title: Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies.
abstract: BACKGROUND
  As for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies.
  
  
  RESULTS
  Starting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance).
  
  
  CONCLUSIONS
  Our association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment.
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.|GQE-Le Moulon, INRA - Univ. Paris-Sud - CNRS - AgroParisTech - Université Paris-Saclay, Ferme du Moulon, F-91190, Gif-sur-Yvette, France.
authors.forename: Stéphane D
authors.initials: SD
authors.lastname: Nicolas
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Jean-Pierre
authors.initials: JP
authors.lastname: Péros
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Lacombe
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Amandine
authors.initials: A
authors.lastname: Launay
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Le Paslier
authors.affiliation: INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France.
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bérard
authors.affiliation: INRA, UR MIAT, F-31326, Castanet-Tolosan, France.
authors.forename: Brigitte
authors.initials: B
authors.lastname: Mangin
authors.affiliation: INRA, Plateforme Génomique, F-31326, Castanet-Tolosan, France.
authors.forename: Sophie
authors.initials: S
authors.lastname: Valière
authors.affiliation: INRA, Plateforme Génomique, F-31326, Castanet-Tolosan, France.|INSERM, UMR1048, F-31432, Toulouse, France.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Martins
authors.affiliation: IFV, UMT Genovigne, F-34060, Montpellier, France.
authors.forename: Loïc
authors.initials: L
authors.lastname: Le Cunff
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Valérie
authors.initials: V
authors.lastname: Laucou
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Roberto
authors.initials: R
authors.lastname: Bacilieri
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.|IRD, UMR IPME, F-34394, Montpellier 5, France.
authors.forename: Alexis
authors.initials: A
authors.lastname: Dereeper
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Philippe
authors.initials: P
authors.lastname: Chatelet
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France.
authors.forename: Patrice
authors.initials: P
authors.lastname: This
authors.affiliation: INRA, UMR AGAP, F-34060, Montpellier, France. doligez@supagro.inra.fr.
authors.forename: Agnès
authors.initials: A
authors.lastname: Doligez
mesh_terms: D017343:Genes, Plant; D005819:Genetic Markers; D014644:Genetic Variation; D055106:Genome-Wide Association Study / Q000379:methods*; D005838:Genotype; D015810:Linkage Disequilibrium; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D013045:Species Specificity; D027843:Vitis / Q000235:genetics*
chemical_list: D005819:Genetic Markers
keywords: Association panel; Genome-wide association studies; Haplotype; Kinship; Linkage disequilibrium; Power; SNP; SSR; Vassal collection; Vitis; sylvestris