Assessment of the Genetic Structure and Diversity of Soybean (Glycine  max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers

Abstract

Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon's diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.

Keywords: AMOVA; Africa; DArT-seq; genetic diversity; population structure; soybean.

Figure 1

Cluster analysis of the 281 soybean genotypes based on unweighted pair-group method with arithmetic means: (A) SNP markers and (B) DArT markers. The different colors indicate the different clusters identified.

Figure 2

Principal component analysis biplot showing the first two components: (A) SNP markers and (B) DArT markers. The blue- and red-filled circles indicate the two groups identified. The black circles also represent the two groups and show the labels of the groups (1 and 2). The black line indicates the sub-group.

Figure 3

Population structure of the soybean accessions: (A) summary plot of estimates of Q for SNP markers; (B) rate of change of the likelihood (∆K) for SNP markers; (C) summary plot of estimates of Q for DArT markers; (D) rate of change of the likelihood (∆K) for DArT markers. The ∆K shows a clear peak at the true value of K.