDF genes are important negative regulators of CONSTANS (CO) transcription, but we found no effect of LATE2 on the transcription of pea CO-LIKE genes, nor on genes in any other families previously implicated in the activation of FT in Arabidopsis. Our results reveal an important component of the pea photoperiod response pathway and support the view that regulation of FTb2 expression by photoperiod occurs via a CO-independent mechanism.

Published
2016

40. De novo construction of a 'Gene-space' for diploid plant genome rich in repetitive sequences by an iterative Process of Extraction and Assembly of NGS reads (iPEA protocol) with limited computing resources

Author

Judith Burstin, Christelle Aluome, Dominique Brunel, Susete Alves Carvalho, Marie-Christine Le Paslier, Grégoire Aubert, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Etude du Polymorphisme des Génomes Végétaux (EPGV), and Institut National de la Recherche Agronomique (INRA)

Subjects
0301 basic medicine, Genotyping Techniques, [SDV]Life Sciences [q-bio], Assembly, Sequence assembly, UniGene, Genomics, Computational biology, Biology, Limited computing resources, Unigene, Genome, Polymorphism, Single Nucleotide, General Biochemistry, Genetics and Molecular Biology, Next-generation sequencing NGS, 03 medical and health sciences, lterative process, Technical Note, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, Sequence (medicine), Repetitive Sequences, Nucleic Acid, Genetics, Medicine(all), gene-space, unigene, next-generation sequencing NGS, assembly, limited computing resources, Contig, Base Sequence, Biochemistry, Genetics and Molecular Biology(all), Peas, Computational Biology, High-Throughput Nucleotide Sequencing, Reproducibility of Results, food and beverages, General Medicine, Diploidy, 030104 developmental biology, Gene-space, [SDE]Environmental Sciences, Iterative process, Algorithms, Genome, Plant, SNP array
Abstract

Background The continuing increase in size and quality of the “short reads” raw data is a significant help for the quality of the assembly obtained through various bioinformatics tools. However, building a reference genome sequence for most plant species remains a significant challenge due to the large number of repeated sequences which are problematic for a whole-genome quality de novo assembly. Furthermore, for most SNP identification approaches in plant genetics and breeding, only the “Gene-space” regions including the promoter, exon and intron sequences are considered. Results We developed the iPea protocol to produce a de novo Gene-space assembly by reconstructing, in an iterative way, the non-coding sequence flanking the Unigene cDNA sequence through addition of next-generation DNA-seq data. The approach was elaborated with the large diploid genome of pea (Pisumsativum L.), rich in repetitive sequences. The final Gene-space assembly included 35,400 contigs (97 Mb), covering 88 % of the 40,227 contigs (53.1 Mb) of the PsCam_low-copy Unigen set. Its accuracy was validated by the results of the built GenoPea 13.2 K SNP Array. Conclusion The iPEA protocol allows the reconstruction of a Gene-space based from RNA-Seq and DNA-seq data with limited computing resources. Electronic supplementary material The online version of this article (doi:10.1186/s13104-016-1903-z) contains supplementary material, which is available to authorized users.

Published
2016

41. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea

Author

Nadim Tayeh, Virginie L’Anthoëne, Alain Baranger, Judith Burstin, Jean-Philippe Rivière, Anne Moussart, Virginie Bourion, Clarice J. Coyne, Martine Roux-Duparque, Pierrick Vetel, Grégoire Aubert, Rebecca J. McGee, Marie-Laure Pilet-Nayel, Pierre Mangin, Christophe Piriou, Aurore Desgroux, Maria J. Manzanares-Dauleux, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, GSP, Domaine Brunehaut, Amélioration des Plantes et Biotechnologies Végétales (APBV), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion (http://www.u949.inserm.fr/), Université de Strasbourg (UNISTRA)-EFS-Institut National de la Santé et de la Recherche Médicale (INSERM), Grain Legume Genet & Physiol Res Unit, United States Department of Agriculture, Washington State University (WSU), USDA Agricultural Research Service [Maricopa, AZ] (USDA), United States Department of Agriculture - USDA (USA), PISOM, Institut National de la Recherche Agronomique (INRA), Ministere de l'Agriculture, de l'Agroalimentaire et de la Foret (FR), INRA, Terres Univia, ANR-09-GENM-026, ANR project GenoPea, Cliquet, Catherine, Génomique et biotechnologies végétales - Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées - - GENOPEA2009 - ANR-09-GENM-0026 - GENOM-BTV - VALID, Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion, United States Department of Agriculture (USDA), ANR-09-GENM-0026,GENOPEA,Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées(2009), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, Amélioration des Plantes et Biotechnologies Végétales ( APBV ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biologie et pharmacologie des plaquettes sanguines: hémostase, thrombose, transfusion ( http://www.u949.inserm.fr/ ), Université de Strasbourg ( UNISTRA ) -EFS-Institut National de la Santé et de la Recherche Médicale ( INSERM ), Washington State University ( WSU ), United States Department of Agriculture ( USDA ), Institut National de la Recherche Agronomique ( INRA ), and Université de Strasbourg (UNISTRA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-EFS

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Root rot, Linkage disequilibrium, Candidate gene, 01 natural sciences, Linkage Disequilibrium, résistance partielle, aphanomyces euteiches, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, GWAS, pisum sativum, Disease Resistance, 2. Zero hunger, Genetics, Vegetal Biology, qtl, [ SDV.BV.PEP ] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Chromosome Mapping, food and beverages, Phenotype, genome wide association study (GWAS), [ SDV.GEN.GPL ] Life Sciences [q-bio]/Genetics/Plants genetics, gène candidat, Aphanomyces euteiches, Research Article, Biotechnology, Genetic Markers, polymorphisme nucléotidique simple (SNP), Quantitative trait loci, Genotype, Plant disease resistance, Aphanomyces, Biology, Quantitative trait locus, Polymorphism, Single Nucleotide, Candidate genes, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Genetic linkage, Pea (Pisum sativum), Marker haplotype, Confidence Intervals, Alleles, Genetic Association Studies, [SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Plant Diseases, Models, Genetic, candidate gene, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, 030104 developmental biology, Haplotypes, Genetic marker, peas, Biologie végétale, 010606 plant biology & botany
Abstract

Background Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. Methods A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. Results GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. Conclusion This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2429-4) contains supplementary material, which is available to authorized users.

Published
2016

42. Génétique et génomique du pois : what else ?

Author

Judith Burstin, Tayeh, Nadim N., Anthony Klein, Virginie Bourion, Jonathan Kreplak, Françoise Jacquin, Susete Alves Carvalho, Christelle Aluome, Sebastien Carrere, Jerome Gouzy, Corinne Cruaud, Gérard Duc, Pascal Gamas, Brunel, Dominique D., Matthieu Falque, Marie-Christine Le Paslier, Patrick Wincker, Aubert, Gregoire G., Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Bayer Cropscience, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), Société Nationale d'Horticulture de France (SNHF). FRA., Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS)

Subjects
pois, [SDV]Life Sciences [q-bio], [SDE]Environmental Sciences, génétique, génomique, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2016

43. Dissecting the proteome of pea mature seeds reveals the phenotypic plasticity of seed protein composition

Author

Nicolas Sommerer, Judith Burstin, Françoise Jacquin, Vincent Savois, Céline Henry, Michael Bourgeois, Valérie Labas, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Sciences Pour l'Oenologie (SPO), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université Montpellier 1 (UM1)-Université de Montpellier (UM)-Institut National de la Recherche Agronomique (INRA), Physiologie de la reproduction et des comportements [Nouzilly] (PRC), Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours (UT)-Centre National de la Recherche Scientifique (CNRS), Biochimie bactérienne (BIOBAC), Institut National de la Recherche Agronomique (INRA), and Institut National de la Recherche Agronomique (INRA)-Institut Français du Cheval et de l'Equitation [Saumur]-Université de Tours-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, 0106 biological sciences, Proteome, Globulin, Environment, CARTE PROTEOMIQUE, 01 natural sciences, Biochemistry, Pisum, 03 medical and health sciences, Sativum, Gene Expression Regulation, Plant, PHENOTYPIC PLASTICITY, Botany, Storage protein, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Electrophoresis, Gel, Two-Dimensional, PREMOBILIZATION, Molecular Biology, Plant Proteins, 030304 developmental biology, 2. Zero hunger, chemistry.chemical_classification, Analysis of Variance, 0303 health sciences, biology, Seed Storage Proteins, Peas, food and beverages, Plant physiology, STORAGE PROTEINS, biology.organism_classification, Phenotype, chemistry, PEA SEED PROTEIN COMPOSITION, Germination, Seeds, biology.protein, 2-DE REFERENCE MAP, 010606 plant biology & botany
Abstract

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; Pea (Pisum sativum L.) is the most cultivated European pulse crop and the pea seeds mainly serve as a protein source for monogastric animals. Because the seed protein composition impacts on seed nutritional value, we aimed at identifying the determinants of its variability. This paper presents the first pea mature seed proteome reference map, which includes 156 identified proteins (http://www.inra.fr/legumbase/peaseedmap/). This map provides a fine dissection of the pea seed storage protein composition revealing a large diversity of storage proteins resulting both from gene diversity and post-translational processing. It gives new insights into the pea storage protein processing (especially 7S globulins) as a possible adaptation towards progressive mobilization of the proteins during germination. The nonstorage seed proteome revealed the presence of proteins involved in seed defense together with proteins preparing germination. The plasticity of the seed proteome was revealed for seeds produced in three successive years of cultivation, and 30% of the spots were affected by environmental variations. This work pinpoints seed proteins most affected by environment, highlighting new targets to stabilize storage protein composition that should be further analyzed.

Published
2009

44. Genomic tools in pea breeding programs: status and perspectives

Author

Nadim Tayeh, Judith Burstin, Thomas D. Warkentin, Isabelle Lejeune-Hénaut, Marie-Laure Pilet-Nayel, Grégoire Aubert, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut Charles Viollette (ICV) - EA 7394 (ICV), Université d'Artois (UA)-Institut National de la Recherche Agronomique (INRA)-Université du Littoral Côte d'Opale (ULCO)-Institut Supérieur d'Agriculture-Université de Lille, University of Saskatchewan [Saskatoon] (U of S), French National Research Agency (ANR) Project Investissements d'Avenir PeaMUST [ANR-11-BTBR-0002], ANR-11-BTBR-0002,PeaMUST,Adaptation multistress et régulations biologiques pour l'amélioration du rendement et de la stabilité du pois protéagineux(2011), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Université du Littoral Côte d'Opale (ULCO)-Université de Lille-Institut National de la Recherche Agronomique (INRA)-Université d'Artois (UA)-Institut Supérieur d'Agriculture, University of Saskatchewan, and Burstin, Judith

Subjects
0106 biological sciences, Mini Review, [SDV]Life Sciences [q-bio], Plant Science, pea (Pisum sativum L.), breeding targets, lcsh:Plant culture, Biology, 01 natural sciences, genotyping platforms, 03 medical and health sciences, Sativum, OTL and association mapping, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, Domestication, Legume, 030304 developmental biology, 2. Zero hunger, 0303 health sciences, Genetic diversity, Resistance (ecology), Abiotic stress, business.industry, food and beverages, genetic diversity, Biotechnology, QTL and association mapping, genetic maps, [SDE]Environmental Sciences, Livestock, genomic resources, business, Genomic selection, 010606 plant biology & botany
Abstract

International audience; Pea (Pisum sativum L.) is an annual cool season legume and one of the oldest domesticated crops. Dry pea seeds contain 22-25% protein, complex starch and fiber constituents, and a rich array of vitamins, minerals, and phytochemicals which make them a valuable source for human consumption and livestock feed. Dry pea ranks third to common bean and chickpea as the most widely grown pulse in the world with more than 11 million tons produced in 2013. Pea breeding has achieved great success since the time of Mendel's experiments in the mid-1800s. However, several traits still require significant improvement for better yield stability in a larger growing area. Key breeding objectives in pea include improving biotic and abiotic stress resistance and enhancing yield components and seed quality. Taking advantage of the diversity present in the pea genepool, many mapping populations have been constructed in the last decades and efforts have been deployed to identify loci involved in the control of target traits and further introgress them into elite breeding materials. Pea now benefits from next-generation sequencing and high-throughput genotyping technologies that are paving the way for genome-wide association studies and genomic selection approaches. This review covers the significant development and deployment of genomic tools for pea breeding in recent years. Future prospects are discussed especially in light of current progress toward deciphering the pea genome.

Published
2015

45. Genetic diversity and trait genomic prediction in a pea diversity panel

Author

Gérard Duc, Marianne Chabert-Martinello, Caroline Pont, Grégoire Aubert, Pauline Salloignon, Judith Burstin, Aurélie Chauveau, Catherine Delaitre, Françoise Jacquin, Mathieu Siol, Jean Bernard Magnin-Robert, Caroline Truntzer, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Université de Bourgogne (UB), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de la Recherche Agronomique (INRA)-Université Blaise Pascal - Clermont-Ferrand 2 (UBP), pea CRB project, FP7-GLIP project, FEDER-Region Bourgogne project 'Qualite de la graine de pois', ANR Bioressources GENOPEA project, and Université Blaise Pascal - Clermont-Ferrand 2 (UBP)-Institut National de la Recherche Agronomique (INRA)

Subjects
Genetic Markers, 0106 biological sciences, Genotype, [SDV]Life Sciences [q-bio], Best linear unbiased prediction, Biology, Polymorphism, Single Nucleotide, 01 natural sciences, 03 medical and health sciences, Sativum, Genetic variation, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Least-Squares Analysis, 030304 developmental biology, 2. Zero hunger, Principal Component Analysis, 0303 health sciences, Genetic diversity, business.industry, Peas, Discriminant Analysis, Genetic Variation, food and beverages, Bayes Theorem, 15. Life on land, Marker-assisted selection, Biotechnology, Phenotype, 13. Climate action, Evolutionary biology, Genetic marker, [SDE]Environmental Sciences, Linear Models, Trait, Rate of evolution, business, Genome, Plant, Microsatellite Repeats, Research Article, 010606 plant biology & botany
Abstract

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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1266-1) contains supplementary material, which is available to authorized users.

Published
2015

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

Author

Jean-Bernard Magnin-Robert, Hervé Houtin, Anthony Klein, Judith Burstin, Céline Rond, Pascal Marget, Nadim Tayeh, Françoise Jacquin, Marianne Chabert-Martinello, Marie-Christine Le Paslier, Grégoire Aubert, Tayeh, Nadim, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), French National Research Agency (ANR) [ANR-09-GENM-026], and Project Investissements d'Avenir PeaMUST [ANR-11-BTBR-0002]

Subjects
[SDV]Life Sciences [q-bio], Population, GenoPea 13.2K SNP Array, Plant Science, Biology, training set, lcsh:Plant culture, genomic selection, chemistry.chemical_compound, Inbred strain, Molecular marker, prediction accuracy, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, lcsh:SB1-1110, education, Genotyping, Selection (genetic algorithm), Original Research, 2. Zero hunger, education.field_of_study, business.industry, Population size, Pea (Pisum sativum L.), Biotechnology, Marker density, chemistry, Test set, [SDE]Environmental Sciences, Trait, pea (Pisum sativum L.), marker density, business
Abstract

International audience; Pea 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.

Published
2015

47. Full-length de novo assembly of RNA-seq data in pea (Pisum sativum L.) provides a gene expression atlas and gives insights into root nodulation in this species

Author

Anthony Klein, Judith Burstin, Patrick Wincker, Karen Boucherot, Corinne Cruaud, Françoise Jacquin, Sandra Moreau, Susete Alves-Carvalho, Jonathan Kreplak, Sébastien Carrère, Grégoire Aubert, Jérôme Gouzy, Anne-Lise Brochot, Pascal Gamas, Chantal Martin, Corinne Da Silva, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Consortium national de recherche en génomique, and Agence Nationale de la Recherche [ANR-09-GENM-026]

Subjects
[SDV]Life Sciences [q-bio], UniGene, Sequence assembly, RNA-Seq, Plant Science, Biology, de novo assembly, nodule development, Plant Root Nodulation, Plant Roots, DNA sequencing, Transcriptome, Gene Expression Regulation, Plant, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, 2. Zero hunger, Whole genome sequencing, cDNA library, Peas, High-Throughput Nucleotide Sequencing, food and beverages, nitrogen symbiotic fixation, Cell Biology, gene expression atlas, RNA, Plant, [SDE]Environmental Sciences, next-generation sequencing, Pisum sativum L
Abstract

Next-generation sequencing technologies allow an almost exhaustive survey of the transcriptome, even in species with no available genome sequence. To produce a Unigene set representing most of the expressed genes of pea, 20 cDNA libraries produced from various plant tissues harvested at various developmental stages from plants grown under contrasting nitrogen conditions were sequenced. Around one billion reads and 100 Gb of sequence were de novo assembled. Following several steps of redundancy reduction, 46 099 contigs with N50 length of 1667 nt were identified. These constitute the 'Caméor' Unigene set. The high depth of sequencing allowed identification of rare transcripts and detected expression for approximately 80% of contigs in each library. The Unigene set is now available online (http://bios.dijon.inra.fr/FATAL/cgi/pscam.cgi), allowing (i) searches for pea orthologs of candidate genes based on gene sequences from other species, or based on annotation, (ii) determination of transcript expression patterns using various metrics, (iii) identification of uncharacterized genes with interesting patterns of expression, and (iv) comparison of gene ontology pathways between tissues. This resource has allowed identification of the pea orthologs of major nodulation genes characterized in recent years in model species, as a major step towards deciphering unresolved pea nodulation phenotypes. In addition to a remarkable conservation of the early transcriptome nodulation apparatus between pea and Medicago truncatula, some specific features were highlighted. The resource provides a reference for the pea exome, and will facilitate transcriptome and proteome approaches as well as SNP discovery in pea.

Published
2015

48. Pea

Author

Thomas D. Warkentin, Petr Smýkal, Clarice J. Coyne, Norman Weeden, Claire Domoney, Deng-Jin Bing, Antonio Leonforte, Zong Xuxiao, Girish Prasad Dixit, Lech Boros, Kevin E. McPhee, Rebecca J. McGee, Judith Burstin, and Thomas Henry Noel Ellis

Published
2015

49. Development of two major resources for pea genomics: the GenoPea 13.2K SNP Array and a high-density, high-resolution consensus genetic map

Author

Anthony Klein, Marie-Christine Le Paslier, Grégoire Aubert, Judith Burstin, Jonathan Kreplak, Hervé Houtin, Alain Baranger, Nadim Tayeh, Françoise Jacquin, Christelle Aluome, Marie-Laure Pilet-Nayel, Chantal Martin, Aurélie Chauveau, Céline Rond, Matthieu Falque, Pascal Marget, Karen Boucherot, Thomas D. Warkentin, Dominique Brunel, Aurélie Bérard, Agroécologie [Dijon], Institut National de la Recherche Agronomique (INRA)-Université de Bourgogne (UB)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Biodiversité, Gènes & Communautés (BioGeCo), Institut National de la Recherche Agronomique (INRA)-Université de Bordeaux (UB), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) (GQE-Le Moulon), Institut National de la Recherche Agronomique (INRA)-Université Paris-Sud - Paris 11 (UP11)-AgroParisTech-Centre National de la Recherche Scientifique (CNRS), Etude du Polymorphisme des Génomes Végétaux (EPGV), Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, University of Saskatchewan [Saskatoon] (U of S), Chercheur indépendant, Agence Nationale de la Recherche, ANR-09-GENM-026, GENOPEA, ANR-09-GENM-0026,GENOPEA,Génomique comparative du cycle de l'azote entre M. truncatula et le pois : étude des potentialités de transfert des connaissances entre espèces modèles et cultivées(2009), Biodiversité, Gènes et Communautés, Centre National de la Recherche Scientifique (CNRS)-AgroParisTech-Université Paris-Sud - Paris 11 (UP11)-Institut National de la Recherche Agronomique (INRA), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Institut National de la Recherche Agronomique ( INRA ), Génétique Quantitative et Evolution - Le Moulon (Génétique Végétale) ( GQE-Le Moulon ), Institut National de la Recherche Agronomique ( INRA ) -Université Paris-Sud - Paris 11 ( UP11 ) -AgroParisTech-Centre National de la Recherche Scientifique ( CNRS ), Etude du Polymorphisme des Génomes Végétaux ( EPGV ), Institut de Génétique, Environnement et Protection des Plantes ( IGEPP ), Institut National de la Recherche Agronomique ( INRA ) -Université de Rennes 1 ( UR1 ), Université de Rennes ( UNIV-RENNES ) -Université de Rennes ( UNIV-RENNES ) -AGROCAMPUS OUEST, University of Saskatchewan [Saskatoon] ( U of S ), Centre National de Génotypage, CEA/DSV/IG, Commissariat à l'énergie atomique et aux énergies alternatives (CEA), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and ANR-11-BTBR-0002,PeaMUST,Adaptation multistress et régulations biologiques pour l'amélioration du rendement et de la stabilité du pois protéagineux(2011)

Subjects
polymorphisme nucléotidique simple (SNP), [ SDV.BV ] Life Sciences [q-bio]/Vegetal Biology, recombinant inbred lines, carte génétique, DNA, Plant, Genotype, GenoPea 13.2K SNP Array, marqueur génomique, Genomics, Plant Science, Computational biology, pea (Pisum sativum L.), Biology, Molecular Inversion Probe, Polymorphism, Single Nucleotide, Genome, Chromosomes, Plant, Gene mapping, Gene Expression Regulation, Plant, single nucleotide polymorphism, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, pisum sativum, Synteny, 2. Zero hunger, Whole genome sequencing, consensus genetic map, synteny, Chromosome Mapping, High-Throughput Nucleotide Sequencing, food and beverages, genome structure and organization, Sequence Analysis, DNA, Cell Biology, Tag SNP, duplication, peas, genetic mapping, Transcriptome, organisation du génôme, Genome, Plant, SNP array
Abstract

International audience; Single nucleotide polymorphism (SNP) arrays represent important genotyping tools for innovative strategies in both basic research and applied breeding. Pea is an important food, feed and sustainable crop with a large (about 4.45 Gbp) but not yet available genome sequence. In the present study, 12 pea recombinant inbred line populations were genotyped using the newly developed GenoPea 13.2K SNP Array. Individual and consensus genetic maps were built providing insights into the structure and organization of the pea genome. Largely collinear genetic maps of 3918-8503 SNPs were obtained from all mapping populations, and only two of these exhibited putative chromosomal rearrangement signatures. Similar distortion patterns in different populations were noted. A total of 12 802 transcript-derived SNP markers placed on a 15 079-marker high-density, high-resolution consensus map allowed the identification of ohnologue-rich regions within the pea genome and the localization of local duplicates. Dense syntenic networks with sequenced legume genomes were further established, paving the way for the identification of the molecular bases of important agronomic traits segregating in the mapping populations. The information gained on the structure and organization of the genome from this research will undoubtedly contribute to the understanding of the evolution of the pea genome and to its assembly. The GenoPea 13.2K SNP Array and individual and consensus genetic maps are valuable genomic tools for plant scientists to strengthen pea as a model for genetics and physiology and enhance breeding.

Published
2015

50. Functional mapping in pea, as an aid to the candidate gene selection and for investigating synteny with the model legume Medicago truncatula

Author

A. Petit, Julie Morin, Marie-Christine Quillet, Judith Burstin, Isabelle Lejeune-Hénaut, Françoise Jacquin, Thierry Huguet, Grégoire Aubert, Catherine Rameau, K. Loridon, UMR 0102 - Unité de Recherche Génétique et Ecophysiologie des Légumineuses, Génétique et Ecophysiologie des Légumineuses à Graines (UMRLEG) (UMR 102), Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Etablissement National d'Enseignement Supérieur Agronomique de Dijon (ENESAD)-Institut National de la Recherche Agronomique (INRA)-AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement, Domaine Brunehaut, Institut National de la Recherche Agronomique (INRA), Stress Abiotiques et Différenciation des Végétaux Cultivés (SADV), Institut National de la Recherche Agronomique (INRA)-Université de Lille, Sciences et Technologies, Unité de recherche Génétique et amélioration des plantes (GAP), Unité mixte de recherche interactions plantes-microorganismes, Institut National de la Recherche Agronomique (INRA)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)

Subjects
Genetic Markers, 0106 biological sciences, Candidate gene, DNA, Plant, Genotype, Positional cloning, Genetic Linkage, Transposon tagging, Single-nucleotide polymorphism, Flowers, QTLS, CARTOGRAPHIE GENETIQUE, Genes, Plant, Models, Biological, Polymorphism, Single Nucleotide, Synteny, 01 natural sciences, Chromosomes, Plant, 03 medical and health sciences, Gene mapping, Databases, Genetic, Medicago truncatula, Genetics, Selection, Genetic, GENETIQUE VEGETALE, Gene, Polymorphism, Single-Stranded Conformational, 030304 developmental biology, 2. Zero hunger, QUANTITATIVE TRAIT LOCI, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, biology, Peas, Chromosome Mapping, food and beverages, General Medicine, biology.organism_classification, Agronomy and Crop Science, Microsatellite Repeats, 010606 plant biology & botany, Biotechnology
Abstract

Publication Inra prise en compte dans l'analyse bibliométrique des publications scientifiques mondiales sur les Fruits, les Légumes et la Pomme de terre. Période 2000-2012. http://prodinra.inra.fr/record/256699; International audience; The identification of the molecular polymorphisms giving rise to phenotypic trait variability—both quantitative and qualitative—is a major goal of the present agronomic research. Various approaches such as positional cloning or transposon tagging, as well as the candidate gene strategy have been used to discover the genes underlying this variation in plants. The construction of functional maps, i.e. composed of genes of known function, is an important component of the candidate gene approach. In the present paper we report the development of 63 single nucleotide polymorphism markers and 15 single-stranded conformation polymorphism markers for genes encoding enzymes mainly involved in primary metabolism, and their genetic mapping on a composite map using two pea recombinant inbred line populations. The complete genetic map covers 1,458 cM and comprises 363 loci, including a total of 111 gene-anchored markers: 77 gene-anchored markers described in this study, 7 microsatellites located in gene sequences, 16 flowering time genes, the Tri gene, 5 morphological markers, and 5 other genes. The mean spacing between adjacent markers is 4 cM and 90% of the markers are closer than 10 cM to their neighbours. We also report the genetic mapping of 21 of these genes in Medicago truncatula and add 41 new links between the pea and M. truncatula maps. We discuss the use of this new composite functional map for future candidate gene approaches in pea.

Published
2006

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