Large-scale eQTL analyses in Atlantic salmon reveal persistent dosage compensation 100 million years after genome duplication

Abstract Whole-genome duplication (WGD) through autopolyploidization has played a role in genome evolution across eukaryotes. A major consequence of WGD is the rewiring of gene regulatory networks, partly driven by selection on dosage balance. In multicellular organisms, evidence for dosage balance selection has relied on comparative patterns of duplicate gene retention and expression, with few studies directly examining regulatory architecture after WGD. Here, we analysed a large-scale eQTL dataset from Atlantic salmon (Salmo salar), which experienced a WGD 100 million years ago. We found that trans-regulatory connections were enriched between duplicated regions, indicating long-term conservation of ancestral interchromosomal regulatory interactions. Overall, 230 duplicated genes (5%) shared eQTLs, suggesting conserved regulatory control. Moreover, 16 gene pairs showed compensatory expression effects mediated by a common regulator, consistent with predictions of the dosage balance hypothesis. These gene pairs were significantly enriched in recently rediploidized regions. Our results indicate long-term maintenance of dosage balance after WGD. Teaser Genetic regulation in Atlantic salmon shows that duplicated genes can remain dosage-balanced across 100 million years of evolution. Competing Interest Statement The authors have declared no competing interest.