Genome-wide single nucleotide polymorphism discovery and validation in adzuki bean

Abstract

Adzuki bean, also known as red bean (Vigna angularis), with 2n = 22 chromosomes, is an important legume crop in East Asian countries, including China, Japan, and Korea. For single nucleotide polymorphism (SNP) discovery, we used Vigna accessions, V. angularis IT213134 and its wild relative V. nakashimae IT178530, because of the lack of DNA sequence polymorphism in the cultivated species. Short read sequences of IT213134 and IT178530 of approximately 37 billion and 35 billion bp were produced using the Illumina HiSeq 2000 system to a sequencing depth of 61.5× and 57.7×, respectively. After de novo assembly was carried out with trimmed HiSeq reads from IT213134, 98,441 contigs of various sizes were produced with N50 of 13,755 bp. Using Burrows–Wheeler Aligner software, trimmed short reads of V. nakashimae IT178530 were successfully mapped to IT213134 contigs. All sequence variations at the whole-genome level were examined between the two Vigna species. Of the 1,565,699 SNPs, 59.4 % were transitions and 40.6 % were transversions. A total of 213,758 SNPs, consisting of 122,327 non-synonymous and 91,431 synonymous SNPs, were identified in coding sequences. For SNP validation, 96 SNPs in the genic region were chosen from among IT213134 contigs longer than 10 kb. Of these 96 SNPs, 88 were confirmed by Sanger sequencing of 10 adzuki bean genotypes from various geographic origins as well as IT213134 and its wild relative IT178530. These genome-wide SNP markers will enrich the existing Vigna resources and, specifically, could be of value for constructing a genetic map and evaluating the genetic diversity of adzuki bean.