Ontogentic shifts in genetic and maternal effects on length and survival in Chinook salmon (Oncorhynchus tshawytscha)

Abstract

Understanding how the interplay between genetic and environmental factors changes over the lifetime of a species is critical when selecting broodstock to optimize production at each life stage and reduce bottlenecks in the production chain. We analyzed changes in environmental, additive genetic, and non-additive genetic contributions in growth and saltwater survival across multiple life stages of Chinook salmon (Oncorhynchus tshawytscha) in an aquaculture facility to assess the importance of each factor throughout life. We used a full-factorial breeding design and followed fish for their entire 3-year life cycle to quantify the dam and sire effect on growth and survival and partition these effects into the respective environmental and genetic components. We show for body size that maternal and non-additive effects are the most important drivers of larval size, explaining a total of 87% of total larval phenotypic variation, but decline with age. Additive genetic effects peak during the juvenile stage, explaining a maximum of 15% of the total variation in size, but are much less important at earlier and later life stages. We saw a similar pattern to saltwater survival—with non-additive effects high (42% of total variance explained) at the earliest stage measured and decreasing in later stages and additive effects playing little role. Unlike growth, there was little maternal influence on survival. Taken together, our results show that maternal and non-additive effects are important drivers of larval size but that additive effects may play a more important role with age. Non-additive effects explained the most phenotypic variance observed for survival, playing a much larger role than maternal or additive effects. Our results add to a growing body of literature suggesting careful crosses of select lines can lead to enhanced growth and survival and that these effects can be tailored to the life stages of most concern for a given system. In this way hatchery managers can best develop breeding lines for specific systems and these lines can have stable effects over many generations. Statement of relevanceThe enclosed manuscript is directly relevant to commercial aquaculture. The study was conducted in a commercial aquaculture facility and the questions we are asking relate to the effects of genetic and non-genetic (maternal) factors in Chinook salmon growth and survival in an aquaculture facility.