title: Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea.
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.
  
  
  CONCLUSIONS
  This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. aurore.desgroux@rennes.inra.fr.|INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France. aurore.desgroux@rennes.inra.fr.
authors.forename: Aurore
authors.initials: A
authors.lastname: Desgroux
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Virginie.Merot@rdto.nestle.com.|Present Address: Nestlé R&D Center Tours, 101 Avenue Gustave Eiffel, 37097, Tours Cedex 2, France. Virginie.Merot@rdto.nestle.com.
authors.forename: Virginie
authors.initials: V
authors.lastname: L'Anthoëne
authors.affiliation: GSP, Domaine Brunehaut, 80200, Estrées-Mons Cedex, France. martine.rouxduparque@ma02.org.|Present Address: Chambre d'Agriculture de l'Aisne, 1 rue René Blondelle, 02007, Laon Cedex, France. martine.rouxduparque@ma02.org.
authors.forename: Martine
authors.initials: M
authors.lastname: Roux-Duparque
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. jean-philippe.riviere@rennes.inra.fr.|PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. jean-philippe.riviere@rennes.inra.fr.
authors.forename: Jean-Philippe
authors.initials: JP
authors.lastname: Rivière
authors.affiliation: INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France. Gregoire.Aubert@dijon.inra.fr.
authors.forename: Grégoire
authors.initials: G
authors.lastname: Aubert
authors.affiliation: INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France. Nadim.Tayeh@dijon.inra.fr.
authors.forename: Nadim
authors.initials: N
authors.lastname: Tayeh
authors.affiliation: PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Anne.Moussard@rennes.inra.fr.|Terres Inovia, 11 rue de Monceau, CS 60003, 75378, Paris Cedex, France. Anne.Moussard@rennes.inra.fr.
authors.forename: Anne
authors.initials: A
authors.lastname: Moussart
authors.affiliation: INRA, Domaine Expérimental d'Epoisses, UE0115, 21110, Bretenières Cedex, France. pierre.mangin@dijon.inra.fr.
authors.forename: Pierre
authors.initials: P
authors.lastname: Mangin
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Pierrick.Vetel@rennes.inra.fr.|PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Pierrick.Vetel@rennes.inra.fr.
authors.forename: Pierrick
authors.initials: P
authors.lastname: Vetel
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Christophe.Piriou@rennes.inra.fr.|PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Christophe.Piriou@rennes.inra.fr.
authors.forename: Christophe
authors.initials: C
authors.lastname: Piriou
authors.affiliation: USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, 99164-6434, USA. Rebecca.McGee@ars.usda.gov.
authors.forename: Rebecca J
authors.initials: RJ
authors.lastname: McGee
authors.affiliation: USDA, ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164-6402, USA. Clarice.Coyne@ars.usda.gov.
authors.forename: Clarice J
authors.initials: CJ
authors.lastname: Coyne
authors.affiliation: INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France. judith.burstin@dijon.inra.fr.
authors.forename: Judith
authors.initials: J
authors.lastname: Burstin
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Alain.Baranger@rennes.inra.fr.|PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Alain.Baranger@rennes.inra.fr.
authors.forename: Alain
authors.initials: A
authors.lastname: Baranger
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. maria.manzanares@agrocampus-ouest.fr.|AgroCampus Ouest, UMR IGEPP 1349 IGEPP, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France. maria.manzanares@agrocampus-ouest.fr.
authors.forename: Maria
authors.initials: M
authors.lastname: Manzanares-Dauleux
authors.affiliation: INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France. Virginie.Bourion@dijon.inra.fr.
authors.forename: Virginie
authors.initials: V
authors.lastname: Bourion
authors.affiliation: INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Marie-Laure.Pilet@rennes.inra.fr.|PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France. Marie-Laure.Pilet@rennes.inra.fr.
authors.forename: Marie-Laure
authors.initials: ML
authors.lastname: Pilet-Nayel
mesh_terms: D000483:Alleles; D044744:Aphanomyces; D002874:Chromosome Mapping; D016001:Confidence Intervals; D060467:Disease Resistance / Q000235:genetics*; D056726:Genetic Association Studies; D005819:Genetic Markers; D005838:Genotype; D006239:Haplotypes; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D018532:Pisum sativum / Q000235:genetics* / Q000382:microbiology; D010641:Phenotype; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci
chemical_list: D005819:Genetic Markers