A major locus on chromosome 14 impacts developmental variation of Atlantic salmon smoltification

Abstract Background Smoltification in anadromous Atlantic salmon is a complex developmental process involving physiological and cellular changes that enable freshwater fish to adapt to seawater. Central to this transformation is the functional transformation of the gill to manage osmoregulatory demands. While environmental cues like photoperiod are known to influence smolt development, the genetic architecture underlying smolt development — particularly related to gill physiology — remains poorly understood. Results A large-scale eQTL analysis across 3,000 Atlantic salmon subjected to three photoperiod regimes, identified over 45,000 significant SNP-gene expression associations in gill tissue. Notably, we discovered a 0.5 Mbp large trans-eQTL hotspot on chromosome 14. This ‘hub-locus’ was associated with expression of more than 2,000 genes across the genome which were significantly enriched for gill cell type specific markers. In addition we found that the hub-locus was associated with somatic growth. Our findings support a “local tissue effect” model, where cis-regulatory or protein sequence variants within the hub-locus modulate cell proliferation and differentiation of gill cell types. Conclusion This work advances our understanding of the genetic basis of smoltification in Atlantic salmon and provides a foundation for future studies using single-cell approaches to resolve cell-type specific mechanisms underlying genetic variation in smolt development.