Transcriptional profiling of two Atlantic salmon strains: implications for reintroduction into Lake Ontario

One of the major challenges facing conservation biology is characterizing the genetic variation underlying adaptation to different environments. Gene expression is the process whereby genomic information is converted into phenotype and quantitative variation in gene expression is linked to phenotypic variation. Identifying gene transcription profiles that provide fitness benefits in specific environments would promote more effective species reintroduction and conservation practices. In this study, we developed a custom oligonucleotide microarray for Atlantic salmon (Salmo salar) and used this microarray to measure gene transcription in gill tissue for two Atlantic salmon strains currently being reintroduced into Lake Ontario: LaHave (anadromous) and Sebago (landlocked). We measured gene transcription in juvenile salmon from each strain that had been reared under the same conditions and identified genes differentially expressed between the two strains. We used the normalized transcription data and microsatellite genotype data to partition the variance into effects of selection versus genetic drift. We found that although there was little genetic differentiation (F (ST) = 0.038) between the two strains, 21 genes were significantly differentially expressed between the two strains, and in all cases the difference was consistent with divergence by selection. We use this analysis to predict the Sebago strain will be more likely to be successfully reintroduced, highlighting how the combination of population genetics with gene expression can help to guide reintroduction efforts