Multiomics Analysis Reveals the Relationship between Muscle Cell Area and Weight in Rainbow Trout

Abstract

Muscle yield in Rainbow Trout is an important and marketable trait. Cell size and count have been proven to influence body size, a process regulated in party by genetic variants linked to growth and nutritional factors. We hypothesized that phenotypic divergence between USDA’s National Center for Cool and Cold Water Aquaculture (NCCCWA) selectively bred high and low fillet yield genetic lines can be explained in part by increased muscle cell size and count. Our investigation found that there was a significant correlation between both cellular filled area and several economically relevant traits, including body weight, muscle weight, visceral weight and body length. A multi-omics approach including transcriptome interrogation and genome wide association study allows us to assess gene expression signatures, and single nucleotide polymorphisms, (SNPs), explaining phenotypic variability. Transcriptome interrogation revealed associations of autophagic and catabolic mechanisms to increased cell size. Homeostatic and developmental pathways were also noted as upregulated in high filled area individuals. In contrast, muscle contractile pathways were noted as downregulated, a phenomenon that may be explained by the interplay of environmental conditions. A total of 728 SNPs 728 surpassed our stringent cutoff for significance when performing genome wide association analysis. The majority of these SNPs cluster on chromosome 2 (n=713) and overlap with notable muscle regulatory genes such as ribosomal RNA processing 15 homolog, Cornichon homolog 4 and fasciculation and elongation protein zeta-2. This work sheds light on the complex genetic architecture underpinning muscle mass accretion in genetically enhanced rainbow trout mediated by enhanced contractile machinery and metabolic support mechanisms