Differential Regulation of Gene Expression over Development in Resident and Migratory Oncorhynchus mykiss

Residency and anadromy represent the extremes of life history variation within salmonids, but the genetic underpinnings of life history variation are still poorly understood, both with regard to the genes involved in differentiation and the timing of the onset of differentiation. Herein, we examine differential gene expression in offspring from migratory and resident O. mykiss, to better understand the identity and timing in differential expression of genes and molecular processes potentially involved in adaptive divergence between life history types. RNA sequencing was conducted in O. mykiss from Sashin Creek and Sashin Lake, Alaska.  Families were reared in a common environment and brains were sampled at 4-6 month intervals from hatch until June of their second year when smoltification or precocious maturation occurs in this system.  A reference transcriptome was created and differential expression analysis was performed including 6 time points.  Differential gene expression between migratory and resident offspring was observed as early as hatch and throughout development, and was highly dependent on both time and sex.  Enrichment of differentially expressed genes was identified for a number of biological pathways, including phototransduction pathways, which can regulate circadian rhythms, ultimately leading to the decision to migrate or remain resident.