Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat

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DOI

https://doi.org/10.1371/journal.pone.0102448

Language of the publication
English
Date
2014-07-21
Type
Article
Author(s)
  • Huang, Yung-Fen
  • Poland, Jesse A.
  • Wight, Charlene P.
  • Jackson, Eric W.
  • Tinker, Nicholas A.
Publisher
Public Library of Science

Abstract

Advances in next-generation sequencing offer high-throughput and cost-effective genotyping alternatives, including genotyping-by-sequencing (GBS). Results have shown that this methodology is efficient for genotyping a variety of species, including those with complex genomes. To assess the utility of GBS in cultivated hexaploid oat (Avena sativa L.), seven bi-parental mapping populations and diverse inbred lines from breeding programs around the world were studied. We examined technical factors that influence GBS SNP calls, established a workflow that combines two bioinformatics pipelines for GBS SNP calling, and provided a nomenclature for oat GBS loci. The high-throughput GBS system enabled us to place 45,117 loci on an oat consensus map, thus establishing a positional reference for further genomic studies. Using the diversity lines, we estimated that a minimum density of one marker per 2 to 2.8 cM would be required for genome-wide association studies (GWAS), and GBS markers met this density requirement in most chromosome regions. We also demonstrated the utility of GBS in additional diagnostic applications related to oat breeding. We conclude that GBS is a powerful and useful approach, which will have many additional applications in oat breeding and genomic studies.

Subject

  • Agriculture

Keywords

  • Oats -- Breeding,
  • Avoine -- Amélioration,
  • Cartes chromosomiques,
  • Gene mapping

Rights

Pagination

1-16

Peer review

Yes

Open access level

Gold

Identifiers

ISSN
1932-6203
1932-6203

Article

Journal title
PLoS ONE
Journal volume
9
Journal issue
7
Article number
e102448
Accepted date
2014-06-19
Submitted date
2013-12-02

Citation(s)

Huang, Y.-F., Poland, J. A., Wight, C. P., Jackson, E. W., & Tinker, N. A. (2014). Using genotyping-by-sequencing (GBS) for genomic discovery in cultivated oat. PLoS ONE, 9(7), Article e102448. https://doi.org/10.1371/journal.pone.0102448

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Collection(s)

Crops and horticulture

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