QTL spanning the TGF-β2 locus is associated with muscle fiber size in rainbow trout

Skeletal muscle growth is a key determinant of body size and market value in salmonid aquaculture, yet the mechanisms linking genomic variation to muscle fiber size, a morphometric indicator of hypertrophic growth, remain poorly resolved. Myofiber cross-sectional area (CSA) provides a quantitative measure of fiber size and a cellular link to macroscopic growth traits. We performed histological phenotyping of white skeletal muscle from rainbow trout (Oncorhynchus mykiss) representing divergent fillet-yield selection lines (ARS-FY-H and ARS-FY-L), quantifying mean myofiber CSA and fiber number using high-throughput image analysis. Genome-wide association analysis (GWAS) was conducted using low-pass whole-genome sequencing (~1×) with genotype imputation and functional variant annotation. RNA sequencing was performed on fish representing high and low CSA extremes to identify differentially expressed genes associated with variation in muscle fiber size. Mean myofiber CSA, a morphometric indicator of hypertrophic growth, was significantly associated with body weight, muscle weight, visceral weight, and body length (p < 0.05), whereas fiber count was not significantly associated with most growth traits, suggesting that variation in fiber size may contribute more substantially to muscle mass variation in this population. GWAS identified 130 SNPs with the predominant association signal occurring on chromosome 2. This signal included a dense primary association block spanning approximately 4.72 Mb. Most associated variants were annotated as noncoding, including intronic, intergenic, and enhancer-associated variants. Multiple associated SNPs overlapped the TGF-β2 locus and annotated enhancer chromatin states in white muscle. Transcriptomic comparisons revealed that high-CSA muscle showed elevated expression of genes related to contractile function, cytoskeletal organization, and translation, whereas low-CSA muscle exhibited upregulation of extracellular matrix and immune-related genes consistent with a tissue-remodeling state. Integration of GWAS, chromatin-state annotation, and transcriptomic profiling identified a chromosome 2 QTL associated with variation in myofiber CSA and highlighted TGF-β2 and other genes within the interval as candidates for further investigation. The overlap of associated variants with annotated regulatory regions and the distinct transcriptional profiles of high- and low-CSA muscle provide supporting evidence for potential regulatory mechanisms underlying variation in muscle fiber size, while fine-mapping and functional validation will be required to identify causal variants and genes.