High-density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia

INTRODUCTION: Common bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies. MATERIALS: Two hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers. RESULTS: The overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classification. Model-based structure analysis delineated the 289 common bean genotypes into six hypothetical ancestoral populations. CONCLUSIONS: The genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing effective collection and conservation for efficient utilization for the improvement of the crop. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11033-023-08498-y.