Assessment of diversity in tropical soybean (Glycine max (L.) Merr.) varieties and elite breeding lines using single nucleotide polymorphism markers
- 1 February 2021
- journal article
- research article
- Published by Cambridge University Press (CUP) in Plant Genetic Resources: Characterization and Utilization
- Vol. 19 (1), 20-28
- https://doi.org/10.1017/S1479262121000034
Abstract
Soybean (Glycine max (L.) Merr.) is an important legume crop with high commercial value widely cultivated globally. Thus, the genetic characterization of the existing soybean germplasm will provide useful information for enhanced conservation, improvement and future utilization. This study aimed to assess the extent of genetic diversity of soybean elite breeding lines and varieties developed by the soybean breeding programme of the International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria. The genetic diversity of 65 soybean genotypes was studied using single-nucleotide polymorphism (SNP) markers. The result revealed that 2446 alleles were detected, and the indicators for allelic richness and diversity had good differentiating power in assessing the diversity of the genotypes. The three complementary approaches used in the study grouped the germplasm into three major clusters based on genetic relatedness. The analysis of molecular variance revealed that 71% (P < 0.001) variation was due to among individual genotypes, while 11% (P < 0.001) was ascribed to differences among the three clusters, and the fixation index (F-ST) was 0.11 for the SNP loci, signifying moderate genetic differentiation among the genotypes. The identified private alleles indicate that the soybean germplasm contains diverse variability that is yet to be exploited. The SNP markers revealed high diversity in the studied germplasm and found to be efficient for assessing genetic diversity in the crop. These results provide valuable information that might be utilized for assessing the genetic variability of soybean and other legume crops germplasm by breeding programmes.Keywords
This publication has 39 references indexed in Scilit:
- Enhancements to the ADMIXTURE algorithm for individual ancestry estimationBMC Bioinformatics, 2011
- Fast model-based estimation of ancestry in unrelated individualsGenome Research, 2009
- adegenet: a R package for the multivariate analysis of genetic markersBioinformatics, 2008
- High-throughput genotyping with the GoldenGate assay in the complex genome of soybeanTheoretical and Applied Genetics, 2008
- Empirical Comparison of Simple Sequence Repeats and Single Nucleotide Polymorphisms in Assessment of Maize Diversity and RelatednessPLOS ONE, 2007
- PLINK: A Tool Set for Whole-Genome Association and Population-Based Linkage AnalysesAmerican Journal of Human Genetics, 2007
- Relationship between Origin and Genetic Diversity in Chinese Soybean GermplasmCrop Science, 2005
- Soybean genetic resources and crop improvementGenome, 1999
- Relationship between Genetic Distance among Parents and Genetic Variance in Populations of SoybeanCrop Science, 1997
- Genetic Base for North American Public Soybean Cultivars Released between 1947 and 1988Crop Science, 1994