Development and characterization of a new set of genomic microsatellite markers in rice bean (Vigna umbellata (Thunb.) Ohwi and Ohashi) and their utilization in genetic diversity analysis of collections from North East India

Abstract

Rice bean [Vigna umbellate (Thumb.) Ohwi and Ohashi] is an underutilized crop believed to be domesticated in the Myanmar-Thailand region of Asia. In India, rice bean is mainly cultivated in the North-Eastern Hills, which is a hotspot for biological diversity. A 5' anchored PCR was used to develop microsatellite markers in rice bean. Twenty-eight specific primer pairs were designed and employed to characterize sixty five ricebean accessions collected from North East India. A total of 179 alleles were amplified with an average of 6.393 alleles per locus. The gene diversity was high (mean 0.534) in the accessions collected from Darjeeling, Nagaland and Manipur, which are bordering areas with East Nepal and Myanmar, respectively. Exceptionally high outcrossing rate was observed in the entire population. Population structure analysis identified three distinct clusters in which accessions collected from areas bordering Myanmar and East Nepal grouped separately. Using a combination of STRUCTURE and Principal Coordinate Analysis, relative affinity of the intermediate accessions could be established. However, differences in allelic counts among populations were non-significant. The results showed that there is a high level of genetic diversity within the accessions, with high outcrossing rate.

Rice bean: a lesser known pulse with well-recognized potential

“…These wild forms occur in natural or disturbed habitats and are intermediate with twining plant types, freely branching, photoperiod sensitive with small seeds. Many intermediate land races are cultivated in northeast India (Iangrai et al 2017). Inter-and intraspecific genetic diversity and inter-species relationships of Vigna species from Thailand and neighbouring region have been assessed using AFLP analysis (Seehalak et al 2006).…”

“…gracilis from which rice bean is believed to have originated is conspecific with the cultivated V. umbellata and widespread in distribution in South and Southeast Asia (Bisht et al 2005;Seehalak et al 2006;Tomooka et al 1991Tomooka et al , 2002a. It is mainly grown in Bhutan, India, Myanmar, Northern Thailand, Southern China, Laos, Vietnam, Indonesia and East Timor (Tian et al 2013;Iangrai et al 2017;Pattanayak et al 2018). The crop was introduced as a garden and cover crop in Fiji, Sri Lanka, Ghana, Jamaica, Mexico and Haiti.…”

“…Genomic studies of rice bean have lagged behind that of other legume crops, such as soybean, common bean, mung bean, and azuki bean due to the lack of polymorphic DNA markers. To date, there are only few reports on the intraspecies molecular diversity in V. umbellata analysed using RAPD, AFLP, ISSR and SSR markers (Bajracharya et al 2008;Muthusamy et al 2008;Thakur et al 2017;Tian et al 2013;Iangrai et al 2017). Ten rice bean landraces from NE India were genotyped with 74 RAPD and 37 ISSR primers (Muthusamy et al 2008).…”

“…Wang et al (2016) also developed and characterized a set of microsatellite markers from a SSR-enriched genomic library of rice bean. Iangrai et al (2017) developed a set of 28 SSR markers and analysed genetic diversity in northeast Indian rice bean accessions. They reported high PIC value for SSR markers, which detected a high genetic diversity among 65 accessions.…”

“…(Tomooka et al 2000;Kashiwaba et al 2003) although resistance to yellow mosaic virus, Cercospora and bacterial leaf spot (Arora et al 1980) and mung bean yellow mosaic virus (Pandiyan et al 2008) has been reported in this crop. In the recent years, some reports on genetic diversity (Tian et al 2013;Iangrai et al 2017;Pattanayak et al 2018), genomics (Somta et al 2006;Isemura et al 2010) and nutritional quality (Katoch 2013;Bepary et al 2017) have been published.…”