Abstract
Eastern Africa is a significant region of common bean (Phaseolus vulgaris L.) production and genetic diversity. Insect pests are a major biotic constraint in subsistence crop production systems. Bean fly (Ophiomyia spencerella) is a serious pest of beans in eastern Africa highlands. Breeding efforts focus on combining adaptability traits with user preferred seed types. However, lack of information on molecular markers linked to genes modulating bean fly resistance has slowed breeding progress. The objectives were to: (i) characterize genetic diversity and uncover putative bean fly resistant genotypes within diverse seed types and market classes and (ii) identify genomic regions controlling bean fly resistance using genome-wide association analysis (GWAS). A set of 276 diverse genotypes comprising local landraces and varieties from Kenya alongside introductions from International Centre for Tropical Agriculture (CIAT), were assembled. The germplasm represented varied bean production ecologies and seed types. Genetic diversity conforming to Andean and Mesoamerican genepools was established. Out of 276 genotypes evaluated, 150 were Andean, 74 were Mesoamerican and 52 were admixed. Twenty-two genotypes were resistant to bean fly. Association mapping results for stem damage score and plant mortality identified six significant single-nucleotide polymorphisms (SNPs) on chromosomes Pv01 and Pv09. The most significant SNP marker was 12 kilobases downstream of Phvul.001G074900 gene with LOD score > 4.0 hence in linkage disequilibrium with the postulated gene. The identified candidate gene is pleiotropic and modulates both flowering time and plant responses to stress. These findings are a key step towards marker-enabled breeding in common bean for sub-Saharan Africa.
Highlights
Common bean was domesticated in two already separated ancestral genepools in Latin America about 7000–8000 years ago (Gepts et al 1986; Gepts and Debouck 1991; Freyre et al 1996; Mamidi et al 2011)
We assembled a total of 276 common bean genotypes which included 259 landrace accessions from Genetic Resources Research Institute (GeRRI) gene bank of the Kenya Agricultural and Livestock Research Organization (KALRO), seven bean fly resistant varieties alongside two resistant landraces from East and Central Africa Bean Research Network (ECABREN) and eight local user preferred varieties developed by Egerton University Kenya (EUK) and KALRO (Table 1 and supplemental Table S1)
The study uncovered the existing sources of resistance to bean fly from a diverse set of bean genetic resources in both Andean and Mesoamerican genepools and associated seed types of major importance in eastern Africa
Summary
Common bean was domesticated in two already separated ancestral genepools in Latin America about 7000–8000 years ago (Gepts et al 1986; Gepts and Debouck 1991; Freyre et al 1996; Mamidi et al 2011). Farmers began to apply selection pressure and to conserve genotypes with valuable traits (Wortmann et al 1998; Sperling 2001). Adoption of crop varieties and continuous selection under different cultivation practices and user preferences create and maintain on-farm genetic diversity of landraces and improved varieties (Worthington et al 2012; Pautasso et al 2013; Soleri et al 2013; Wilkus et al 2018). Landraces are valuable sources of genes for improvement of modern cultivars for resistance or tolerance to production challenges including insect pest, disease, low soil fertility, drought and other effects arising from climate variability (Kimani et al 2001; Blair et al 2010; Ddamulira et al 2014; Assefa et al 2019; Piechota et al 2019)
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