Exploring the genetic base of the soybean germplasm from Africa, America and Asia as well as mining of beneficial allele for flowering and seed weight

Abstract

Genetic diversity is the foundation for any breeding program. The present study analyzed the genetic base of 163 soybean genotypes from three continents viz. Africa, America and Asia using 68 trait-linked simple sequence repeats (SSR) markers. The average number of alleles among the germplasm from the three continents followed the trend as Asia (9) > America (8) > Africa (7). Similar trends were observed for gene diversity (0.76 > 0.74 > 0.71) and polymorphism information content (PIC) (0.73 > 0.71 > 0.68). These findings revealed that soybean germplasm from Asia has wider genetic base followed by America, and least in Africa. The 163 genotypes were grouped into 4 clusters by phylogenetic analysis, whereas model-based population structure analysis also divided them into 4 subpopulations comprising 80.61% pure lines and 19.39% admixtures. The genotypes from Africa were easily distinguished from those of other two continents using phylogenetic analysis, indicating important role of geographyical differentiation for this genetic variability. Our results indicated that soybean germplasm has moved from Asia to America, and from America to Africa. Analysis of molecular variance (AMOVA) showed 8.41% variation among the four subpopulations, whereas 63.12% and 28.47% variation existed among and within individuals in the four subpopulations, respectively. Based on the association mapping, a total of 21 SSR markers showed significant association with days to flowering (DoF) and 100-seed weight (HSW). Two markers Satt365 and Satt581 on chromosome 6 and 10, respectively, showed pleiotropic effect or linkage on both traits. Genotype A50 (Gakuran Daizu/PI 506679) from Japan has 8 out of the 13 beneficial alleles for increased HSW. The diverse genotypes, polymorphic SSR markers and desirable alleles identified for DoF and HSW will be used in future breeding programs to improve reproductive, yield and quality traits.

Keywords: Cluster; Desirable alleles; Polymorphism information content; Principal coordinate analysis; Simple sequence repeats.

Fig. 1

Summary of number of alleles, gene diversity and polymorphism information content (PIC) among the 163 germplasm. All in the X-axis represent the whole of 163 germplasm used in this study, whereas Africa, America and Asia represent 53, 53 and 57 germplasm assembled from each continent, respectively

Fig. 2

Neighbor-joining tree constructed by Nei (1972) genetic distance among the 163 genotypes assembled from Africa, America and Asia. Each cluster is represented by one color in the clade: yellow, green, ash and purple color represent Cluster I, II, III and IV obtained by Nei’s genetic distances and visualized in MEGA software, respectively. Germplasm marked with blue circle, red triangle and pink star represent germplasm from Africa (Af1–53), America (Am1–53) and Asia (As1–57) continent, respectively

Fig. 3

Model based population structure of all 163 germplasm. The four colors (red, green, blue and yellow) represent four inferred ancestral population based on membership coefficient (Q) obtained from STRUCTURE software. The red, green, blue and yellow represent subpopulation 1, 2, 3 and 4, respectively. Each accession is represented by a vertical bar. Af1–53, Am1–53 and As1–57 in each column represent accessions assembled from Africa, America and Asia continents, respectively

Fig. 4

Linkage disequilibrium (LD) among the four subpopulations obtained from the model-based population structure analysis implemented in STRUCTURE software