Rapid Genomic Characterization of the Genus Vitis

• DOI: 10.1371/journal.pone.0008219
• Publication Date: 2010-01-12T23:22:28Z
• Authors: Sean Myles; Jer-Ming Chia; Bonnie Hurwitz; Charles Simon; Gan Yuan Zhong; Edward Buckler; Doreen Ware
• Keywords: SNP genotyping; Linkage Disequilibrium

Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating mapping agriculturally important phenotypes. The first step in optimizing design studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment population structure pattern linkage disequilibrium (LD) species interest. In present study, we provide such an grapevine (genus Vitis), world's most economically fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches SNP calling, identified hundreds thousands SNPs validated subset these on 9K genotyping array. demonstrate that array provides sufficient resolution distinguish among cultivars, between species, even diverse species. show there is substantial sharing find relationships cultivars agree well their proposed geographic origins using principal components analysis (PCA). Levels LD domesticated are low at short ranges, but persists above background levels 3 kb. While arrays useful assessing decay across large numbers samples, suggest whole-genome will become method choice high-diversity plant This study demonstrates can move quickly towards next-generation sequencing. Our sets stage future work other high diversity significant enhancement current resources available community.