Molecular characterization and genetic diversity analysis of soybean (Glycine max (L.) Merr.) germplasm accessions in India

Abstract

Molecular characterization and genetic diversity among 82 soybean accessions was carried out by using 44 simple sequence repeat (SSR) markers. Of the 44 SSR markers used, 40 markers were found polymorphic among 82 soybean accessions. These 40 polymorphic markers produced a total of 119 alleles, of which five were unique alleles and four alleles were rare. The allele number for each SSR locus varied between two to four with an average of 2.97 alleles per marker. Polymorphic information content values of SSRs ranged from 0.101 to 0.742 with an average of 0.477. Jaccard's similarity coefficient was employed to study the molecular diversity of 82 soybean accessions. The pairwise genetic similarity among 82 soybean accessions varied from 0.28 to 0.90. The dendrogram constructed based on genetic similarities among 82 soybean accessions identified three major clusters. The majority of genotypes including four improved cultivars were grouped in a single subcluster IIIa of cluster III, indicating high genetic resemblance among soybean germplasm collection in India.

Genetic diversity analysis among soybean genotypes using SSR markers in Uganda

“…Bisen et al (2015) detected 2.22 alleles per locus with an average PIC value of 0.199 using 16 SSR markers on 38 soybean varieties in active seed multiplication chain together with all varieties developed and released by JNKVV in India. The average polymorphic information content (PIC) (a measure of the allelic diversity of SSRs) observed in this study was 0.573 which was consistent with previous studies (Widaningsih et al, 2014;Kumawat et al, 2015;Ghosh et al, 2014;Wang et al, 2010). A total of 20 markers excluding BE806308 had the PIC values greater than 0.4 indicating that these markers were highly informative for discriminating and distinguishing released varieties and elite genotypes, and these markers with high PIC values occurred on 14 separate linkage groups indicating that molecular polymorphism was spread across different regions of the genome (Song et al, 2010).…”

“…Allelic richness (average number of alleles per locus) is an effective index for diversity evaluation but it is largely dependent on the sample size (Hipparagi et al, 2017), suggesting that to improve the allelic richness more genotypes need to be introduced into the breeding program to be able to enhance genetic diversity (Widaningsih et al, 2014). The number of alleles observed in this study is comparable to those reported by Kumawat et al (2015) on 82 indigenous and exotic soybean accessions of different maturity groups and source in India where 2.9 alleles were detected per locus with an average polymorphic information content (PIC) value of 0.58. Similarly, Hipparagi et al (2017) also reported 2.61 alleles with an average PIC value of 0.36 among 75 soybean genotypes assayed by 21 SSR markers in India.…”

“…The PIC was highest for the SSR primer Satt411 (0.741) and was lowest for the primer BE806308 (0.208) indicating that primer Satt411 was highly informative, effective and useful tool to determine the genetic differences among the released varieties and elite soybean genotypes and to study the phylogenetic relationship. Previous study by Kumawat et al (2015) reported the PIC value of 0.50 for SSR primer Satt411 and 0.41 for primer BE806308 on genetic diversity analysis of 82 soybean accessions in India.…”

“…Soybean being a self-pollinated crop has narrow genetic base (Kumawat et al, 2015). In the recent past, the soybean breeding program in Uganda focused on targeted hybridization using few selected genotypes as parental lines such as Duiker, GC001, UG05 and MNG.…”

“…Among the different DNA markers are; Amplified Fragment Length Polymorphisms (AFLPs), Single Nucleotide Polymorphisms (SNPs), Restriction Fragment Length Polymorphisms (RFLPs), Microsatellites/ Simple Sequence Repeats (SSRs) and Randomly Amplified Polymorphic DNAs (RAPDs) have been widely used in studying genetic diversity in soybeans, each with its own merits and demerits (Khare et al, 2013;Chakraborty et al, 2018). For molecular characterization and genetic diversity studies in soybean, SSR markers have been considered as the molecular markers of choice because of their abundance, codominance, high reproducibility (Kujane et al, 2019;Koutu et al, 2019), high polymorphism compared to RFLPs, AFLPs and RAPDs (Kumawat et al, 2015;Chakraborty et al, 2018;Moniruzzaman et al, 2019) and have much greater ability to identify unique alleles in parental and elite soybean germplasm than any other markers (Tantasawat et al, 2011). Therefore, the objective of this study was to determine the level genetic diversity that exists among released and elite soybean genotypes in Uganda based on the SSRs molecular markers.…”