Dissecting the genetic basis for migration in rainbow and steelhead trout (Oncorhynchus mykiss)

Across their natural and introduced ranges, salmonids exhibit diverse life histories, from purely anadromous populations and species, to those that vary in the timing of their migration to the sea, to those that vary in whether or not they migrate or remain in freshwater for all of their lives. In crosses between migratory steelhead and non-migratory rainbow O. mykiss from the Sashin Creek, Alaska system, we have identified several QTL for traits associated with smoltification, with some overlap with genome regions previously identified in the same species for similar traits.  However, such QTL frequently span large genome regions making determining which gene(s) underlie these QTL difficult. Here we present data from a genome wide association study (GWAS) in two divergent natural populations of O. mykiss; from Sashin Creek, Alaska, and Little Sheep Creek, Oregon.  Using next-generation sequence data we found ~25, 000 SNPs of which 906 were found to be statistically associated (p-value < 0.001) with migration. By taking advantage of recent mapping studies we were able to determine the position of 2,630 SNPs in the O. mykiss genome. Several SNPs that produced a significant p-value from the GWAS were found to be located in genome regions that contain QTL for traits associated with smoltification; reinforcing the importance of these genome regions. These studies will ultimately help us understand the genetic determinants of migration and residency in this species, and will be an important framework in which to study the evolution of migratory and resident life history diversity in the salmonid fishes.