Genetic Signal at the TGF-β2 Locus Shapes Muscle Fiber Size in Rainbow Trout

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The rainbow trout study adds to a growing body of work showing that the cellular architecture of muscle, rather than simply the number of cells it contains, can be a decisive factor in how an animal grows. Skeletal muscle in fish, as in other vertebrates, enlarges through two processes that operate in parallel: hyperplasia, the recruitment of new muscle fibers from pools of satellite cells, and hypertrophy, the expansion of existing fibers in diameter. In salmonids, hyperplasia continues well into adult life, which is one reason these species can sustain growth over long periods and reach large sizes. The finding that myofiber cross-sectional area, but not fiber count, tracked closely with body weight, muscle weight, and body length in the studied population suggests that hypertrophic capacity may be the more consequential lever in this particular genetic context. That interpretation carries practical weight for breeding programs, because it implies that selection acting on the genetic determinants of fiber enlargement could translate into measurable gains in fillet weight, the trait that ultimately determines market value in the aquaculture sector.

The chromosome 2 signal described in the study is notable for its structure. A dense block of associated variants spanning roughly 4.72 megabases is characteristic of a quantitative trait locus in which many correlated markers ride along with the true causal mutation, a phenomenon driven by linkage disequilibrium, the non-random association of alleles across a chromosomal region. In outbred populations such as the divergent fillet-yield selection lines used here, the extent of linkage disequilibrium determines how finely a association signal can be localized. The authors’ use of low-pass whole-genome sequencing at approximately one-fold coverage, followed by genotype imputation, represents a pragmatic compromise between the cost of deep sequencing and the resolution needed to catalog variation across the genome. Imputation accuracy in such designs depends heavily on a well-characterized reference panel, and for rainbow trout, ongoing efforts to build genomic resources for the species have made this approach increasingly viable. Still, the authors are careful to note that fine-mapping and functional validation will be needed to separate the causal variant or variants from their linked neighbors.

The predominance of noncoding annotations among the associated variants, including intronic, intergenic, and enhancer-proximal sites, fits a pattern that has emerged repeatedly from genome-wide association studies of complex traits across the tree of life. Most of the heritable variation underlying quantitative traits resides not in protein-coding sequences but in regulatory elements that modulate when, where, and how strongly genes are expressed. The overlap of associated SNPs with annotated enhancer chromatin states in white muscle is particularly suggestive, because enhancers active in the tissue where a trait is expressed are strong candidates for the regulatory architecture underlying that trait. Chromatin-state annotation, typically derived from assays that map histone modifications or accessible chromatin, provides a functional filter that can prioritize variants within a broad association signal. In this study, the convergence of association statistics, enhancer annotation, and the TGF-β2 locus within the same interval builds a circumstantial but coherent case for a regulatory mechanism acting on that gene or on neighboring genes within the block.

Transforming growth factor beta 2 belongs to a family of secreted signaling molecules with well-documented roles in development, cell proliferation, and tissue homeostasis. The TGF-β superfamily includes members with diverse and sometimes opposing effects on muscle: some, such as myostatin, are potent negative regulators of muscle mass whose inhibition has been pursued as a strategy for enhancing growth in livestock and aquaculture species, while others participate in the activation and differentiation of muscle satellite cells. TGF-β2 itself has been implicated in the regulation of cell proliferation and extracellular matrix production in multiple tissues, and its expression dynamics during muscle growth and remodeling have been described in several vertebrate systems. The association signal overlapping the TGF-β2 locus in rainbow trout therefore connects to a biologically plausible candidate, though the authors appropriately frame this as a hypothesis requiring functional validation rather than a settled conclusion. It remains possible that the causal variant acts on a different gene within the interval, or that multiple variants in the region contribute jointly to the observed phenotypic variation.

The transcriptomic comparisons between high- and low-cross-sectional-area muscle add a complementary dimension to the genetic findings. The observation that high-CSA muscle shows elevated expression of genes related to contractile function, cytoskeletal organization, and translation is consistent with a tissue state in which fibers are actively enlarging and maintaining their contractile apparatus. Protein synthesis machinery, including ribosomal components and translation factors, would be expected to be upregulated in growing fibers, and cytoskeletal genes support the structural changes that accompany hypertrophic expansion. Conversely, the upregulation of extracellular matrix and immune-related genes in low-CSA muscle suggests a tissue-remodeling state, one in which the architecture surrounding fibers is being modified and inflammatory or repair processes are more active. Such a profile could reflect slower fiber growth, ongoing turnover, or a response to cellular stress. These transcriptional contrasts do not by themselves establish causality, since differential expression can be a consequence rather than a cause of differing fiber sizes, but they provide a molecular signature that can be compared against the genetic association signal to identify genes whose regulation and expression both point in the same direction.

The histological phenotyping approach used in the study deserves attention for its methodological rigor. Quantifying mean myofiber cross-sectional area from histological sections requires careful standardization of sampling location, section orientation, and staining protocol, because fiber diameter varies across the muscle and with the plane of section. High-throughput image analysis, as employed here, reduces the observer bias that can affect manual measurements and enables the processing of the large sample numbers needed for genetic association studies. The choice of white skeletal muscle as the target tissue is relevant to aquaculture practice, since white muscle constitutes the bulk of the fillet. Fiber size distributions in fish muscle are typically skewed, with a majority of small fibers and a smaller number of large ones, and mean cross-sectional area captures the central tendency of that distribution while remaining sensitive to shifts in the upper tail where hypertrophic enlargement is most visible.

The divergent selection lines used in the study, ARS-FY-H and ARS-FY-L, were established to create genetic contrast in fillet yield, and their use here illustrates how long-term selection experiments can generate populations that are particularly informative for dissecting the genetic basis of commercially relevant traits. Divergent lines accumulate allele frequency differences at loci responding to selection, which increases the statistical power of association mapping relative to unselected populations. The fact that fiber size, rather than fiber number, emerged as the trait more strongly associated with growth in this population may partly reflect the selection history of these lines, and the authors’ caution about generalizing to other populations is warranted. Replication in independent populations, including commercial strains and wild-derived lines, would help establish how broadly the chromosome 2 signal applies and whether the same locus contributes to variation in fiber size across the species.

From an applied perspective, the identification of a quantitative trait locus for muscle fiber size opens several avenues for aquaculture genetics. Marker-assisted selection could incorporate variants within the associated block into breeding indices, provided that the association is robust across populations and that the effect size justifies inclusion. Genomic selection, which uses dense marker panels to predict breeding values without requiring knowledge of causal variants, could also benefit from the inclusion of this locus in training populations. The low-pass sequencing approach demonstrated here is particularly relevant to breeding applications, since it offers a cost-effective route to genome-wide genotyping in species for which commercial SNP arrays may be limited or outdated. As sequencing costs continue to decline, the combination of low-pass genotyping, imputation, and histological phenotyping could be scaled to larger populations, increasing the resolution of association mapping and the accuracy of genomic prediction.

The study also contributes to a broader comparative understanding of muscle growth genetics. Loci associated with muscle fiber characteristics have been described in livestock species, including cattle, pigs, and chickens, where they influence meat quality and growth traits. In fish, the genetic architecture of muscle growth has been explored through quantitative trait locus mapping in species such as tilapia and Atlantic salmon, though the cellular phenotypes underlying those signals have often remained indirect. By connecting a genomic association directly to a cellular morphometric measure, the rainbow trout study provides a more mechanistically grounded link between genotype and phenotype than is typical in aquaculture genomics. This kind of integration, spanning histology, genomics, chromatin annotation, and transcriptomics, reflects a methodological trend in quantitative genetics toward multi-layered evidence that can constrain the space of plausible causal mechanisms.

Several questions remain open. The functional role of TGF-β2 in rainbow trout muscle growth has not been directly tested, and experimental approaches such as gene knockdown, overexpression, or genome editing in zebrafish or in trout cell lines would be needed to establish whether variation in this gene’s activity produces the fiber size differences observed. The identity of the enhancer elements carrying the associated variants, and the genes they regulate, requires chromatin conformation assays or reporter studies to resolve. Whether the same locus influences fiber number, fiber type composition, or other muscle characteristics in addition to cross-sectional area is also unresolved. And the relationship between fiber size and fillet texture, a trait of growing interest to processors and consumers, could be explored using the same histological framework. These directions, together with fine-mapping within the 4.72-megabase block, define the agenda that the authors themselves lay out for moving from association to mechanism.

In the context of salmonid aquaculture, where growth rate and fillet characteristics determine profitability, the study’s findings sit within a research program supported by the United States Department of Agriculture’s National Institute of Food and Agriculture, reflecting public investment in the genetic improvement of food fish species. The collaboration between the University of Maryland, Auburn University, and the USDA Agricultural Research Service’s National Center for Cool and Cold Water Aquaculture combines expertise in genomics, quantitative genetics, and cold-water fish husbandry, a combination that the complexity of the trait demands. As genomic resources for rainbow trout continue to mature, including reference genomes, imputation panels, and chromatin maps for commercially relevant tissues, the kind of integrative analysis demonstrated here is likely to become a standard tool for connecting genetic variation to the cellular and molecular processes that drive growth in aquaculture species.

Subject of Research: Genomics

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

Article References: Raghu, A., Raymo, G., O. Ahmed, R., Ali, A., Leeds, T., & Salem, M. (2026). QTL spanning the TGF-β2 locus is associated with muscle fiber size in rainbow trout. BMC Genomics. https://doi.org/10.1186/s12864-026-13463-7

Image Credits: AI Generated

DOI: 10.1186/s12864-026-13463-7

Keywords: rainbow trout, TGF-β2, GWAS, muscle fiber size, aquaculture, QTL, transcriptomics, genomics, spanning, TGF-, locus, associated