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1. 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

2. A local score approach improves GWAS resolution and detects minor QTL: application to Medicago truncatula quantitative disease resistance to multiple Aphanomyces euteiches isolates

Author

Christophe Jacquet, Maxime Bonhomme, Marie-Laure Pilet-Nayel, Yacine Badis, Hélène Navier, Henri Miteul, Bernard Dumas, Ahmed Hajri, Deborah A. Samac, María Inés Fariello, Alain Baranger, Evolution et Diversité Biologique (EDB), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Génétique Cellulaire (LGC), 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-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Pathologie Végétale (PaVé), Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST, Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, HEC Paris - Recherche - Hors Laboratoire, Ecole des Hautes Etudes Commerciales (HEC Paris), Supélec Sciences des Systèmes [Gif-sur-Yvette] (E3S), SUPELEC, ANR-16-CE20-0017-01, Agence Nationale de la Recherche (French National Research Agency), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), 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 Toulouse III - Paul Sabatier (UT3), USDA ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN, 55108, USA, Evolution des Interactions Plantes-Microorganismes, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Universidad de la República [Montevideo] (UDELAR), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, United States Department of Agriculture (USDA), Interactions Microbiennes dans la Rhizosphère et les Racines, ANR-16-CE20-0017,DeCoD,Détection de réseaux de gènes Coadaptés par analyse de la Diversité génétique à l'échelle du génome: application à la légumineuse modèle Medicago truncatula(2016), ANR-10-GENM-0007,Immunit-Ae,Diversité des composants génétiques et des mécanismes de résistance à Aphanomyces euteiches chez les légumineuses.(2010), and ANR-10-LABX-0041,TULIP,Towards a Unified theory of biotic Interactions: the roLe of environmental(2010)

Subjects
0106 biological sciences, 0301 basic medicine, Candidate gene, Linkage disequilibrium, Genetic Linkage, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Locus (genetics), Aphanomyces, Plant disease resistance, Quantitative trait locus, Plant Roots, Polymorphism, Single Nucleotide, 010603 evolutionary biology, 01 natural sciences, Chromosomes, Plant, Linkage Disequilibrium, Article, 03 medical and health sciences, Medicago truncatula, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, ComputingMilieux_MISCELLANEOUS, Genetics (clinical), Disease Resistance, Plant Diseases, Genetic association, biology, Chromosome Mapping, food and beverages, biology.organism_classification, [SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy, Phenotype, 030104 developmental biology, Aphanomyces euteiches, Genome-Wide Association Study
Abstract

International audience; Quantitative trait loci (QTL) with small effects, which are pervasive in quantitative phenotypic variation, are difficult to detect in genome-wide association studies (GWAS). To improve their detection, we propose to use a local score approach that accounts for the surrounding signal due to linkage disequilibrium, by accumulating association signals from contiguous single markers. Simulations revealed that, in a GWAS context with high marker density, the local score approach outperforms single SNP p-value-based tests for detecting minor QTL (heritability of 5-10%) and is competitive with regard to alternative methods, which also aggregate p-values. Using more than five million SNPs, this approach was applied to identify loci involved in Quantitative Disease Resistance (QDR) to different isolates of the plant root rot pathogen Aphanomyces euteiches, from a GWAS performed on a collection of 174 accessions of the model legume Medicago truncatula. We refined the position of a previously reported major locus, underlying MYB/NB-ARC/tyrosine kinase candidate genes conferring resistance to two closely related A. euteiches isolates belonging to pea pathotype I. We also discovered a diversity of minor resistance QTL, not detected using p-value-based tests, some of which being putatively shared in response to pea (pathotype I and III) and/or alfalfa (race 1 and 2) isolates. Candidate genes underlying these QTL suggest pathogen effector recognition and plant proteasome as key functions associated with M. truncatula resistance to A. euteiches. GWAS on any organism can benefit from the local score approach to uncover many weak-effect QTL.

Published
2019

3. 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, Virginie Bourion, 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, 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), Institut de Recherche en Horticulture et Semences (IRHS), AGROCAMPUS OUEST-Institut National de la Recherche Agronomique (INRA)-Université d'Angers (UA), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), 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), 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, 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), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
0106 biological sciences, 0301 basic medicine, Candidate gene, disease resistance, root rot, [SDV.SA.AGRO]Life Sciences [q-bio]/Agricultural sciences/Agronomy, Genome-wide association study, Plant Science, Quantitative trait locus, Plant disease resistance, lcsh:Plant culture, 01 natural sciences, root system architecture, Pisum sativum, GWAS, root, rot, 03 medical and health sciences, Genetic variation, lcsh:SB1-1110, Genetic variability, Allele, Original Research, 2. Zero hunger, Genetics, biology, food and beverages, 15. Life on land, biology.organism_classification, 030104 developmental biology, Aphanomyces euteiches, 010606 plant biology & botany
Abstract

Desgroux, Aurore;Baudais, Valentin N;Aubert, Veronique;Le Roy, Gwenola;de Larambergue, Henri;Miteul, Henri;Aubert, Gregoire;Boutet, Gilles;Duc, Gerard;Baranger, Alain;Burstin, Judith;Manzanares-Dauleux, Maria;Pilet-Nayel, Marie-Laure;Bourion, Virginie;Journal Article;Switzerland;Front Plant Sci. 2018 Jan 5;8:2195. doi: 10.3389/fpls.2017.02195. eCollection 2017.; International audience; 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

4. High-density genome-wide association mapping implicates an F-box encoding gene in Medicago truncatula resistance to Aphanomyces euteiches

Author

Marie-Laure Pilet-Nayel, Hélène Navier, Ahmed Hajri, Joëlle Ronfort, Maxime Bonhomme, Christophe Jacquet, Concetta Burgarella, Peter Tiffin, Frédéric Debellé, Henri Miteul, Alain Baranger, Joann Mudge, Roman Briskine, Nathalie Chantret, Olivier André, Jean Marie Prosperi, Yacine Badis, Bernard Dumas, Nevin D. Young, Laboratoire de Recherche en Sciences Végétales (LRSV), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, 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), Department of Computer Science and Engineering, University of Minnesota [Twin Cities], University of Minnesota System-University of Minnesota System, National Center for Genome Resources, Laboratoire des interactions plantes micro-organismes (LIPM), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Recherche Agronomique (INRA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), AGROCAMPUS OUEST-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National de la Recherche Agronomique (INRA), Department of Plant Biology, CNRS, Universite Paul Sabatier, INRA, French Agence Nationale de la Recherche [ANR-10-GENM-0007], US National Science Foundation [IOS-1237993], NGCR, Evolution des Interactions Plantes-Microorganismes, Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), 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), University of Minnesota [Twin Cities] (UMN), National center for genome resources (NCGR), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Interactions Microbiennes dans la Rhizosphère et les Racines, ANR-10-GENM-0007,Immunit-Ae,Diversité des composants génétiques et des mécanismes de résistance à Aphanomyces euteiches chez les légumineuses.(2010), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), 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 Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST

Subjects
Candidate gene, Genome-wide association study, F-box protein, Cytokinins, Transcription, Genetic, Physiology, health care facilities, manpower, and services, [SDV]Life Sciences [q-bio], education, Colony Count, Microbial, Single-nucleotide polymorphism, Locus (genetics), partial resistance, Ralstonia, Plant Science, Aphanomyces, Quantitative trait locus, Genes, Plant, Aphanomyces euteiches, Gene Expression Regulation, Plant, Medicago truncatula, oomycete, RNA, Messenger, Gene, health care economics and organizations, Disease Resistance, Plant Diseases, Plant Proteins, Genetics, biology, F-Box Proteins, Chromosome Mapping, biology.organism_classification, root, Up-Regulation, Mutation, Root Nodules, Plant, Signal Transduction, Transcription Factors
Abstract

Summary � The use of quantitative disease resistance (QDR) is a promising strategy for promoting durable resistance to plant pathogens, but genes involved in QDR are largely unknown. To identify genetic components and accelerate improvement of QDR in legumes to the root pathogen Aphanomyces euteiches, we took advantage of both the recently generated massive genomic data for Medicago truncatula and natural variation of this model legume. � A high-density (� 5.1 million single nucleotide polymorphisms (SNPs)) genome-wide association study (GWAS) was performed with both in vitro and glasshouse phenotyping data collected for 179 lines. � GWAS identified several candidate genes and pinpointed two independent major loci on the top of chromosome 3 that were detected in both phenotyping methods. Candidate SNPs in the most significant locus (r 2 = 23%) were in the promoter and coding regions of an F-box protein coding gene. Subsequent qRT-PCR and bioinformatic analyses performed on 20 lines demonstrated that resistance is associated with mutations directly affecting the interaction domain of the F-box protein rather than gene expression. � These results refine the position of previously identified QTL to specific candidate genes, suggest potential molecular mechanisms, and identify new loci explaining QDR against A. euteiches.

Published
2014

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

Author

Virginie L’Anthoëne, R. Esnault, Lyndon D. Porter, Anne Moussart, Martine Roux-Duparque, Isabelle Le Goff, G. Morin, Bernard Tivoli, Céline Hamon, Anthony Klein, Régine Delourme, Jean-Philippe Rivière, Pierre Mangin, Clarice J. Coyne, Alain Baranger, Marie-Laure Pilet-Nayel, Caroline Onfroy, Rebecca J. McGee, Angélique Lesné, Henri Miteul, Kevin E. McPhee, Amélioration des Plantes et Biotechnologies Végétales (APBV), 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), United States Department of Agriculture (USDA), 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 expérimental d'Époisses - UE0115 U2E (DIJ EPOISSES), Institut National de la Recherche Agronomique (INRA), North Dakota State University (NDSU), GSP, Domaine Brunehaut, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), 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)-Institut National de la Recherche Agronomique (INRA), Union Nationale Interprofessionnelle des plantes riches en Protéines (UNIP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Terres Inovia

Subjects
0106 biological sciences, Genotype, Genetic Linkage, Quantitative Trait Loci, Aphanomyces, Quantitative trait locus, 01 natural sciences, Plant Roots, Chromosomes, Plant, 03 medical and health sciences, Inbred strain, Genetics, Root rot, Crosses, Genetic, 030304 developmental biology, Plant Diseases, 2. Zero hunger, 0303 health sciences, Genetic diversity, [SDV.GEN]Life Sciences [q-bio]/Genetics, Resistance (ecology), biology, Peas, food and beverages, Chromosome Mapping, General Medicine, biology.organism_classification, Immunity, Innate, United States, Phenotype, Epistasis, Aphanomyces euteiches, France, Agronomy and Crop Science, 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; Partial resistances, often controlled by quantitative trait loci (QTL), are considered to be more durable than monogenic resistances. Therefore, a precursor to developing efficient breeding programs for polygenic resistance to pathogens should be a greater understanding of genetic diversity and stability of resistance QTL in plants. In this study, we deciphered the diversity and stability of resistance QTL to Aphanomyces euteiches in pea towards pathogen variability, environments and scoring criteria, from two new sources of partial resistance (PI 180693 and 552), effective in French and USA infested fields. Two mapping populations of 178 recombinant inbred lines each, derived from crosses between 552 or PI 180693 (partially resistant) and Baccara (susceptible), were used to identify QTL for Aphanomyces root rot resistance in controlled and in multiple French and USA field conditions using several resistance criteria. We identified a total of 135 additive-effect QTL corresponding to 23 genomic regions and 13 significant epistatic interactions associated with partial resistance to A. euteiches in pea. Among the 23 additive-effect genomic regions identified, five were consistently detected, and showed highly stable effects towards A. euteiches strains, environments, resistance criteria, condition tests and RIL populations studied. These results confirm the complexity of inheritance of partial resistance to A. euteiches in pea and provide good bases for the choice of consistent QTL to use in marker-assisted selection schemes to increase current levels of resistance to A. euteiches in pea breeding programs

Published
2010

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

Author

Anne Moussart, Bernard Tivoli, Isabelle Le Goff, Céline Hamon, Caroline Onfroy, Alain Baranger, Henri Miteul, Jean-Marie Prosperi, Marie-Laure Pilet-Nayel, Ronan Lecointe, Régine Delourme, Gwenaëlle Deniot, Amélioration des Plantes et Biotechnologies Végétales (APBV), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Diversité et adaptation des plantes cultivées (UMR DIAPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2), 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), and Université Montpellier 2 - Sciences et Techniques (UM2)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)

Subjects
0106 biological sciences, Genetic Markers, Genetic Linkage, Population, Molecular Sequence Data, Locus (genetics), Quantitative trait locus, Aphanomyces, Genes, Plant, 01 natural sciences, Chromosomes, Plant, 03 medical and health sciences, Gene interaction, Inbred strain, Gene Expression Regulation, Plant, Medicago truncatula, Genetics, Gene Regulatory Networks, GENETIQUE VEGETALE, education, Crosses, Genetic, 030304 developmental biology, Plant Diseases, 2. Zero hunger, 0303 health sciences, education.field_of_study, [SDV.GEN]Life Sciences [q-bio]/Genetics, biology, fungi, food and beverages, Chromosome Mapping, Epistasis, Genetic, General Medicine, biology.organism_classification, Immunity, Innate, Phenotype, Genetic Loci, Epistasis, Aphanomyces euteiches, Agronomy and Crop Science, 010606 plant biology & botany, Biotechnology
Abstract

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

Published
2009

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