title: Genetic diversity, linkage disequilibrium, population structure and construction of a core collection of Prunus avium L. landraces and bred cultivars.
abstract: BACKGROUND
  Depiction of the genetic diversity, linkage disequilibrium (LD) and population structure is essential for the efficient organization and exploitation of genetic resources. The objectives of this study were to (i) to evaluate the genetic diversity and to detect the patterns of LD, (ii) to estimate the levels of population structure and (iii) to identify a 'core collection' suitable for association genetic studies in sweet cherry.
  
  
  RESULTS
  A total of 210 genotypes including modern cultivars and landraces from 16 countries were genotyped using the RosBREED cherry 6 K SNP array v1. Two groups, mainly bred cultivars and landraces, respectively, were first detected using STRUCTURE software and confirmed by Principal Coordinate Analysis (PCoA). Further analyses identified nine subgroups using STRUCTURE and Discriminant Analysis of Principal Components (DAPC). Several sub-groups correspond to different eco-geographic regions of landraces distribution. Linkage disequilibrium was evaluated showing lower values than in peach, the reference Prunus species. A 'core collection' containing 156 accessions was selected using the maximum length sub tree method.
  
  
  CONCLUSIONS
  The present study constitutes the first population genetics analysis in cultivated sweet cherry using a medium-density SNP (single nucleotide polymorphism) marker array. We provided estimations of linkage disequilibrium, genetic structure and the definition of a first INRA's Sweet Cherry core collection useful for breeding programs, germplasm management and association genetics studies.
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. jacampoy@bordeaux.inra.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. jacampoy@bordeaux.inra.fr.
authors.forename: José Antonio
authors.initials: JA
authors.lastname: Campoy
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. emilie.lerigoleur@univ-tlse2.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. emilie.lerigoleur@univ-tlse2.fr.|Current address: CNRS, UMR 5602 GEODE, Géographie de l'environnement, F-31058, Toulouse, France. emilie.lerigoleur@univ-tlse2.fr.
authors.forename: Emilie
authors.initials: E
authors.lastname: Lerigoleur-Balsemin
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. christma@bordeaux.inra.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. christma@bordeaux.inra.fr.
authors.forename: Hélène
authors.initials: H
authors.lastname: Christmann
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. rbeauvie@bordeaux.inra.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. rbeauvie@bordeaux.inra.fr.
authors.forename: Rémi
authors.initials: R
authors.lastname: Beauvieux
authors.affiliation: INRA, UAR 0415 SDAR, Services Déconcentrés d'Appui à la Recherche, F 33140, Villenave d'Ornon, France. nabil.girollet@bordeaux.inra.fr.|Current address: INRA, ISVV, UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, F 33140, Villenave d'Ornon, France. nabil.girollet@bordeaux.inra.fr.
authors.forename: Nabil
authors.initials: N
authors.lastname: Girollet
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. jqueroga@bordeaux.inra.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. jqueroga@bordeaux.inra.fr.
authors.forename: José
authors.initials: J
authors.lastname: Quero-García
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. dirlewan@bordeaux.inra.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. dirlewan@bordeaux.inra.fr.
authors.forename: Elisabeth
authors.initials: E
authors.lastname: Dirlewanger
authors.affiliation: INRA, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. teresa.barreneche@bordeaux.inra.fr.|University Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France. teresa.barreneche@bordeaux.inra.fr.
authors.forename: Teresa
authors.initials: T
authors.lastname: Barreneche
mesh_terms: D001947:Breeding; D014644:Genetic Variation; D015810:Linkage Disequilibrium; D000068220:Prunus avium / Q000235:genetics*