Partitioning Transcriptional Variance in Fish: Patterns of Population and Family Divergence

A fundamental question in genetics is how genetic architecture (relative contribution of variance components) determines phenotype, and thus what role genetic architecture plays in the response to selection and trait evolution. Such questions are the basis of quantitative genetics, and have been widely explored for many traits in a variety of taxa.  However, the genetic architecture of gene transcription (viewed as a phenotype) has received relatively little attention, despite an expectation for strong family and population effects.  Here we partition variation in gene transcription (measured using qRT-PCR) into additive, non-additive and maternal variance components. Specifically, we measure gene transcription relating to saltwater tolerance in steelhead trout (Oncorhynchus mykiss) and immune function in Chinook salmon (Oncorhynchus tshawytscha). We also explore the nature of population effects on disease response gene expression across many genes using a custom Chinook salmon microarray. We find evidence for strong non-additive effects contributing to the observed variation in gene transcription, but weak and variable additive variance components. We also find only weak evidence for consistent additive population effects, calling into question the concept of local adaptation by selection on additive traits.  Our results have important implications for our understanding of salmon gene transcription evolution in that it underscores the prevalence of non-additive genetic effects in salmon.  Although rapid evolution may be facilitated by such a non-traditional genetic architecture, it is not encouraging for breeders interested in mean-trait selection for improving performance in farmed salmon stocks.