Gene Expression in Early Development of Rainbow Trout with Divergent Life Histories

Salmonids display a wide variety of life history strategies, both within and across populations.  Residency and anadromy represent the extremes of life history variation within salmonids, and the ecology of these life history differences has been well studied.  However, 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.  By examining transcriptome level differences across several time points during development we hope to understand both which genes are involved in the process of life history determination, and when in development the differentiation is initiated.

We conducted RNAseq Illumina sequencing on offspring from migratory and resident crosses of O. mykiss from Sashin Creek and Sashin Lake, Alaska.  Full sibling anadromous/anadromous (AxA) and resident/resident crosses (RxR) were made and the offspring were raised in a common environment at the Little Port Walter Marine Station, Alaska.  RNA was extracted from samples taken at four month intervals from hatch until June of their first year.  A de novo reference transcriptome was created and consisted of 431,000 contigs with a mean length of 1161 bp.  Differential expression analysis was performed on between 80,000 and 97,000 contigs that met count thresholds at each timepoint.   Between 2,200 and 3,00 contigs showed differential expression between AxA and RxR crosses at each time point, with 1,500 contigs showing differential expression at two or more time points.  BLAST annotation of differentially expressed contigs found hits to 31 genes associated with life history divergence in other studies.  These results confirm large scale differences in gene expression between AxA and RxR crosstypes during early development.