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

doi:10.1016/j.cj.2015.09.004

CORC > 中国农业科学院 > 作物科学研究所

	Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library
	Wang Lixia 1; Kim Kyung Do 2; Gao Dongying 2; Chen Honglin 1; Wang Suhua 1; Lee Sukha 3; Jackson Scott A 2; Cheng Xuzhen 1
刊名	The Crop Journal
	2016
卷号	4 期号:1 页码:40-47
关键词	Vigna umbellata SSR Distribution and frequency Mapping Primer design
ISSN号	2095-5421
DOI	10.1016/j.cj.2015.09.004
英文摘要	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.
语种	中文
内容类型	期刊论文
源URL	[http://ir.nais.net.cn/handle/2HMLN22E/131160]
专题	作物科学研究所
作者单位	1.Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081; 2.Center for Applied Genetic Technologies, University of Georgia, USA, Athens, 30602; 3.Plant Genomics and Breeding Institute, Seoul National University, Republic of Korea, Seoul, 151-921
推荐引用方式 GB/T 7714	Wang Lixia,Kim Kyung Do,Gao Dongying,et al. Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library[J]. The Crop Journal,2016,4(1):40-47.
APA	Wang Lixia.,Kim Kyung Do.,Gao Dongying.,Chen Honglin.,Wang Suhua.,...&Cheng Xuzhen.(2016).Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library.The Crop Journal,4(1),40-47.
MLA	Wang Lixia,et al."Analysis of simple sequence repeats in rice bean (Vigna umbellata) using an SSR-enriched library".The Crop Journal 4.1(2016):40-47.