Comparison of the hypothalamic and pituitary transcriptome between six6 genotypes in one-year-old salmon

Sexual maturation is a key life-history trait in Atlantic salmon (Salmo salar) that influences reproductive success. Previous studies have identified the six6 genomic region as a major genetic determinant of sea age at maturity in Atlantic salmon. The six6 gene encodes a transcription factor expressed in the hypothalamus and pituitary, two key components of the hypothalamic–pituitary–gonadal (HPG) axis that regulates reproductive development. Although six6 expressions have been studied in different tissues and life stages, little is known about whether gene expressions in the hypothalamus and pituitary differ among Atlantic salmon carrying different six6 genotypes. To address this, transcriptomes of the hypothalamus (n = 40) and pituitary (n = 35) were compared among one-year-old Atlantic salmon carrying early-maturation (EE), heterozygous (EL), and late-maturation (LL) six6 genotypes. Gene expression was quantified using 3′ RNA sequencing, and differential gene expression was analyzed using DESeq2 while accounting for family effects and including body length as a covariate. Differential gene expression analysis identified only a limited number of genes associated with six6 genotype. In the hypothalamus, eomes, LOC106584459, and LOC106598272 were associated with female genotype comparisons, while only a single genotype-associated gene was detected in males. In the pituitary, differential expression was restricted to two uncharacterized genes (LOC106591957 and LOC106563368), which were detected across genotype and sex comparisons. Overall, six6 genotype was associated with only subtle transcriptional differences in the hypothalamus and pituitary at this developmental stage. Further studies across multiple developmental stages are needed to better understand when genotype-associated transcriptional differences occur and how they contribute to variation in maturation timing in Atlantic salmon.