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Rapid Genomic Characterization of the Genus Vitis

Author

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

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.

Suggested Citation

  • Sean Myles & Jer-Ming Chia & Bonnie Hurwitz & Charles Simon & Gan Yuan Zhong & Edward Buckler & Doreen Ware, 2010. "Rapid Genomic Characterization of the Genus Vitis," PLOS ONE, Public Library of Science, vol. 5(1), pages 1-9, January.
  • Handle: RePEc:plo:pone00:0008219
    DOI: 10.1371/journal.pone.0008219
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    References listed on IDEAS

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    1. David Altshuler & Victor J. Pollara & Chris R. Cowles & William J. Van Etten & Jennifer Baldwin & Lauren Linton & Eric S. Lander, 2000. "An SNP map of the human genome generated by reduced representation shotgun sequencing," Nature, Nature, vol. 407(6803), pages 513-516, September.
    2. Magnus Nordborg & Detlef Weigel, 2008. "Next-generation genetics in plants," Nature, Nature, vol. 456(7223), pages 720-723, December.
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    Cited by:

    1. Nami Goto-Yamamoto & Jason Sawler & Sean Myles, 2015. "Genetic Analysis of East Asian Grape Cultivars Suggests Hybridization with Wild Vitis," PLOS ONE, Public Library of Science, vol. 10(10), pages 1-9, October.
    2. Agota Fodor & Vincent Segura & Marie Denis & Samuel Neuenschwander & Alexandre Fournier-Level & Philippe Chatelet & Félix Abdel Aziz Homa & Thierry Lacombe & Patrice This & Loic Le Cunff, 2014. "Genome-Wide Prediction Methods in Highly Diverse and Heterozygous Species: Proof-of-Concept through Simulation in Grapevine," PLOS ONE, Public Library of Science, vol. 9(11), pages 1-14, November.
    3. David VLK & Jana ŘEPKOVÁ, 2017. "Application of next-generation sequencing in plant breeding," Czech Journal of Genetics and Plant Breeding, Czech Academy of Agricultural Sciences, vol. 53(3), pages 89-96.
    4. Jason Sawler & Bruce Reisch & Mallikarjuna K Aradhya & Bernard Prins & Gan-Yuan Zhong & Heidi Schwaninger & Charles Simon & Edward Buckler & Sean Myles, 2013. "Genomics Assisted Ancestry Deconvolution in Grape," PLOS ONE, Public Library of Science, vol. 8(11), pages 1-1, November.

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