Rapid genomic characterization of the genus Vitis

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

Research output: Contribution to journalArticle

145 Citations (Scopus)

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.

Original languageEnglish (US)
Article numbere8219
JournalPLoS One
Volume5
Issue number1
DOIs
StatePublished - Jan 13 2010
Externally publishedYes

Fingerprint

Vitis
Crops
linkage disequilibrium
Genes
Linkage Disequilibrium
genomics
Single Nucleotide Polymorphism
Vitis vinifera
genotyping
chromosome mapping
Polymorphism
Genome
genome
population structure
crops
genetic polymorphism
Fruits
Principal component analysis
Technology
fruit crops

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Myles, S., Chia, J. M., Hurwitz, B. L., Simon, C., Zhong, G. Y., Buckler, E., & Ware, D. (2010). Rapid genomic characterization of the genus Vitis. PLoS One, 5(1), [e8219]. https://doi.org/10.1371/journal.pone.0008219

Rapid genomic characterization of the genus Vitis. / Myles, Sean; Chia, Jer Ming; Hurwitz, Bonnie L; Simon, Charles; Zhong, Gan Yuan; Buckler, Edward; Ware, Doreen.

In: PLoS One, Vol. 5, No. 1, e8219, 13.01.2010.

Research output: Contribution to journalArticle

Myles, S, Chia, JM, Hurwitz, BL, Simon, C, Zhong, GY, Buckler, E & Ware, D 2010, 'Rapid genomic characterization of the genus Vitis', PLoS One, vol. 5, no. 1, e8219. https://doi.org/10.1371/journal.pone.0008219
Myles S, Chia JM, Hurwitz BL, Simon C, Zhong GY, Buckler E et al. Rapid genomic characterization of the genus Vitis. PLoS One. 2010 Jan 13;5(1). e8219. https://doi.org/10.1371/journal.pone.0008219
Myles, Sean ; Chia, Jer Ming ; Hurwitz, Bonnie L ; Simon, Charles ; Zhong, Gan Yuan ; Buckler, Edward ; Ware, Doreen. / Rapid genomic characterization of the genus Vitis. In: PLoS One. 2010 ; Vol. 5, No. 1.
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