title: Genome-wide association links candidate genes to resistance to Plum Pox Virus in apricot (Prunus armeniaca).
abstract: In fruit tree species, many important traits have been characterized genetically by using single-family descent mapping in progenies segregating for the traits. However, most mapped loci have not been sufficiently resolved to the individual genes due to insufficient progeny sizes for high resolution mapping and the previous lack of whole-genome sequence resources of the study species. To address this problem for Plum Pox Virus (PPV) candidate resistance gene identification in Prunus species, we implemented a genome-wide association (GWA) approach in apricot. This study exploited the broad genetic diversity of the apricot (Prunus armeniaca) germplasm containing resistance to PPV, next-generation sequence-based genotyping, and the high-quality peach (Prunus persica) genome reference sequence for single nucleotide polymorphism (SNP) identification. The results of this GWA study validated previously reported PPV resistance quantitative trait loci (QTL) intervals, highlighted other potential resistance loci, and resolved each to a limited set of candidate genes for further study. This work substantiates the association genetics approach for resolution of QTL to candidate genes in apricot and suggests that this approach could simplify identification of other candidate genes for other marked trait intervals in this germplasm.
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.|UMR 1202 BIOGECO, INRA, F-33610, Cestas, France.|UMR 1202 BIOGECO, Université de Bordeaux, F-33400, Talence, France.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Mariette
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.|Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France.
authors.forename: Fabienne
authors.initials: F
authors.lastname: Wong Jun Tai
authors.affiliation: UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France.|CEP INNOVATION, INRA, 23 rue Jean Baldassini, F-69364, LYON Cedex 7, France.
authors.forename: Guillaume
authors.initials: G
authors.lastname: Roch
authors.affiliation: Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France.
authors.forename: Aurélien
authors.initials: A
authors.lastname: Barre
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Chague
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Decroocq
authors.affiliation: Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Groppi
authors.affiliation: UMR 1202 BIOGECO, INRA, F-33610, Cestas, France.|UMR 1202 BIOGECO, Université de Bordeaux, F-33400, Talence, France.
authors.forename: Yec'han
authors.initials: Y
authors.lastname: Laizet
authors.affiliation: UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France.
authors.forename: Patrick
authors.initials: P
authors.lastname: Lambert
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.
authors.forename: David
authors.initials: D
authors.lastname: Tricon
authors.affiliation: Bordeaux Bioinformatics Center CBiB, Université de Bordeaux, 351 cours de la Libération, F-33405, Talence, France.
authors.forename: Macha
authors.initials: M
authors.lastname: Nikolski
authors.affiliation: UR1052 GAFL, Domaine Saint Maurice, INRA, CS60094, F-84143, Montfavet, France.
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Audergon
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.|University of Kentucky, 106 T. P. Cooper Hall, Lexington, KY, 40546-0073, USA.
authors.forename: Albert G
authors.initials: AG
authors.lastname: Abbott
authors.affiliation: UMR 1332 Biologie du Fruit et Pathologie, Equipe de Virologie, INRA, Université de Bordeaux, CS20032, F-33882, Villenave d'Ornon, France.
authors.forename: Véronique
authors.initials: V
authors.lastname: Decroocq
mesh_terms: D002874:Chromosome Mapping; D060467:Disease Resistance / Q000235:genetics; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D054884:Host-Pathogen Interactions / Q000235:genetics; D015810:Linkage Disequilibrium; D010935:Plant Diseases / Q000235:genetics* / Q000821:virology*; D017801:Plum Pox Virus / Q000472:pathogenicity*; D020641:Polymorphism, Single Nucleotide; D000068219:Prunus armeniaca / Q000235:genetics* / Q000821:virology*; D040641:Quantitative Trait Loci
keywords: Plum Pox Virus (PPV) resistance; Prunus species; candidate genes; genome-wide association study (GWAS); genome-wide resequencing; sharka; single nucleotide polymorphism (SNP)