Molecular characterization and genetic diversity studies of Indian soybean (Glycine max (L.) Merr.) cultivars using SSR markers

Abstract

Background The genetic base of soybean cultivars in India has been reported to be extremely narrow, due to repeated use of few selected and elite genotypes as parents in the breeding programmes. This ultimately led to the reduction of genetic variability among existing soybean cultivars and stagnation in crop yield. Thus in order to enhance production and productivity of soybean, broadening of genetic base and exploring untapped valuable genetic diversity has become quite indispensable. This could be successfully accomplished through molecular characterization of soybean genotypes using various DNA based markers. Hence, an attempt was made to study the molecular divergence and relatedness among 29 genotypes of soybean using SSR markers. Methods and results A total of 35 SSR primers were deployed to study the genetic divergence among 29 genotypes of soybean. Among them, 14 primer pairs were found to be polymorphic producing a total of 34 polymorphic alleles; and the allele number for each locus ranged from two to four with an average of 2.43 alleles per primer pair. Polymorphic information content (PIC) values of SSRs ranged from 0.064 to 0.689 with an average of 0.331. The dendrogram constructed based on dissimilarity indices clustered the 29 genotypes into two major groups and four sub-groups. Similarly, principal coordinate analysis grouped the genotypes into four major groups that exactly corresponded to the clustering of genotypes among four sub-groups of dendrogram. Besides, the study has reported eight unique and two rare alleles that could be potentially utilized for genetic purity analysis and cultivar identification in soybean. Conclusion In the present investigation, two major clusters were reported and grouping of large number of genotypes in each cluster indicated high degree of genetic resemblance and narrow genetic base among the genotypes used in the study. With respect to the primers used in the study, the values of PIC and other related parameters revealed that the selected SSR markers are moderately informative and could be potentially utilized for diversity analysis of soybean. The clustering pattern of dendrogram constructed based on SSR loci profile displayed good agreement with the cultivar’s pedigree information. High level of genetic similarity observed among the genotypes from the present study necessitates the inclusion of wild relatives, land races and traditional cultivars in future soybean breeding programmes to widen the crop gene pool. Thus, hybridization among diverse gene pool could result in more heterotic combinations ultimately enhancing genetic gain, crop yield and resistance to various stress factors.

Genetic diversity in early maturity Chinese and European elite soybeans: A comparative analysis

“…While the mean number of SSR alleles per locus was 5.5 across the two populations of the present study (Suppl. Table 3) and similar to the sets of Žulj Mihaljević et al (2020) or Tavaud-Pirra et al (2009), numbers of alleles were lower in Serbian (Tomicic et al 2015) and Indian (Kumar et al 2022) sets of elite cultivars. In contrast, the numbers of alleles were considerably higher in several sets of soybean accessions originating from Korea (Hwang et al 2020;Lee et al 2014;Song et al 2013).…”

Genetic variability, combining ability and molecular diversity-based parental line selection for heterosis breeding in field corn (Zea mays L.)

“…Although per se performance of female inbred lines plays crucial role in economic seed production of any hybrids, breeder may tend to select even poor performing female parents, if genetic distance between the parents is high, will be explore for heterosis breeding programme [26,27]. The extent of heterosis has been reported to vary with genetics of traits under consideration [28][29][30][31][32].…”

Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes

“…SSRs have been deemed as promising candidate markers for population genetics and germplasm identification in plants due to their hypervariability, high information content and codominance [ 45 , 46 , 47 ]. With the rapid development of next-generation sequencing technology, whole-genome SSR identification becomes much more effective and comprehensive [ 2 , 48 ].…”