Genetic diversity and population structure analysis in cultivated soybean (Glycine max [L.] Merr.) using SSR and EST-SSR markers

Abstract

Soybean (Glycine max) is an important legume that is used to fulfill the need of protein and oil of large number of population across the world. There are large numbers of soybean germplasm present in the USDA germplasm resources. Finding and understanding genetically diverse germplasm is a top priority for crop improvement programs. The current study used 20 functional EST-SSR and 80 SSR markers to characterize 96 soybean accessions from diverse geographic backgrounds. Ninety-six of the 100 markers were polymorphic, with 262 alleles (average 2.79 per locus). The molecular markers had an average polymorphic information content (PIC) value of 0.44, with 28 markers ≥ 0.50. The average major allele frequency was 0.57. The observed heterozygosity of the population ranged from 0–0.184 (average 0.02), while the expected heterozygosity ranged from 0.20–0.73 (average 0.51). The lower value for observed heterozygosity than expected heterozygosity suggests the likelihood of a population structure among the germplasm. The phylogenetic analysis and principal coordinate analysis (PCoA) divided the total population into two major groups (G1 and G2), with G1 comprising most of the USA lines and the Australian and Brazilian lines. Furthermore, the phylogenetic analysis and PCoA divided the USA lines into three major clusters without any specific differentiation, supported by the model-based STRUCTURE analysis. Analysis of molecular variance (AMOVA) showed 94% variation among individuals in the total population, with 2% among the populations. For the USA lines, 93% of the variation occurred among individuals, with only 2% among lines from different US states. Pairwise population distance indicated more similarity between the lines from continental America and Australia (189.371) than Asia (199.518). Overall, the 96 soybean lines had a high degree of genetic diversity.

Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers

“…The average PIC for the 25 SSRs studied was 0.625, indicating a high polymorphic level. Among twenty-five SSRs, Satt371, Satt243, Satt244, Satt458, and Sat288 were previously successfully used to assess genetic diversity in different soybean collections [55][56][57][58][59]. The results showed that only five SSRs were required to distinguish all nineteen accessions from Kazakhstan (Figure S2, which is comparable with reports using other crops [60].…”

Understanding genetic diversity in drought-adaptive hybrid parental lines in pearl millet

“…Q1 contained most of the R-lines (pollinators), while Q2 possessed all Blines except for one R-line (Fig 3A and 3B). Individuals with a score for clusters membership coefficient more than 0.80 are considered as pure, while those who scored less than 0.80 was considered as admixture [41,42]. In the case of the R-lines cluster (Q1), 67 accessions were identified, out of which 58 were pure and nine were admixtures.…”

Diversity Analysis of 53 Soybean Accessions Introduced from China Based on Morphological Characteristics and SSR Markers

“…In addition to being used for genetic diversity analysis [12], molecular markers can also be used in gene mapping analysis [34,35], fingerprinting analysis [36], and mutant gene detection [37]. The use of molecular markers in soybean genetic diversity analysis was carried out in previous studies including Rani et al [38] on 96 soybean accessions with 96 SSR and EST-SSR markers, Jain et al [39] on 24 soybean genotypes with 18 RAPD markers, Sulistyo et al [40] on 40 soybean accessions with 13 SSR markers, Slamet et al [41] on 40 soybean genotypes using 20 SSR markers, and Agam et al [42] on 11 mutant soybean genotypes with 12 RAPD markers.…”