Modern durum and common wheat cultivars were developed from ancient wheat ancestors by natural and artificial selection of agronomic and domestication traits, which ultimatey decreased their genetic diversity and made them more susceptible to various biotic and abiotic stresses. At present, new sources of resistance need to be introgressed into future wheat cultivars to combat the effect of the disease stem rust caused by the biotrophic fungal pathogen Puccinia graminis f.sp. tritici (Pgt). In this dissertation, I first analyzed the domestication-related traits in a tetraploid recombinant inbred line (RIL) population developed from a cross between the durum wheat line Rusty and the cultivated emmer accession PI 193883 (referred to as the RP883 population). Second, the RP883 population and a double haploid (DH) population (referred to as the LP749 population) derived from a cross between the durum cultivar Lebsock and the Triticum. turgidium ssp. carthlicum accession PI 94749, and nine durum wheat cultivars were screened with Pgt races TMLKC, TTKSK, TRTTF, and TTTTF. Domestication-related trait analysis in the RP883 population showed vernalization (Vrn-A1) and domestication (Q) genes had a pleiotrophic effect on spike length, spikelet per spike, spike compactness, and threshability. Additionally, an interaction and dosage effect of three free-threshing trait governing loci, teneacious glume Tg2A and Tg2B, and q, revealed that mutation in all three loci are required to attain complete free threshability. The stem rust analysis done in the RP883 population showed two Sr gene regions conferring resistance against TMLKC, TTKSK, and TRTTF: one novel gene region on chromosome 2BL (Sr883) and likely a new allele or gene residing in close proximity to the Sr13 gene on 6AL. The second stem rust study using the LP749 population and nine durum wheat cultivars showed that most likely the U.S. durum germplasm carries the four major Sr genes, Sr7a (4AL), Sr8155B1 (6AS), Sr13 (6AL), and likely Sr9e (2BL) against TTKSK, TRTTF, and TTTTF. In conclusion, results obtained from this domestication study provide knowledge about different stages in wheat evolution. Both stem rust studies revealed genetic diversity in the tetraploid wheat gene pool and indicate their utility in future breeding programs.