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United States Department of Agriculture

Agricultural Research Service

Research Project: IDENTIFICATION OF FUNCTIONAL SEQUENCE IN PLANT GENOMES THROUGH BIOINFORMATIC, GENOMIC, AND GENETIC APPROACHES Title: Rapid genomic characterization of the genus Vitis

Authors
item Myles, Sean -
item Chia, Jer-Ming -
item Hurwitz, Bonnie -
item Simon, Charles
item Zhong, Gan-Yuan
item Buckler, Edward
item Ware, Doreen

Submitted to: PLoS One
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 16, 2009
Publication Date: January 13, 2010
Citation: Myles, S., Chia, J., Hurwitz, B., Simon, C.J., Zhong, G., Buckler IV, E.S., Ware, D. 2010. Rapid genomic characterization of the genus Vitis. PLoS One. 5(1):e8219.

Interpretive Summary: The grapevine (genus Vitis) is the world’s most economically important fruit crop, yet many questions remain about its genetic diversity and population structure. We have generated DNA sequence from 17 grapevine accessions. With this DNA sequence information, we were able to identify more than 70,000 single nucleotide polymorphisms(SNPs) that segregate across the genus Vitis. This information will be useful for genetic mapping studies that identify relationships between genes and traits with the aim of improving the grapevine through breeding. We also designed a SNP genotyping microarray that allows us to distinguish genetically between wild and cultivated varieties, among wild species and also among V. vinifera cultivars. We find that genetic relationships among the V. vinifera cultivars agrees well with geographical origins of these varieties. This resource will prove valuable for assessing germplasm collections in the future.

Technical 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 resolution to distinguish among V. vinifera cultivars, between V. vinifera and wild Vitis species, and even among diverse wild Vitis species. Using principal components analysis (PCA), we show that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins. Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3kb. While genotyping arrays are useful for assessing population structure and the decay of LD across large numbers of samples, we suggest that whole-genome sequencing will become the genotyping method of choice for genome-wide genetic mapping studies in high-diversity plant species.

Last Modified: 12/22/2014