Leeds, T. | bioRxiv Science

bioRxiv2026

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

BackgroundSkeletal muscle growth is a key determinant of body size and market value in salmonid aquaculture, yet the mechanisms linking genomic variation to muscle fiber hypertrophy remain poorly resolved. Myofiber cross-sectional area (CSA) provides a quantitative cellular proxy for fiber size and a direct link to macroscopic growth traits. MethodsWe 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 ([~]1x) with genotype imputation and functional variant annotation. RNA sequencing was performed on fish representing high and low CSA extremes to identify differentially expressed genes and enriched biological pathways. ResultsMean myofiber CSA was significantly associated with body weight, muscle weight, visceral weight, and body length (p < 0.05), while fiber count showed no significant association with most growth traits, implicating hypertrophy as the primary driver of muscle mass variation. GWAS identified a significant QTL spanning [~]4.76 Mb on chromosome 2 (117 significant SNPs; Bonferroni-adjusted P [≤] 0.05; {lambda} = 1.02). Associated variants were predominantly noncoding, enriched in intronic, intergenic, and enhancer-annotated regions. A high density of SNPs colocalized with the TGF-{beta}2 locus, overlapping strong and genic enhancer elements in white muscle. Transcriptomic comparisons revealed that high-CSA muscle showed elevated expression of genes related to contractile function, cytoskeletal organization, and translation, while low-CSA muscle exhibited upregulation of extracellular matrix and immune-related genes consistent with a tissue remodeling state. ConclusionsNoncoding regulatory variation within a significant QTL spanning the TGF-{beta}2 locus is associated with distinct transcriptional programs linked to muscle fiber hypertrophy in rainbow trout. By integrating genetic variation, chromatin-state annotation, and transcriptomic profiling, this study identifies candidate regulatory loci associated with variation in muscle cellularity and growth-related phenotypes in rainbow trout.

genomics↗

bioRxiv2018

Genome-wide association analysis with a 50K transcribed gene SNP-chip identifies QTL affecting muscle yield in rainbow trout

Detection of coding/functional SNPs that change the biological function of a gene may lead to identification of putative causative alleles within QTL regions and discovery of genetic markers with large effects on phenotypes. Two bioinformatics pipelines, GATK and SAMtools, were used to identify ~21K transcribed SNPs with allelic imbalances associated with important aquaculture production traits including body weight, muscle yield, muscle fat content, shear force, and whiteness in addition to resistance/susceptibility to bacterial cold-water disease (BCWD). SNPs were identified from pooled RNA-Seq data collected from ~620 fish, representing 98 families from growth- and 54 families from BCWD-selected lines with divergent phenotypes. In addition, ~29K transcribed SNPs without allelic-imbalances were strategically added to build a 50K Affymetrix SNP-chip. SNPs selected included two SNPs per gene from 14K genes and ~5K non-synonymous SNPs. The SNP-chip was used to genotype 1728 fish. The average SNP calling-rate for samples passing quality control (QC; 1,641 fish) was [≥] 98.5%. Genome-wide association (GWA) study on 878 fish (representing 197 families from 2 consecutive generations) with muscle yield phenotypes and genotyped for 35K polymorphic markers (passing QC) identified several QTL regions explaining together up to 28.40% of the additive genetic variance for muscle yield in this rainbow trout population. The most significant QTLs were on chromosomes 14 and 16 with 12.71% and 10.49% of the genetic variance, respectively. Many of the annotated genes in the QTL regions were previously reported as important regulators of muscle development and cell signaling. No major QTLs were identified in a previous GWA study using a 57K genomic SNP chip on the same fish population. These results indicate improved detection power of the transcribed gene SNP-chip in the target trait and population, allowing identification of large-effect QTLs for important traits in rainbow trout.

genomics↗