Transcriptomic Profiles of Rainbow Trout (Oncorhynchus mykiss) Selectively Bred for High and Low Fillet Yield

The fillet yield phenotype is a trait that can be improved in aquaculture species through conventional selective breeding. This approach was applied to rainbow trout for three consecutive generations of selection to produce a high-yield line (HY) that exhibits 2.5 percentage points higher fillet yield compared to a low-yield line (LY). To characterize the genetic and physiological mechanisms contributing to the HY phenotype, transcriptomic analysis of liver and skeletal muscle was performed at three stages of development, 2 g, 60 g, and 300 g, which corresponded to 35, 208, and 277 days post-hatch. Functional analysis of differentially expressed genes (DEG) suggests that increased muscle yield in the HY line is partially driven by greater hyperplasia at 60 g; although, higher rates of protein accretion, primarily attributed to lower rates of protein degradation, promote muscle cell hypertrophy during all stages of development. Additionally, DEGs support reductions in glycolysis in the HY muscle, with increased activity of the more efficient citric acid cycle and oxidative phosphorylation reactions for energy production compared to the LY line. In the liver, DEGs indicate unique nutrient utilization mechanisms in the HY line that support reduced visceral adiposity compared to the LY line. These findings provide insight into the physiology and metabolism driving the high fillet yield phenotype; this information is useful for the development of genomic markers to enhance breeding strategies toward the improvement of performance traits.