Genome-Wide Association Study of Resistance to Bean Fly and Population Structure of Market Classes of Common Bean

Abstract

Organization (BecA-ILRI) Hub, Nairobi. Received _____________. *Corresponding Author (pookwiri@yahoo.com). Core Ideas• GWAS revealed major loci associated with bean fly resistance on chromosome 01.• New sources of resistance to bean fly were uncovered from different market classes.• Genetic diversity uncovered is based on recent farmer preferences selection events. Abstract Common bean (Phaesolus vulgaris L.) distribution across eastern, central and southernAfrica 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 F ST 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. Abbreviations BAK1, brassinosteroid insensitive 1-associated receptor kinase 1; BLASTn, basic local alignment search tool for nucleotide; BLASTx basic local alignment search tool for translated nucleotide; BR, brassinosteroid; BSM, bean stem maggot; CIAT, International

Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean

“…Several other reports have alluded that populations derived from Meso-American gene pool had faster LD decay compared to the Andean gene pool [ 73 , 74 ]. Markers for BDS and PC were identified on Pv01 , similar to reports by Ojwang et al [ 36 ]. This suggests that chromosome Pv01 harbours genes controlling bean fly resistance.…”

“…Genome-wide association studies (GWAS) based on linkage disequilibrium (LD) complements conventional linkage mapping to identify genomic regions controlling quantitative traits of interest [ 26 ]. GWAS has been used in common bean to identify genes associated with cooking time [ 27 ], days to flowering [ 28 ], yield-related traits [ 29 ], and resistance to angular leaf spot [ 30 ], anthracnose [ 31 ], common bacterial blight [ 32 ], soybean cyst nematodes [ 33 , 34 ], bruchids [ 35 ] and bean fly [ 36 ]. [Ojwang, Eldridge [ 36 ]] identified five significant SNP markers linked to bean fly resistance in common bean on chromosome Pv01 , and one of the markers was reportedly linked to an immune response gene PHAVU_001G075500g [ 37 ].…”

“…[Ojwang, Eldridge [ 36 ]] identified five significant SNP markers linked to bean fly resistance in common bean on chromosome Pv01 , and one of the markers was reportedly linked to an immune response gene PHAVU_001G075500g [ 37 ]. This was the first identified gene associated with bean fly resistance [ 36 ].…”

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress

“…Several GWASs in common bean are based on analysis combining collections of Andean and Mesoamerican germplasms, providing a broad perspective over the common bean diversity ( Perseguini et al, 2016 ; Raggi et al, 2019 ; Ojwang et al, 2019 ; Tigist et al, 2019 ). However, each gene pool has been domesticated for specific agronomic, morphological, and physiological and under diverse edaphoclimatic conditions ( Rendón-Anaya et al, 2017 ).…”