Genome-wide mapping of quantitative trait loci that can be used in marker-assisted selection for resistance to bacterial cold water disease in two commercial rainbow trout breeding populations

Bacterial cold water disease (BCWD), caused by Flavobacterium psychrophilum, is a frequent and problematic disease in rainbow trout (Oncorhynchus mykiss) aquaculture. A focus of our research is to improve genetic resistance against this disease in commercial populations. Commercial rainbow trout breeding is complicated by multiple populations that spawn naturally at different times of the year and often multiple year-classes are maintained. Previously, we found that resistance to BCWD in the 2013 year-class (YC) of the Troutlodge May spawning breeding population was controlled by oligogenic inheritance of five to six moderate to large effect QTL and many small effect loci. In the current study, we performed genome-wide association analyses using rainbow trout from YC 2015 and YC 2016 strains that were separated as two closed breeding populations for seven generations. Our results confirmed that resistance to BCWD in the even-year strain (YC 2016) is also controlled by oligogenic inheritance of nine QTLs with moderate-large effects that individually explained 2.1% - 34.7% of the additive genetic variance. The nine QTL regions detected in YC 2016 strain jointly explained up to 88% of the additive genetic variance and the five detected QTLs in YC 2015 strain jointly explained up to 61% of the genetic variance. The largest effect and most significant QTL is shared between the two YC strains on chromosome Omy25. This QTL was previously shown to be useful for marker-assisted selection (MAS) in the odd-year strain and it should also be the best candidate for MAS in the even-year strain. On the other hand, two other moderate-large effect QTL were not shared by the two YC strains, demonstrating that differences in the trait genetic architecture can exist between populations that were originated from the same source due to founders' effect and genetic drift in small populations.