In a global aquaculture sector that requires increasingly efficient production to meet protein demand, every gram of product counts. Fillet yield—the proportion of edible fillet weight to the total body weight of the fish—is a critical factor for the profitability of any operation. However, improving this trait through selective breeding is a challenge, as it traditionally requires sacrificing the candidates to be measured.
A recent study published in Marine Biotechnology by researchers from the USDA’s National Center for Cool and Cold Water Aquaculture (NCCCWA) has shed light on the fundamental biological differences that drive higher yield. Using transcriptomic analysis, scientists have identified which genes and metabolic pathways are activated differently in trout selected for three generations for high fillet yield (HY line) compared to a low-yield line (LY line). The findings not only explain why these trout are meatier but also open the door to developing genomic tools for more precise and efficient selection.
A generational study to decipher success
To understand the basis of the high-yield phenotype, researchers applied a genetic selection program for three consecutive generations. This effort resulted in a trout line (HY) that exhibits 2.5 percentage points higher fillet yield compared to the low-yield line (LY).
The core of the study involved analyzing gene expression (transcriptomics) in two key tissues: skeletal muscle and liver. This analysis was performed at three crucial developmental stages, defined by the fish’s weight: 2 g (hyperplasia phase, or creation of new muscle cells), 60 g (mixed hyperplasia and hypertrophy phase), and 300 g (hypertrophy phase, or growth in the size of existing cells).
What makes the high-yield trout different?
The study identified a total of 3,663 genes that were expressed differently between the HY and LY lines in the various tissues and growth stages. These genetic differences translate into concrete physiological advantages.
Muscle growth: more cells and less degradation
Contrary to what one might think, the advantage of the HY line is not solely due to a higher rate of protein synthesis, but more significantly, to a lower rate of protein degradation.
- More muscle cells (hyperplasia): At 60 g, the analysis suggests that the HY line exhibits greater muscle cell proliferation. This means that from an early stage, these fish are building a foundation with more muscle fibers.
- Less protein degradation: The most consistent finding across all growth stages is that the HY line has lower activity in protein degradation processes, such as autophagy. Essentially, these fish are more efficient at conserving the muscle they have already built, which promotes hypertrophy (larger cells) and net protein accretion.
A more efficient energy metabolism in the muscle
Energy is a finite resource, and how the organism manages it is key. The study revealed that the muscle of high-yield trout uses energy in a smarter way.
- Less reliance on glycolysis: Surprisingly, a reduction in the activity of the glycolytic pathway—the process that breaks down glucose for quick energy—was detected in the HY line. While this might seem counterintuitive, it indicates a strategic metabolic shift.
- Greater Krebs cycle activity: The HY line compensates for this reduction by relying more on efficient pathways like the citric acid cycle (TCA) and oxidative phosphorylation. This allows them to generate more energy from the same substrates, freeing up resources that can be directed toward muscle growth instead of just maintenance. A key gene, acly, associated with this cycle, was previously shown to account for up to 8% of the genetic variance for muscle yield.
The role of the liver: less visceral fat and different nutrient use
Fillet yield is not just a matter of muscle. The liver, as the metabolic center, plays a crucial role in how nutrients are partitioned. The study found that the HY line trout exhibits unique nutrient utilization mechanisms in the liver that lead to reduced visceral adiposity compared to the LY line.
This means that selection for higher fillet yield not only promotes muscle growth but also favors a leaner overall phenotype, with less fat accumulated around the internal organs—a desirable trait for both product quality and fish health.
Practical implications for trout aquaculture
The results of this research have a direct and practical impact on the sector.
- Genetic selection validation: It confirms that conventional selection for fillet yield is effective and that its physiological effects begin to manifest at very early growth stages (from 60 g).
- Toward genomic selection: The identification of specific genes and metabolic pathways (like those related to protein degradation or energy metabolism) provides clear candidates for the development of genomic markers.
- Greater efficiency and sustainability: The use of these markers would allow producers to select the best broodstock without needing to sacrifice them, accelerating genetic progress and improving production efficiency.
Conclusion: toward a more precise selection
This study demonstrates that the success of genetic selection for higher fillet yield in rainbow trout is the result of a complex symphony of physiological adjustments. It is not a single factor but a combination of increased muscle cell creation, a notable reduction in protein degradation, and more efficient muscle energy metabolism.
This knowledge is fundamental to moving from phenotype-based selection to precision genomic selection, allowing the aquaculture industry to produce higher-quality and more profitable fish in a more sustainable and effective way.
Contact
Beth M. Cleveland
National Center for Cool and Cold Water Aquaculture, USDA/ARS
Kearneysville, WV, 25430, USA
Email: beth.cleveland@usda.gov
Reference (open access)
Mankiewicz, J.L., Gao, G., Leeds, T. et al. Transcriptomic Profiles of Rainbow Trout (Oncorhynchus mykiss) Selectively Bred for High and Low Fillet Yield. Mar Biotechnol 27, 102 (2025). https://doi.org/10.1007/s10126-025-10479-0
Editor at the digital magazine AquaHoy. He holds a degree in Aquaculture Biology from the National University of Santa (UNS) and a Master’s degree in Science and Innovation Management from the Polytechnic University of Valencia, with postgraduate diplomas in Business Innovation and Innovation Management. He possesses extensive experience in the aquaculture and fisheries sector, having led the Fisheries Innovation Unit of the National Program for Innovation in Fisheries and Aquaculture (PNIPA). He has served as a senior consultant in technology watch, an innovation project formulator and advisor, and a lecturer at UNS. He is a member of the Peruvian College of Biologists and was recognized by the World Aquaculture Society (WAS) in 2016 for his contribution to aquaculture.
