"Common bean (Phaseolus vulgaris. L.) is a cheap source of protein, energy, and micronutrients including iron, zinc, vitamins, and dietary fiber for millions in the developing world. Bean production is constrained by a number of abiotic and biotic stresses, and drought stress has become the most important abiotic stress negatively affecting subsistence farming systems particularly in Africa. The overall goal of this study was to explore additional genetic diversity for drought tolerance within the Andean gene pool, and understand the genetic control of drought responses using genomic and phenometric tools. The first objective focused on the determination of the genetic architecture of yield component and photosynthetic traits at pod filling stage under terminal drought stress using a genome-wide association study (GWAS). This study involved 256 common bean genotypes from the Andean gene pool that were evaluated for two seasons (2016 and 2017) under stress and non-stress at two locations (Kasese and Namulonge) in Uganda. Several significant marker-trait associations were identified for agronomic and photosynthetic traits under drought stress conditions. Overlapping GWAS signals were detected for yield components and partitioning traits on chromosomes Pv02, Pv06, and Pv11 respectively, while colocalized signals for photosynthetic traits were identified on Pv03, Pv04, and Pv11 under drought stress conditions. Positional candidate genes, including Phvul.006G117500 encoding, plant invertase/pectin methylesterase inhibitor (INH/PMEI) superfamily protein, a positive regulator of carbon partitioning and sink strength in the reproductive stage, and Phvul.011G210000, encoding DNAJ heat shock N-terminal domain-containing protein, were identified. The second objective focused on identifying quantitative trait loci (QTL) associated with drought tolerance in a Portillo x Red Hawk recombinant inbred line (RIL) mapping population. 97 F4:7 RILs were evaluated under drought stress and non-stress conditions in the field for two seasons (2016 and 2017), at Kasese and one season (2017) at Namulonge in Uganda. Thirty-two significant QTL signals were identified for phenology, yield components and partitioning traits measured under drought and non-stress conditions. Colocalized QTL signals were identified for phenology, yield component traits and partitioning traits on Pv01, Pv02, Pv03, Pv04, Pv06 and Pv11. Functional annotation of positional candidate genes identified within the colocalized peak regions were consistent with the functional similarity or pleiotropic effects of those genes on the associated traits, and could be validated for marker assisted breeding. The third objective focused on the use photosynthetic traits and visual scores for high throughput screening for drought tolerance at the seedling stage. Three hundred genotypes were evaluated under stress and non-stress conditions in the green house at Namulonge, Uganda. Drought stress was applied by withholding water 21 days after planting. Significant genetic variability was observed among accessions for photosynthetic traits during early stages of drought stress, suggesting that substantial genetic variability exists among common bean genotypes from the Andean gene pool for photosynthetic traits under drought conditions at the seedling stage. Slow wilting was positively associated with recovery and could be used to identify drought tolerant genotypes at the seedling stage. The results from GWAS, QTL analysis and high throughput screening for drought tolerance at seedling stage will facilitate the screening of germplasm, and use of marker assisted breeding for drought tolerance, to improve the genetic gain for yield under drought stress in the Andean gene pool of common bean."--Pages ii-iii.
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