The aquaculture industry has vastly expanded in recent years and accounts for half of seafood consumed globally . With this expansion, sustainable shifts in aquaculture must be made to access nutrients essential to human health in response to a decline in marine resources for aquafeeds. Along with shifts in aquafeed composition, selective breeding programs aid in eliminating mortality rates in fish populations aimed for the marketplace. Rainbow trout are a staple aquaculture species and serve as a non-model organism to investigate toxicology, evolutionary biology, and nutritional programming. Understanding the impacts of nutritional programming in aquaculture species will aid in understanding the effects of broodstock nutrition on offspring growth performance via inherited epigenetic mechanisms while providing information regarding potential mechanisms of maternal effects. Therefore, this project focuses on the interactions between maternal nutrition and genetic selection utilizing rainbow trout, Oncorhynchus mykiss, used within the industry – disease-resistant selected rainbow trout maintained by the National Center for Cool and Cold- Water Aquaculture. The overall project objective includes identifying specific genes and gene pathways in offspring affected by maternal dietary intake of choline supplementation during oogenesis. To accomplish this, global and local DNA methylation patterns were analyzed in trout offspring and compared to global transcriptomic data from corresponding samples. Treatment effects on the methylome and transcriptome were analyzed to identify potential mechanisms altered by maternal choline intake and establish links between epigenetic modifications in the genome and phenotype of the offspring. Results indicate that several metabolic and tissue-specific pathways are under, at least, partial maternal regulation.