Rapid Genomic Characterization of the Genus Vitis

Myles, S., Chia, J. M., Hurwitz, B. L., Simon, C., Zhong, G. Y., Buckler, E., Ware, D. H. (January 2010) Rapid Genomic Characterization of the Genus Vitis. PLoS ONE, 5 (1). ISSN 1932-6203

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URL: https://www.ncbi.nlm.nih.gov/pubmed/20084295
DOI: 10.1371/journal.pone.0008219

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. We show that there is substantial sharing of polymorphism between V. vinifera and wild Vitis species and find that genetic relationships among V. vinifera cultivars agree well with their proposed geographic origins using principal components analysis (PCA). Levels of LD in the domesticated grapevine are low even at short ranges, but LD persists above background levels to 3 kb. 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. This study demonstrates that we can move quickly towards genome-wide studies of crop species using next-generation sequencing. Our study sets the stage for future work in other high diversity crop species, and provides a significant enhancement to current genetic resources available to the grapevine genetic community.

Item Type: Paper
Uncontrolled Keywords: REDUCED REPRESENTATION SNP DISCOVERY GENETIC-STRUCTURE VINIFERA L. WIDE ASSOCIATION CHALLENGES LIBRARIES SUCCESS TRAITS MAIZE
Subjects: organism description > plant > maize
bioinformatics > genomics and proteomics > annotation > sequence annotation
bioinformatics > genomics and proteomics > analysis and processing > Sequence Data Processing
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
organism description > plant > Vitus
CSHL Authors:
Communities: CSHL labs > Ware lab
Depositing User: CSHL Librarian
Date: 13 January 2010
Date Deposited: 03 Oct 2011 15:05
Last Modified: 23 Feb 2017 16:34
PMCID: PMC2805708
Related URLs:
URI: http://repository.cshl.edu/id/eprint/15490

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