Common bean (Phaseolus vulgaris L.) is one of the most important food legumes grown worldwide but drought stress is a major limiting factor in common bean production. Drought events, both intermittent and terminal, affect over 60% of the annual dry bean production worldwide. The development of drought tolerant varieties is essential to enhance performance under stressed and non-stressed conditions. However, breeding for drought tolerance in common bean poses difficulties, primarily from large environmental and temporal variation which make drought stress highly difficult to observe. This dissertation contains three research chapters, the objectives in the first chapter were to explore the genetic variation present within a 96-entry diversity panel and use genomewide association (GWAS) analysis to identify candidate regions associated with drought tolerance traits and agronomic performance in common bean genotypes from the Middle American gene pool. A number of marker trait associations under irrigated or rainfed were found that included shoot biomass at harvest, shoot biomass at flowering, seed size, lodging score, leaf elongation rate and wilting score. Population structure in the panel was also studied and this suggested different levels of genetic admixture or purity among the Mesoamerican and Durango races. In the second chapter, we used yield, agronomic and root architecture data from evaluations of the Mesoamerican common bean diversity panel grown under rainfed and irrigated treatments in two Michigan locations to assess the genotype x environment interaction (GE), stability and performance of the germplasm using GGE biplots. We also studied root architecture traits to determine which traits contribute most to yield under drought across two different environments. Environmental differences were found among the treatments and locations in terms of their ability to discriminate the genotypes tested. Variation in genotype stability was found across environments and differential performance under treatments was found. Genotype-by-trait biplot analysis allowed for the identification of relevant traits associated with higher yield under rainfed and irrigated conditions. In the third chapter, we constructed three small red-seeded recombinant inbred line (RIL) populations with a common parent and performed joint interval mapping analysis as a modified Nested Association Mapping (NAM) population for agronomic traits and performance under rainfed conditions. The objective was to identify novel sources of improved performance and quantitative trait loci (QTL) associated with desirable traits under rainfed and water-sufficient conditions in small red bean breeding materials adapted to temperate zones. A number of QTL were found for yield, days to flowering, lodging score, and seed size and canopy height. Progeny with superior performance under drought conditions were also identified in one of the populations. This study was the first application of a NAM design for joint linkage QTL analysis of economic traits in common bean.
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