Data for: Large-effect loci control maturation age through functionally modular and interacting gene regulatory networks in Atlantic salmon

Understanding how genetic variation is translated into phenotypic variation remains a central challenge in biology. In Atlantic salmon (Salmo salar), age at maturity is a key life-history trait strongly associated with two large-effect loci linked to the transcriptional regulators vgll3 and six6. But how do they together shape age at maturity through transcriptomic layer remains poorly understood. Here, we analysed gonadal transcriptomes from 89 individuals of a single full-sib family carrying homozygous combinations of early (E) and late (L) maturation alleles at both loci. We integrated expression, alternative splicing, networks and linkage disequilibrium (LD) analyses to characterized genotype-associated transcriptomic variation.