Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis).

Honglin Chen,Xuzhen Cheng,Prakit Somta,Lixia Wang,Suhua Wang,Liping Liu,Mukesh Jain

doi:10.1371/journal.pone.0131939

Abstract

The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is an important grain legume of Asia. It is cultivated mainly in China, Japan and Korea. Despite its importance, few genomic resources are available for molecular genetic research of adzuki bean. In this study, we developed EST-SSR markers for the adzuki bean through next-generation sequencing. More than 112 million high-quality cDNA sequence reads were obtained from adzuki bean using Illumina paired-end sequencing technology, and the sequences were de novo assembled into 65,950 unigenes. The average length of the unigenes was 1,213 bp. Among the unigenes, 14,547 sequences contained a unique simple sequence repeat (SSR) and 3,350 sequences contained more than one SSR. A total of 7,947 EST-SSRs were identified as potential molecular markers, with mono-nucleotide A/T repeats (99.0%) as the most abundant motif class, followed by AG/CT (68.4%), AAG/CTT (30.0%), AAAG/CTTT (26.2%), AAAAG/CTTTT (16.1%), and AACGGG/CCCGTT (6.0%). A total of 500 SSR markers were randomly selected for validation, of which 296 markers produced reproducible amplicons with 38 polymorphic markers among the 32 adzuki bean genotypes selected from diverse geographical locations across China. The large number of SSR-containing sequences and EST-SSR markers will be valuable for genetic analysis of the adzuki bean and related Vigna species.

Highlights

The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is a diploid crop (2n = 2x = 22) with a genome size of approximately 500 Mb
Sequencing and de novo assembly of Illumina paired-end reads from adzuki bean transcriptomes
De novo transcriptome sequencing has proven to be a crucial tool in many organisms and an effective way to develop molecular markers [12, 13, 24, 25]

Summary

Introduction

The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is a diploid crop (2n = 2x = 22) with a genome size of approximately 500 Mb. The adzuki bean (Vigna angularis (Ohwi) Ohwi and Ohashi) is a diploid crop (2n = 2x = 22) with a genome size of approximately 500 Mb It is an important temperate legume, with high nutritional value, grown for human consumption. Adzuki bean has been widely grown in East Asian countries, especially in China, Japan and Korea, for thousands of years [1]. In these countries, the adzuki bean is the second-most important legume crop after soybean. PLOS ONE | DOI:10.1371/journal.pone.0131939 July 6, 2015

Methods

Results

Conclusion