Distribution and analysis of SSR in mung bean (Vigna radiata L.) genome based on an SSR-enriched library

Abstract Simple sequence repeats (SSR) are widely distributed in plant genomes, have been popular genetic markers and can be involved in gene function. We report an SSR analysis of mung bean (Vigna radiata L.), based on an SSR-enriched library. A total of 308,509 SSRs (56.9 % simple and 43.1 % compound) were discovered from 167,628 sequences. Both di- and tri-nucleotide were the most prevalent repeat types (each accounts for 48.6 %). The most frequent motifs were AAC/GTT, accounting for 45.14 % of all, followed by AC/GT at 41.80 %. After filtering the SSRs, 70,104 flanking sequences were used as BLAST queries and corresponded to 574 non-redundant gene ontology terms against the protein database from Arabidopsis thaliana. The three main categories were biological processes (23.8 %), cellular components (44.4 %) and molecular functions (31.8 %). A total of 6,100 non-repeated primer pairs were designed and validated by PCR analysis. The results showed that 60 % of primers were effective in mung bean and 35.2, 34.0 and 25.9 % could be transferred to rice bean, adzuki bean and cowpea, respectively. 9.1 % of the 6,100 displayed polymorphism between a wild and cultivated mung bean genotype, and 367 were mapped onto chromosomes using a RIL population derived from a wild × a cultivated cross. However, only 49 of 1,700 effective primer pairs showed polymorphism among 32 Chinese cultivated mung bean accessions. A total of 46,565 loci on mung bean chromosomes from the draft genome were hit by the 70,104 flanking sequences using BLASTn. The present study, especially the newly published 387 markers that have been validated and mapped, will significantly enhance genetic linkage map construction, QTL mapping and marker-assisted selection in mung bean and breeding in closely related crop species.

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