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Abstract
Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a warm season annual legume mainly grown in East Asia. Only scarce genomic resources are currently available for this legume crop species and no simple sequence repeat (SSR) markers have been specifically developed for rice bean yet. In this study, approximately 26 million high quality cDNA sequence reads were obtained from rice bean using Illumina paired-end sequencing technology and assembled into 71,929 unigenes with an average length of 986 bp. Of these unigenes, 38,840 (33.2%) showed significant similarity to proteins in the NCBI non-redundant protein and nucleotide sequence databases. Furthermore, 30,170 (76.3%) could be classified into gene ontology categories, 25,451 (64.4%) into Swiss-Prot categories and 21,982 (55.6%) into KOG database categories (E-value < 1.0E-5). A total of 9,301 (23.5%) were mapped onto 118 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) pathway database. A total of 3,011 genic SSRs were identified as potential molecular markers. AG/CT (30.3%), AAG/CTT (8.1%) and AGAA/TTCT (20.0%) are the three main repeat motifs. A total of 300 SSR loci were randomly selected for validation by using PCR amplification. Of these loci, 23 primer pairs were polymorphic among 32 rice bean accessions. A UPGMA dendrogram revealed three major clusters among 32 rice bean accessions. The large number of SSR-containing sequences and genic SSRs in this study will be valuable for the construction of high-resolution genetic linkage maps, association or comparative mapping and genetic analyses of various Vigna species.
Highlights
There are currently 21 species in the genus Vigna subgenus Ceratotropis that are distributed across a wide region of Asia
25.95 million clean reads with a GC content of 47.87% was obtained for the ‘Jingfan No 1’ variety
No genome or transcriptome sequences of rice bean have been developed until now and they have only been developed from mung bean [5] and adzuki bean [1]
Summary
There are currently 21 species in the genus Vigna subgenus Ceratotropis that are distributed across a wide region of Asia. Mung bean (V. radiata), adzuki bean (V. angularis), rice bean (V. umbellata), and black gram (V. mungo) are the four most economically important cultivated species in Asian countries. Rice bean (Vigna umbellata (Thunb.) Ohwi & Ohashi) is a short-day, warm-season annual legume that is cultivated mainly in Nepal, Bhutan, northeast India, Myanmar, southern China, northern Thailand, Laos, Vietnam, Indonesia and East Timor [1]. Rice bean has a high yield potential and good nutritional quality. It is mainly grown for human consumption and is important as a fodder, green manure and vegetable. Rice bean has been sometimes substituted for adzuki bean (Vigna angularis (Willd.) Ohwi & Ohashi) in the making of pastry [1]
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