Development and characterization of genic SSR markers for mungbean (Vigna radiata (L.) Wilczek)

Abstract

Mungbean (Vigna radiata (L.) Wilczek) is an important food legume, but has limited genomic resources. In this study, the development of genic SSR markers from mungbean transcriptome sequences and their transferability to related Vigna species is presented. A total of 12,596 EST sequences from mungbean genotype ‘Jangan’ were searched for the presence of SSRs and 2,299 SSR motifs from 1,848 SSR containing unique ESTs were identified with an average of one SSR per 3.4 kb. Trinucleotide motifs (48 %) were the most abundant repeats followed by di- (25 %), tetra- (15 %), hexa- (7 %) and penta- (5 %) nucleotide repeats. Based on these SSR containing sequences, PCR primer pairs were successfully designed for 1,742 SSR loci and randomly selected 100 primer pairs were further used for characterization. Sequences analyses indicate that about 45 % of the SSR motifs were present in the coding sequences (CDS) and 55 % were located in the untranslated regions (UTRs). Trinucleotide repeats (62 %) were preferentially present in the CDS. Randomly selected 27 SSR markers were used to study the genetic relationship among 20 mungbean genotypes. Twenty one (78 %) genic SSR markers showed polymorphism and the number of alleles ranged from two to six with an average PIC value of 0.34. Cluster analysis based on similarity coefficient clearly separated the cultivated and the wild genotypes into separate groups. Transferability study showed that 97 % SSR markers were transferable to eight other Vigna species, hereby expanding their utility. This study gives an insight into frequency, type and distribution of SSRs in the genic region of mungbean and report the development of a large set of SSR markers for mungbean. These genic SSR markers will provide an important genomic resource for qualitative and quantitative traits mapping, marker assisted selection and genetic diversity studies in mungbean and related Vigna species.