In commercial production, shrub willow grown as a biomass bioenergy crop can potentially remain in the field for more than 20 years. In these dense plantations, biotic stressors can flourish, impacting biomass yield. Among the most impactful are willow leaf rusts caused by Melampsora spp. As a macrocyclic and heteroecious rust, breeding for resistance is challenging. Most of the research into the Melampsora and Salix pathosystem centers around European species, however, revealing a need for the characterization of resistance of their North American counterparts. Two mapping populations have been generated for the species S. purpurea, which has high quality reference genomes and is naturalized in North America. The first is an F2 population, while the second is the Salix F1 hybrid common parent population with eight families. In this population, four females from S. suchowensis, S. viminalis, and S. integra were crossed with a male S. purpurea, while four males from S. suchowensis, S. viminalis, S. udensis, and S. koriyanagi were crossed with a female S. purpurea. The objectives of this research were to 1) identify the temporal, gene-level response to infection and candidate genes associated with resistance to M. americana within the S. purpurea F2 population, 2) describe the relatedness within, produce linkage maps, and map the sex determination regions within the Salix F1 hybrid mapping population and within those same linkage maps 3) identify QTL for leaf rust severity in addition to a multitude of agronomically important traits. Analysis of 3′ RNA-Seq conducted with genotypes resistant to M. americana showed a more coordinated response to infection compared to susceptible genotypes leading to the identification of candidate genes involved in plant defense. The production of 16 linkage maps facilitated the mapping of the sex determination regions to the maternal chromosome 15 in each pedigree, revealing that these species use a ZW system. Through the analysis of 41 traits, 87 QTL were mapped in the F1 hybrid common parent population, including five leaf rust QTL. Future studies should focus on candidate gene and QTL validation in order to expedite the introgression of resistance into North American Salix.