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

Abdulwahab S. Shaibu,Sanusi G. Mohammed,Alpha Y. Kamara,Lucky O. Omoigui,Ibrahim B. Mohammed,Benjamin Karikari,Hassan Ibrahim,Zainab L. Miko,Hauwa L. Yusuf

doi:10.3390/plants11010068

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.

Highlights

IntroductionThe average worldwide yields of soybean increased from 2183 kg ha−1 in 1994 to 2769 kg ha−1 in 2019, with an annual increase of 26 kg ha−1 [1]
The single nucleotide polymorphism (SNP) were distributed across the 20 soybean chromosomes (Figure S1a), with Gm18 having the highest number of SNPs (533), while
The estimated genetic diversities were comparable between SNP and diversity array technology (DArT) markers

Summary

Introduction

The average worldwide yields of soybean increased from 2183 kg ha−1 in 1994 to 2769 kg ha−1 in 2019, with an annual increase of 26 kg ha−1 [1]. This shows that there is still considerable potential for increasing soybean yield. The use of new sources of genetic variation to develop improved varieties is enhanced when the selection of parental genotypes is based on both phenotypic and genetic diversity [2]. Determining the variation in the soybean germplasm is important for the effective selection of parental lines for hybridization and the development of improved varieties

Objectives

Methods

Results

Discussion

Conclusion