Molecular Breeding

, Volume 33, Issue 4, pp 769–778

Genome-wide single nucleotide polymorphism and Insertion-Deletion discovery through next-generation sequencing of reduced representation libraries in common bean

  • Xiaolu Zou
  • Chun Shi
  • Ryan S. Austin
  • Daniele Merico
  • Seth Munholland
  • Frédéric Marsolais
  • Alireza Navabi
  • William L. Crosby
  • K. Peter Pauls
  • Kangfu Yu
  • Yuhai Cui
Article

DOI: 10.1007/s11032-013-9997-7

Cite this article as:
Zou, X., Shi, C., Austin, R.S. et al. Mol Breeding (2014) 33: 769. doi:10.1007/s11032-013-9997-7

Abstract

Single nucleotide polymorphisms (SNPs) and insertions-deletions (InDels) are valuable molecular markers for genomics and genetics studies and molecular breeding. The advent of next-generation sequencing techniques has enabled researchers to approach high-throughput and cost-effective SNP and InDel discovery on a genomic scale. In this report, 36 common bean genotypes grown in Canada were used to construct reduced representation libraries for next-generation sequencing. Using 76 million sequence reads generated by the Illumina HiSeq 2000 Sequencing System, we identified a total of 43,698 putative SNPs and 1,267 putative InDels. Of the SNPs, 43,504 were bi-allelic and 194 were tri-allelic, and the InDels comprised 574 insertions and 693 deletions. The putative bi-allelic SNPs were distributed across all 11 chromosomes with the highest number of SNPs observed in chromosome 2 (4,788), and the lowest in chromosome 10 (2,941). With the aid of the recent release of the first chromosome-scale version of Phaseolus vulgaris, 24,907 bi-allelic SNPs, 79 tri-allelic SNPs, 315 insertions, and 377 deletions were located in 8,758, 77, 273, and 364 genes, respectively. Among these 24,907 bi-allelic SNPs, 7,168 nonsynonymous bi-allelic SNPs were identified within 36 common bean genotypes that were located in 4,303 genes. A total of 113 putative SNPs were randomly chosen for validation using high-resolution melt analysis. Of the 113 candidate SNPs, 105 (92.9 %) contained the predicted SNPs.

Keywords

Single nucleotide polymorphism Insertion Deletion Next-generation sequencing Phaseolus vulgaris L. 

Supplementary material

11032_2013_9997_MOESM1_ESM.docx (102 kb)
Supplementary material 1 (DOCX 101 kb)

Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • Xiaolu Zou
    • 1
  • Chun Shi
    • 2
  • Ryan S. Austin
    • 1
  • Daniele Merico
    • 3
  • Seth Munholland
    • 5
  • Frédéric Marsolais
    • 1
  • Alireza Navabi
    • 2
    • 4
  • William L. Crosby
    • 5
  • K. Peter Pauls
    • 4
  • Kangfu Yu
    • 2
  • Yuhai Cui
    • 1
  1. 1.Southern Crop Protection and Food Research CentreAgriculture and Agri-Food CanadaLondonCanada
  2. 2.Greenhouse and Processing Crops Research CentreAgriculture and Agri-Food CanadaHarrowCanada
  3. 3.The Centre for Applied GenomicsThe Hospital for Sick ChildrenTorontoCanada
  4. 4.Department of Plant AgricultureUniversity of GuelphGuelphCanada
  5. 5.Department of Biological SciencesUniversity of WindsorWindsorCanada

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