Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

Abstract

Knowledge of genetic diversity in plant germplasm and the relationship between genetic factors and phenotypic expression is vital for crop improvement. This study's objectives were to understand the extent of genetic diversity and population structure in 60 common bean genotypes from East and Southern Africa. The common bean genotypes exhibited significant (p<0.05) levels of variability for traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield per hectare in kilograms (GYD). About 47.82 per cent of the variation among the genotypes was explained by seven principal components (PC) associated with the following agronomic traits: NPP, NFF (nodes to first flower), DTF, GH (growth habit) and GYD. The SNP markers revealed mean gene diversity and polymorphic information content values of 0.38 and 0.25, respectively, which suggested the presence of considerable genetic variation among the assessed genotypes. Analysis of molecular variance showed that 51% of the genetic variation were between the gene pools, while 49% of the variation were within the gene pools. The genotypes were delineated into two distinct groups through the population structure, cluster and phylogenetic analyses. Genetically divergent genotypes such as DRK57, MW3915, NUA59, and VTTT924/4-4 with high yield and agronomic potential were identified, which may be useful for common bean improvement.

Morpho-agronomic and genetic variation among Phaseolus vulgaris landraces from selected provinces of South Africa

“…3) indicated that the landraces (P. vulgaris landraces and the two out-groups (P. coccineus and P. lunatus)) could be divided into two subpopulations with admixed landraces between the subpopulations. The results were similar to the population structure of P. vulgaris germplasm in Malawi, where delta K was the highest at K = 2 (Nkhata et al 2020). At the K = 3 levels, where the population was modelled to evaluate more genetic variations of the subpopulations and the admixtures, 38 landraces were grouped into two subpopulations based on the Bayesian genotype clustering approach.…”

“…The lower heterozygosity values in the current study were probably caused by P. vulgaris as a naturally self-pollinating plant and most loci were probably homozygous (Nkhata et al 2020). The polymorphic information content (PIC) values show how beneficial specific markers are in diversification research (Nkhata et al 2020). The PIC that ranged from 0.00 to 0.58 among the P. vulgaris landraces in the current study (Table 4) was within a range from 0.00 to 0.96 recorded among the Brazilian landraces (Burle et al 2010).…”

“…These differences were probably caused by unequal numbers (7 and 58) of detected SSR loci. The lower heterozygosity values in the current study were probably caused by P. vulgaris as a naturally self-pollinating plant and most loci were probably homozygous (Nkhata et al 2020). The polymorphic information content (PIC) values show how beneficial specific markers are in diversification research (Nkhata et al 2020).…”

“…According to the clustering analysis among P. vulgaris from Turkey, the populations that demonstrated high similarity and high gene flow were geographically close (Bilir et al 2019). These results show large variations in seed coats but had a high degree of similarity that probably emerged from gene introgressions due to random bee pollination in the fields in the same geographical areas (Musango et al 2016) or through natural crosspollination (Nkhata et al 2020).…”

Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits

“…For common bean, DArTseq now provides an efficient and cost-effective strategy to generate SNPs for large-scale genome-wide studies [24]. For these analyses to be useful for future breeding programs, the results must be compared with the results of the morphological analyses to assist breeders in selecting source material [31].…”