Using Random Forest to Identify Loci Linked to Resistance to Infectious Hematopoietic Necrosis Virus in Two Populations of Steelhead

Predicting the ecology and evolution of infectious diseases requires an understanding of factors that affect both pathogen transmission and host response. In wild populations, both factors might be mediated by a population’s resistance to this disease.  If genetic variation for resistance can be characterized across populations, then models aimed at predicting the spread of a pathogen can be improved. Infectious hematopoietic necrosis virus (IHNV) is a virus endemic to the Pacific Northwest of the United States and can have devastating consequences on populations of steelhead. Here, we aimed to identify the genetic variation underlying disease resistance in two types of crosses from two recently diverged steelhead populations that exhibit different degrees of resistance to IHNV. We conducted IHNV challenges and genotyped 380 individuals, resistant and susceptible to the virus, with the 50K SNP chip available for Oncorhynchus mykiss. We used Random Forest with about 30,000 polymorphic loci to identify loci and regions of the genomes involved in resistance to IHNV. The results from this study will be used to determine if these loci are also linked to IHNV resistance in other steelhead populations.