Identification of haplotypes associated with resistance to bacterial cold water disease in rainbow trout

Bacterial cold water disease (BCWD) is an important disease in rainbow trout aquaculture. Previously, we have identified and validated two major QTL (quantitative trait loci) for BCWD resistance, located on chromosomes Omy08 and Omy25, respectively, in the odd-year Troutlodge May spawning population. We also demonstrated that marker-assisted selection for BCWD resistance using the favorable haplotypes associated with the two major QTL is feasible. The goals of this study were to identify additional SNPs associated with BCWD resistance using whole-genome sequencing of pooled samples, and to refine the haplotypes associated with BCWD resistance in rainbow trout.