Abstract
Genus Vigna represented by more than 100 species is a source of nutritious edible seeds and sprouts that are rich sources of protein and dietary supplements. It is further valuable because of therapeutic attributes due to its antioxidant and anti-diabetic properties. A highly diverse and an extremely ecological niche of different species can be valuable genomic resources for productivity enhancement. It is one of the most underutilized crops for food security and animal feeds. In spite of huge species diversity, only three species of Vigna have been sequenced; thus, there is a need for molecular markers for the remaining species. Computational approach of microsatellite marker discovery along with evaluation of polymorphism utilizing available genomic data of different genotypes can be a quick and an economical approach for genomic resource development. Cross-species transferability by e-PCR over available genomes can further prioritize the potential SSR markers, which could be used for genetic diversity and population differentiation of the remaining species saving cost and time. We present VigSatDB—the world’s first comprehensive microsatellite database of genus Vigna, containing >875 K putative microsatellite markers with 772 354 simple and 103 865 compound markers mined from six genome assemblies of three Vigna species, namely, Vigna radiata (Mung bean), Vigna angularis (Adzuki bean) and Vigna unguiculata (Cowpea). It also contains 1976 validated published markers. Markers can be selected on the basis of chromosomes/location specificity, and primers can be generated using Primer3core tool integrated at backend. Efficacy of VigSatDB for microsatellite loci genotyping has been evaluated by 15 markers over a panel of 10 diverse genotype of V. radiata. Our web genomic resources can be used in diversity analysis, population and varietal differentiation, discovery of quantitative trait loci/genes, marker-assisted varietal improvement in endeavor of Vigna crop productivity and management.
Highlights
Genus Vigna is one of the most important Fabaceae family crops, which is mostly found in tropical regions and warm temperate region of Asia and Africa [1], but some of its species are found in America [2]
We report here first comprehensive web genomic resource of genus Vigna covering three of its commercially important species
VigSatDB contains a total of 876 219 putative microsatellite DNA markers, which includes 1976 validated published markers
Summary
Genus Vigna is one of the most important Fabaceae family crops, which is mostly found in tropical regions and warm temperate region of Asia and Africa [1], but some of its species are found in America [2]. Genus Vigna having more than 100 species is one of the most underutilized leguminous crop for human food and animal feeds, as only 10 species are domesticated [5]. Mungbean (Vigna radiata), cowpea (Vigna unguiculata), adzuki bean (Vigna angularis) and urdbean (Vigna mungo) are the major domesticated species. Since more than 90 species of this genus are well adaptive to very extreme ecological niches like marine beach, deserts and swamps, they could be a potential source of genomic resource for productivity enhancement [6]
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