Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

BMC Plant Biology

Research Article

Loïc Le Cunff¹  Sophie Valière²  Frédéric Martins³  Jean-Pierre Péros⁴  Valérie Laucou⁴  Roberto Bacilieri⁴  Agnès Doligez⁴  Thierry Lacombe⁴  Amandine Launay⁴  Philippe Chatelet⁴  Patrice This⁴  Stéphane D. Nicolas⁵  Alexis Dereeper⁶  Brigitte Mangin⁷  Marie-Christine Le Paslier⁸  Aurélie Bérard⁸ 

[1] IFV, UMT Genovigne, F-34060, Montpellier, France;INRA, Plateforme Génomique, F-31326, Castanet-Tolosan, France;INRA, Plateforme Génomique, F-31326, Castanet-Tolosan, France;INSERM, UMR1048, F-31432, Toulouse, France;INRA, UMR AGAP, F-34060, Montpellier, France;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;INRA, UMR AGAP, F-34060, Montpellier, France;IRD, UMR IPME, F-34394, Montpellier 5, France;INRA, UR MIAT, F-31326, Castanet-Tolosan, France;INRA, US1279 EPGV, CEA-IG/CNG, F-91057, Evry, France;

关键词: Vitis;    Association panel;    Linkage disequilibrium;    Power;    Genome-wide association studies;    SSR;    SNP;    sylvestris;    Vassal collection;    Haplotype;    Kinship;   

DOI  :  10.1186/s12870-016-0754-z

 received in 2015-11-16, accepted in 2016-03-14,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundAs 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.ResultsStarting 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).ConclusionsOur 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.

【 授权许可】

CC BY   
© Nicolas et al. 2016