Article

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 ZouAffiliated withSouthern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada
  • , Chun ShiAffiliated withGreenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada
  • , Ryan S. AustinAffiliated withSouthern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada
  • , Daniele MericoAffiliated withThe Centre for Applied Genomics, The Hospital for Sick Children
  • , Seth MunhollandAffiliated withDepartment of Biological Sciences, University of Windsor
  • , Frédéric MarsolaisAffiliated withSouthern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada
  • , Alireza NavabiAffiliated withGreenhouse and Processing Crops Research Centre, Agriculture and Agri-Food CanadaDepartment of Plant Agriculture, University of Guelph
  • , William L. CrosbyAffiliated withDepartment of Biological Sciences, University of Windsor
  • , K. Peter PaulsAffiliated withDepartment of Plant Agriculture, University of Guelph
    • , Kangfu YuAffiliated withGreenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada
    • , Yuhai CuiAffiliated withSouthern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada Email author 

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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.