Rauf, Yahya2024-01-052024-01-052019-05https://hdl.handle.net/11299/259640University of Minnesota Ph.D. dissertation. May 2019. Major: Applied Plant Sciences. Advisor: James Anderson. 1 computer file (PDF); xvii , 186 pages.Cereal rusts are among the most important fungal diseases worldwide and pose a major threat to global food security. Wheat is attacked by three rusts known as stripe rust, leaf rust, and stem rust caused by fungal pathogens, Puccinia striiformis f. sp. tritici (Pst), Puccinia triticina (Pt), and Puccinia graminis f. sp. tritici (Pgt), respectively. These pathogens are widely distributed across the world, produce spores with the ability to travel long distances, rapidly multiply under favorable environmental conditions, and evolve new races that overcome the resistant genes in cultivated varieties. The rapid appearance of new races of rust pathogens with virulence for the major seedling resistance genes in wheat has intensified the focus to breeding for durable resistance. Durable rust resistance is more likely to be of adult plant resistance (APR) rather than seedling resistance, and not associated with the genes conferring hypersensitive reaction. Two projects were developed to identify and map the genetic sources and dissect the mechanism of APR to rusts. The first project utilized a bi-parental mapping population derived from a cross of COPIO x Apav#1. It consisted of 178, F4:F5 recombinant inbred lines (RIL) developed at the International Maize and Wheat Improvement Centre (CIMMYT) in Mexico. The objectives of this study were to map the APR genes in ‘COPIO’ and to understand the genetic relationship of APR genes conferring resistance to all three rusts. The parents of the RIL mapping population were tested against selected Pgt, Pst, and Pt races at the seedling stage and were also assayed for the known APR genes and 2NS/2AS translocation using molecular markers. The RIL population was also evaluated under field conditions in six environments for leaf and stem rust and nine environments for stripe rust. Genotyping of the population and parents was carried out through genotyping-by-sequencing (GBS) and 762 resulting polymorphic markers each representing a unique locus, were used for the downstream QTL mapping analysis. Molecular characterization and quantitative/qualitative analysis revealed that COPIO harbors some important pleiotropic and APR genes along with qualitative genes for Pgt, Pst, and Pt. Pleiotropic gene Lr46/Yr29/Sr58 on chromosome 1BL reduced disease severities of all three rusts with R2 values ranging from 10 to 42%. The APR genes Sr2/Yr30 for stem and stripe rust along with either a new gene for leaf rust resistance or due to pleiotropic effects of Sr2/Yr30 resulted in reduced severities of all three rusts. The 2NS/2AS translocation segment on chromosome 2AS containing the race-specific resistance genes Sr38, Lr37, and Yr17 is present in COPIO. A new putative stripe rust APR QTL (QYr.umn.2A) in the same region, along with partial effects of Yr17, significantly reduced stripe rust severities in all nine environments. We also postulated the presence of Lr13 on chromosome 2B and Yr31, Yr45, and Yr60 on chromosomes 2B, 3D, and 4B respectively in COPIO. This study also detected minor effect QTL, both previously reported (for stem rust; QSr.umn.3B.2; QSr.umn.4B, for stripe rust; QYr.umn.1A; QYr.umn.3B.3) and potentially new sources of resistance (for stem rust; QSr.umn.2A.3; QSr.umn.7A, for leaf rust; QLr.umn.2A.1, QLr.umn.3B, for stripe rust; QYr.umn.1B.1; QYr.umn.3A.2) in COPIO. These QTLs are also contributing quantitative resistance to all three rusts in COPIO. Our findings show that wheat line COPIO contains pleiotropic, APR and seedling genes along with small to medium effect QTL that are working in combination to enhance genetic resistance against rust pathogens. Broad spectrum resistance against wheat rust diseases in COPIO makes it a valuable source of resistance and its utilization in recombination breeding can potentially enhance durable resistance. Development of diagnostic markers, particularly for the 2A QTL (QYr.umn.2A), will be useful for marker assisted selection in breeding programs. The second project involved a bi-parental mapping population developed by crossing a wheat line ‘MN06113-8’ and cultivated wheat variety ‘Sabin’. The wheat breeding program at the University of Minnesota previously mapped a large effect stem rust APR QTL (QSr.umn-2B.2) on chromosome 2B in wheat line ‘MN06113-8’. This QTL is effective against the North American, Kenyan and Ethiopian stem rust pathogen races. The objectives of this study were to:1) understand the genetics of APR to wheat stem rust in the breeding line ‘MN06113-8’ and cultivated wheat variety ‘Sabin’; and 2) validate 2B QTL in MN06113-8. A total of 184 recombinant inbred lines (RILs) from the cross Sabin/MN06113-8 were tested in stem rust nurseries in Kenya, Ethiopia and Saint Paul. Both parental lines were highly susceptible to Ug99 races TTKSK, TTKST, and TTKTT at the seedling stage but MN06113-8 exhibited adult plant resistance (APR) in Kenya and Ethiopia under field testing conditions. Genotyping by sequencing (GBS) was used to genotype the population and both parents. A total of 4,100 polymorphic GBS markers were assigned to 21 wheat chromosomes to develop the linkage maps. The GBS single nucleotide polymorphism (SNP) markers covered 2,931 cM of the genome with an average of 0.71 markers cM-1. Composite interval mapping detected six quantitative trait loci (QTL) on chromosomes 2A, 3B, 4A, 4B, and 6B associated with stem rust resistance. Among these seven QTL, three were detected in African environments and four were detected in Saint Paul against the North American stem rust pathogen races. We could not validate QSr.umn-2B.2, discovered in a previous study involving MN06113-8 because the QTL region was monomorphic in our population. A large effect QTL (QSr.umn.3B) was mapped on chromosome 3B conferring resistance to Ug99 and North American Pgt races. The QTL (QSr.umn.4A.1) detected in Kenya on chromosome 4A has not been previously reported. Development of diagnostic markers and pyramiding of these genes through marker assisted selection will accelerate the development of durable rust resistance.enPlant BreedingPlant GeneticsQTL mappingWheat RustsThesis or Dissertation