rapid genomic characterization of the genus vitis快速属葡萄的基因组特征.pdfVIP

Rapid Genomic Characterization of the Genus Vitis 1. 2. 2 3,4 3,4 Sean Myles , Jer-Ming Chia , Bonnie Hurwitz , Charles Simon , Gan Yuan Zhong , Edward Buckler1,4*, Doreen Ware2,4* 1 Institute for Genomic Diversity, Cornell University, Ithaca, New York, United States of America, 2 Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, United States of America, 3 New York State Agricultural Experiment Station, Geneva, New York, United States of America, 4 United States Department of Agriculture, Agricultural Research Service, Ithaca, New York, United States of America Abstract Next-generation sequencing technologies promise to dramatically accelerate the use of genetic information for crop improvement by facilitating the genetic mapping of agriculturally important phenotypes. The first step in optimizing the design of genetic mapping studies involves large-scale polymorphism discovery and a subsequent genome-wide assessment of the population structure and pattern of linkage disequilibrium (LD) in the species of interest. In the present study, we provide such an assessment for the grapevine (genus Vitis), the world’s most economically important fruit crop. Reduced representation libraries (RRLs) from 17 grape DNA samples (10 cultivated V. vinifera and 7 wild Vitis species) were sequenced with sequencing-by-synthesis technology. We developed heuristic approaches for SNP calling, identified hundreds of thousands of SNPs and validated a subset of these SNPs on a 9K genotyping array. We demonstrate that the 9K SNP array provides sufficient