RNA-seq reveals differential gene expression in the brains of juvenile resident and migratory smolt rainbow trout (Oncorhynchus mykiss)

Many migratory traits are heritable, but there is a paucity of evidence identifying the molecular mechanisms underlying differentiation in alternative migratory tactics, or in linking variation in gene expression to migratory behaviors. To that end, we examined differential gene expression in the brain transcriptome between young steelhead trout that had undergone the smoltification process, and resident rainbow trout (Oncorhynchus mykiss) from Sashin Creek, Alaska. Samples were sequenced from two time points: immediately before (at 20 months of age) and during (2 years of age) the presumed peak of smoltification. Smolt and resident individuals came from two genetic crosses, one where both parents were migratory, and another where both parents were residents. A total of 533 (1.9%) genes were differentially expressed between crosses, or between smolt and resident samples. These genes include some candidate migratory genes (such as POMC), as well as genes with no previous known involvement in the migratory process. Progeny from resident parents showed more upregulated genes than progeny from migrant parents at both time points. Pathway analysis showed enrichment in 227 biological pathways between cross type, and 171 biological pathways were enriched between residents and smolts. Enriched pathways had connections to many biofunctions, and most were only enriched in one contrast. However, pathways connected to phototransduction were enriched between both cross type and migratory tactics in 11 out of 12 contrasts, suggesting there are fundamental differences in how smolts and residents process light in the brain. The genes and pathways described herein constitute an a priori candidate list for future studies of migration in other populations of O. mykiss, and other migratory species.