Melampsora spp. willow rust is the most threatening disease of Salix spp. shrub willow for short rotation coppice bioenergy feedstock production. Control of this pathogen is limited to host resistance via breeding and polyculture, as application of fungicides are economically limiting for this cropping system. Previous work has investigated the population of Melampsora rust in the northeast US, while simultaneously identifying QTL’s for resistance to this rust in Salix spp. breeding populations. We have built upon our understanding of this pathosystem by using RNAseq methods to investigate host resistance though eQTL analysis in order to discover essential transcription factors associated with rust resistance. An F2 mapping population was surveyed for rust susceptibility and 60 S. purpurea genotypes (30 resistant and 30 susceptible to rust) were artificially inoculated in a greenhouse with M. americana. A preliminary experiment identified 2 and 3 days post inoculation as the time points with the greatest number of differentially expressed genes, therefore these timepoints were used in the eQTL experiment. RNA has been extracted and data analysis is ongoing to identify QTL’s for variation in gene expression between the resistant and susceptible pools. This work will identify markers associated with transcription factors that regulate the resistance response, providing important information for future breeding work.