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Research paper | Open Access

Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library

Lixia Wanga, Kyung Do Kimb, Dongying Gaob, Honglin Chena, Suhua Wanga, SukHa Leec, Scott A. Jacksonb, Xuzhen Chenga( )
Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Center for Applied Genetic Technologies, University of Georgia, 30602 Athens, GA, USA
Plant Genomics and Breeding Institute, Seoul National University, Seoul 151-921, Republic of Korea

Peer review under responsibility of Crop Science Society of China and Institute of Crop Science, CAAS.

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Abstract

Rice bean (Vigna umbellata Thunb.), a warm-season annual legume, is grown in Asia mainly for dried grain or fodder and plays an important role in human and animal nutrition because the grains are rich in protein and some essential fatty acids and minerals. With the aim of expediting the genetic improvement of rice bean, we initiated a project to develop genomic resources and tools for molecular breeding in this little-known but important crop. Here we report the construction of an SSR-enriched genomic library from DNA extracted from pooled young leaf tissues of 22 rice bean genotypes and developing SSR markers. In 433,562 reads generated by a Roche 454 GS-FLX sequencer, we identified 261,458 SSRs, of which 48.8% were of compound form. Dinucleotide repeats were predominant with an absolute proportion of 81.6%, followed by trinucleotides (17.8%). Other types together accounted for 0.6%. The motif AC/GT accounted for 77.7% of the total, followed by AAG/CTT (14.3%), and all others accounted for 12.0%. Among the flanking sequences, 2928 matched putative genes or gene models in the protein database of Arabidopsis thaliana, corresponding with 608 non-redundant Gene Ontology terms. Of these sequences, 11.2% were involved in cellular components, 24.2% were involved molecular functions, and 64.6% were associated with biological processes. Based on homolog analysis, 1595 flanking sequences were similar to mung bean and 500 to common bean genomic sequences. Comparative mapping was conducted using 350 sequences homologous to both mung bean and common bean sequences. Finally, a set of primer pairs were designed, and a validation test showed that 58 of 220 new primers can be used in rice bean and 53 can be transferred to mung bean. However, only 11 were polymorphic when tested on 32 rice bean varieties. We propose that this study lays the groundwork for developing novel SSR markers and will enhance the mapping of qualitative and quantitative traits and marker-assisted selection in rice bean and other Vigna species.

Keywords

MappingSSRVigna umbellataDistribution and frequencyPrimer design

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The Crop Journal
Volume 4 Issue 1,
February 2016
Pages 40-47
DOI: 10.1016/j.cj.2015.09.004
Cite this article:
Wang L, Kim KD, Gao D, et al. Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library. The Crop Journal, 2016, 4(1): 40-47. https://doi.org/10.1016/j.cj.2015.09.004

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Received: 23 April 2015
Revised: 28 September 2015
Accepted: 27 November 2015
Published: 04 December 2015
© 2015 Crop Science Society of China and Institute of Crop Science, CAAS.

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
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