Macharia, Godwin Kamau.2013-06-122013-06-122013-04https://hdl.handle.net/11299/150970University of Minnesota Ph.D. dissertation. April 2013. Major: Applied plant sciences. Advisor: James A. Anderson. 1 computer file (PDF); x, 197 pages, appendices I-V.Despite recognition as key bread wheat producers in sub-Saharan Africa, for decades Ethiopia and Kenya have relied on imports to meet local consumption needs. The challenges posed by pests and diseases as exemplified by repeated attacks by the Russian Wheat Aphid, and the new highly virulent race TTKSK (Ug99) of stem rust, have been strong yield barriers. To change this trend, it is important that breeding populations that combine desirable alleles for yield, disease, and pest resistance are developed followed by selection, promotion and adoption of superior cultivars. In the first chapter of this thesis, SNP- based characterization of population structure and diversity in a comprehensive panel of 297, mainly East Africa lines are described. Four to seven subpopulations were identified largely consistent with line breeding era. The oldest East Africa germplasm was found to be most diverse based on several summary statistics. Present day germplasm including that in commercial production was associated with relatively high allelic diversity too. Methods used to detect signatures of past selection successfully identified outlier SNPs possibly under positive selection which could have played an important role in increasing the adaptive range of bread wheat in East Africa. Long range linkage disequilibrium consistent with past observations for this species, was detected and is described in chapter two. Over 50 QTL for adult plant resistance (APR) to stem, leaf and stripe rusts are reported from mixed model association mapping. Similarly, APR previously observed in the cultivar Kenya- Nyangumi was dissected leading to the detection of 15 minor QTL across all rusts. These results are presented in chapter three. In chapter four, results for high and low molecular weight glutenin subunit alleles, puroindoline proteins, grain hardness and other bread making quality-determining traits that were characterized amongst 216 Ethiopia and Kenya bread wheat lines are discussed.en-USAssociation mappingDiversityGrain qualityRust diseasesSNPWheatThesis or Dissertation