Common bean (Phaesolus vulgaris L.) distribution across eastern, central and southern Africa region is widely driven by choice of grain types, which is affecting the genetic composition and adaptation to target production environments for biotic and abiotic constraints. Two bean fly species, Ophiomyia spencerella and Ophiomyia phaseoli are harmful insect pests of beans causing significant yield losses. Our objectives were to assess the population structure of common bean germplasm of different market classes and to identify polymorphic loci associated with resistance to O. spencerella. The study was carried out on a diversity panel of 284 genotypes using 9040 SNP markers. The genotypes were differentiated in to 14 distinct clusters. The mean FST of 0.4849, revealed major differentiation among the populations. Andean gene pool was more diverse compared to Mesoamerica gene pool which could be attributed to preference for large seeded cultivars. Multi-dimensional scaling and structure analyses revealed admixture among seed types. From genome wide association studies (GWAS), major genomic regions associated with O. spencerella resistance were identified on chromosome 1 (Pv01). The most significant SNP on Pv01 was aligned to gene PHAVU_001G075500g that is related to the Interleukin-1 receptor-associated kinase (IRAK) pathway, critical in regulating inherent immune responses to disease infection and insect herbivore attack. The diversity uncovered on the basis of market classes of beans and the presence of QTL regions associated with resistance to bean fly could serve as a valuable genetic resource for improvement of beans of different seed types in eastern and southern Africa region.nnCore IdeasO_LIGWAS revealed major loci associated with bean fly resistance on chromosome 01.nC_LIO_LINew sources of resistance to bean fly were uncovered from different market classes.nC_LIO_LIGenetic diversity uncovered is based on recent farmer preferences selection events.nC_LI
