Genetic Diversity and Population Structure of Ugandan Soybean (Glycine max L.) Germplasm Based on DArTseq

Abstract

Soybean (Glycine max (L.) is an important oil crop with production below the real need in Africa. To increase the production, substantial upgrading must be accomplished by enlarging the genetic potential of new cultivars that relays on the parents' genetic diversity. We aimed to assess the genetic diversity and the population structure of soybean accessions, therefore, evaluate soybean value in terms of use for breeding purposes. To accomplish this, a set of 282 soybean accessions were genotyped using the Diversity Array Technology Sequencing with a high throughput of the Single-nucleotide polymorphisms (SNPs). A total of 6,935 high-quality SNPs were identi ed across the whole soybean genome. The mean value of genetic diversity, major alleles frequency, minor alleles frequency, expected heterozygosity, and the polymorphism information content was respectively estimated at 0.35, 0.77, 0.22, 0.33, and 0.29. The analysis of molecular variance reveals that the variance among the populations is lower than the variance within the populations. The soybean accessions could be classi ed into two groups based on the model-based population structure and the principal coordinate analysis or into three groups based on the discriminant analysis of the principal component and the Neighbor-joining tree. The information provided in this study will be helpful for breeders.

Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean

“…The knowledge of the population structure and familial relationships (i.e., kinship) in an association panel is important to prevent false associations in a GWAS [ 39 ]. Population structure and admixture for this population were reported in a previous study [ 40 ]. From our study, 113 putative candidate genes encoding for several proteins ( Table 6 ) were discovered as major contributors to the resistance to Coniothyrium glycines , the causal agent of red leaf blotch disease in soybean production.…”

Characterization of the Moroccan Barley Germplasm Preserved in the Polish Genebank as a First Step towards Selecting Forms with Increased Drought Tolerance

“…As described in the introduction, Morocco is located within a biodiversity hotspot, and diverse eco-geographical conditions and traditional agriculture have facilitated the emergence and survival of landraces adapted to multiple stresses [45]. High-throughput DArTseq analysis, which is commonly used to assess the genetic diversity of different plant species, was used here [70][71][72][73][74][75][76][77][78]. DArTseq analysis has previously been used to describe variation in other accessions from the NCPRG, i.e., native landraces and from several other countries, as well as cultivars bred and grown in Poland over the last 120 years [55,64].…”

Phenotypic Diversity and Relationships of Fruit Traits in Persimmon (Diospyros kaki Thunb.) Germplasm Resources

“…The study of phenotypic diversity can elucidate the structure and laws of population variation and thereby provide an important basis for the formation mechanism of complex traits through the deep excavation of genetic resources [15]. Genetic diversity is characterized by analyzing variations at the DNA level, phenotypes, and physiological characteristics [16][17][18][19]. The genetic diversity in persimmon germplasm resources has recently been reported from a study mainly focusing on the phenotypic diversity of the leaves and some fruit traits [20], the variation in the flavonoid and polyphenol contents [21], and the variation in the ascorbic acid content of the leaves [22].…”