Genetic diversity and population structure analysis of Kala bhat (Glycine max (L.) Merrill) genotypes using SSR markers

Yegappa Hipparagi,Rakesh Singh,Debjani Roy Choudhury,Veena Gupta

doi:10.1186/s41065-017-0030-8

Yegappa Hipparagi, Rakesh Singh + Show 2 more

Open Access

https://doi.org/10.1186/s41065-017-0030-8

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Abstract

BackgroundKala bhat (Black soybean) is an important legume crop in Uttarakhand state, India, due to its nutritional and medicinal properties. In the current study, the genetic variabilities present in Kala bhat were estimated using SSR markers and its variability was compared with other improved soybean varieties cultivated in Uttarakhand state, India.ResultsSeventy-five genotypes cultivated in different districts of Uttarakhand were collected, and molecular analysis was done using 21 SSR markers. A total of 60 alleles were amplified with an average of 2.85 alleles per locus. The mean value of gene diversity and PIC was estimated to be 0.43 and 0.36, respectively. The unrooted phylogenetic tree grouped soybean genotypes into three major clusters, where, yellow seed coat (improved varieties) genotypes were grouped in one cluster, while reddish brown (improved varieties) and Kala bhat showed intermixing. Population structure divided the soybean genotypes into six different populations. AMOVA analysis showed 12% variance among the population, 66% variance among individual and 22% variance was observed within individuals. Principal Coordinate Analysis (PCoA) also showed that yellow seed coat genotypes were grouped in one cluster, whereas, the Kala bhat showed scattered distribution and few genotypes of Kala bhat showed grouping with red and yellow genotypes.ConclusionsThe different genetic diversity parameters used in the present study indicate that Kala bhat genotypes were more diverse than the yellow seed coat and brown seed coat colour genotypes. Therefore, Kala bhat genotypes can be a good source for the soybean breeding programme due to its better genetic diversity as well as its medicinal properties.

Highlights

Kala bhat (Black soybean) is an important legume crop in Uttarakhand state, India, due to its nutritional and medicinal properties
Total 21 Simple sequence repeats (SSR) primers were used for genetic diversity study of 75 soybean genotypes
The maximum polymorphic information content (PIC) was observed for primer Satt 180 (0.66) and the minimum was observed for Satt285 and Satt389 (0.10) with a mean value of 0.36. (Table 2)

Summary

Introduction

Kala bhat (Black soybean) is an important legume crop in Uttarakhand state, India, due to its nutritional and medicinal properties. The genetic variabilities present in Kala bhat were estimated using SSR markers and its variability was compared with other improved soybean varieties cultivated in Uttarakhand state, India. The wild and cultivated soybeans showed significant phenotypic diversity but the small reproductive difference, and they have very similar genomes in both its size and content [2]. Soybean is grown under varied climatic conditions and geographical locations in India. It occupies an area of 10.8 million hectare and accounting. Evaluation of genetic diversity is enhanced by the use of DNA markers. Among different DNA markers, restriction fragment length polymorphisms (RFLPs), random amplified polymorphic DNAs (RAPDs), amplified fragment length polymorphisms (AFLPs), single nucleotide polymorphisms (SNPs) and microsatellites or simple sequence repeats

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