Fillet yield and quality traits are some of the most important traits for genetic improvement in rainbow trout breeding programs. The host genetics and gut microbiome are known contributors to the regulation of these traits. While most studies investigate them separately, a simultaneous holistic look into these two components may provide insights into the interplay between hosts’ genetics and the microbiomes and how they influence these traits. We analyzed the host transcriptome, host genome, and gut microbiome of rainbow trout fish families that are divergent for these traits. The transcriptome analysis revealed gene expression patterns and identified several differentially expressed genes (DEGs). To prioritize candidate genes, we performed eQTL mapping, identifying DEGs whose expression patterns are regulated by genetic variants. Further, we performed an association analysis between gene expression and phenotypic traits, and only those DEGs whose expressions are correlated with the phenotypic traits and are regulated by cis-eQTL variants are prioritized as candidate genes. Potential candidate genes for growth traits were identified for body weight (ubiquitin-protein ligase E3A (UBE3A), collagen alpha-1 (XXV1) chain (COL26A1), protein phosphatase inhibitor 2 (PPI-2)); muscle yield (PDZ domain-containing protein 11 (PDZK11), pex5-related protein-like (PEX5-L), Synaptic vesicle glycoprotein 2Ca (SVC2C)) and condition factor (Synaptic vesicle glycoprotein 2Ca (SVC2C), Sodium-dependent neutral amino acid transporter SLC6A17, and Meiosis-specific coiled-coil domain-containing protein (MEIOC)). Our microbiome analysis revealed microbiome biomarkers with the potential to improve body weight, muscle yield, and body condition factor. Integrated gene-microbiome analysis identifies Clostridium species (C. beijerinckii, C. intestinale, C.isatidis, C. saccharobutylicum, C. taeniosporum, C. gasigenes) enriched in high muscle yield rainbow trout family to be positively correlated with PEX5-L, and PDZK genes identified as muscle yield candidate genes. Separately, we performed genome-wide association analysis that revealed candidate genes for fatty acid profiles, muscle fiber size, fiber density, and fillet color. These results provide new insights into the relationship and interaction between host genetics and the microbiome and how these biomarkers could be targeted for selective modification to improve fillet yield and quality traits in rainbow trout.
KEYWORDS—Fillet yield, Quality traits; microbiome; genes