Genome-wide association studies (GWAS) to identify key genomic regions and candidate genes associated with feed intake and efficiency in Atlantic salmon (Salmo salar)

Improving feed efficiency is a key focus in Atlantic salmon breeding programs. It helps maintain production levels while reducing feed costs, which account for over 50 % of total production expenses. Despite its importance, our understanding of the genetic factors regulating feed intake and efficiency in salmon is limited, largely due to the challenges in measuring feed intake at the individual level. In this study, we aimed to 1) identify the genetic architecture influencing individual feed intake (IFI), feed conversion ratio (FCR), and residual feed intake (RFI) in salmon, and 2) map genetic variants to uncover candidate genes and biological pathways associated with these traits. Genome-wide association studies (GWAS) and candidate gene identification analysis were performed on 700 Atlantic salmon smolts, which were genotyped with MOWI's in-house 55 K SNP array and phenotyped for IFI, FCR and RFI at three measurement time points using an X-ray imaging method. GWAS revealed a polygenic genetic architecture of all the traits, with no large-effect QTLs identified. However, nine chromosome-wide significant and independent QTLs were detected. Among them, four independent QTLs located on chromosomes Ssa12 and Ssa13 were identified for IFI, while five positioned on chromosomes Ssa07 and Ssa13 were linked with both feed efficiency traits, i.e. FCR and RFI. Furthermore, twenty-one putative candidate genes were identified within ±50 Kb genomic regions flanking these top QTLs. Most of the candidate genes associated with IFI, such as Foxr1, gnai2b, collagen alpha-1(IX) and protein phosphatase-1 , are involved in neurodevelopment, growth and signalling. In contrast, genes related to feed efficiency, including Acox3, SENP3, GDAP1, and mGluRs, are primarily associated with lipid metabolism and energy homeostasis. In addition, several genes identified for feed efficiency showed significant gene enrichment in interrelated gene ontology (GO) terms affiliated with fatty acid metabolism and transportation, suggesting potential mechanisms for regulating feed efficiency. This study identified key genomic loci and candidate genes potentially associated with feed intake and efficiency, which provides a genomic foundation for improving feed efficiency in Atlantic salmon. However, functional validations are required to validate these findings and fully understand the underlying mechanisms regulating feed intake and efficiency in salmon. • Individual feed intake and efficiency have a polygenic genetic architecture in Atlantic salmon. • Key genomic regions on Ssa 07, Ssa 12 and Ssa 13 are significantly associated with feed efficiency traits. • Neuronal signalling is central to regulating feed intake, where lipid metabolism influences feed efficiency.