Stripe rust (Puccinia striiformis f. sp. tritici) and Septoria tritici blotch (Zymoseptoria tritici) are a constant and significant threat to wheat production, significantly reducing wheat quality and yield. Wheat is responsible for 20% of the world’s human calorie intake, and wheat production must increase to supply the demand of the world’s growing population. Both stripe rust and Septoria tritici blotch (STB) are critical foliar diseases of wheat in the Pacific Northwest (PNW). Increasing stripe rust and STB resistance through plant breeding is the most cost-effective, sustainable, and environmentally friendly approach to manage these diseases. A recombinant inbred line population was developed from a cross between ‘Madsen’ and ‘Foote’ soft white winter wheat cultivars to study stripe rust and STB resistance. Foote (PI 599663) was initially resistant to stripe rust but is now considered susceptible to new, virulent strains of the pathogen. However, Foote has maintained moderate resistance to STB in the PNW. Madsen (PI 511673) has provided effective resistance to stripe rust, but it is considered moderately susceptible to STB. The recombinant inbred line (RIL) population, consisting of 217 lines, was phenotyped across multiple environments for stripe rust and STB response and genotyped using Illumina HiSeq 3000 Sequencing. The 217 lines were also phenotyped for seedling resistance for stripe rust in growth chambers against a bulk population of spores collected from the field in 2012 and a single isolate of race Pstv-37. Pstv-37 has been the most abundant race in the PNW in the last six years. The STACKS and Bfctools programs were used for calling genotype variation. The best linear unbiased prediction (BLUP) was calculated across environments and used to detect QTL resistance. Results of quantitative trait locus (QTL) analysis indicated minor alleles for adult plant resistance to STB in wheat chromosomes 4B, 5A, 6B, 6D and 7DS. Stacking these genes is the best strategy to develop durable resistance to STB. For wheat stripe rust in the field, major alleles for resistance were identified in wheat chromosome 2AS, which is likely the known stripe rust resistance gene Yr17, and in 1AS. Two minor QTL were found in 2AS/2DS and 4DL. For the growth chamber study, four QTL were found in 1B, 2B, 6B, and 7B, with the identified QTL dependent on the stripe rust race used for screening. Combining Yr17, 1AS, and the other QTLs will lead to developing durable resistance to individual cultivars. The QTL identified in this thesis could help to develop breeder-friendly molecular markers for use in genotypic selection for improved STB and stripe rust resistance in whea
