We are using Atlantic salmon as a model to study the transcriptional dynamic change of reproductive tissues (gonad and pituitary) on sexual maturation. We used Atlantic salmon from two age cohorts that were raised in common garden hatchery conditions, with natural temperature and photo period. We sequenced polyadenylated RNA from eight pituitary samples collected from 4-year-old immature males and 90 gonadal samples were collected from 1-year-old individuals, including immature ovaries (n=36), immature testis (n=28), and mature testis (n=26).

Purpose: Sexual maturation is a key developmental process important for reproductive success. Variation in maturity age underlies much of adaptive diversity and can evolve rapidly to optimize lifetime fitness given the environmental context. The importance of understanding the molecular mechanisms of maturation in marine fish species facing global change is underlined by a strong allometric relationship between age (and therefore size) at maturity and fecundity - evolution of maturation age is a key factor determining population growth and resilience in fishes. Atlantic salmon (*Salmo salar*) is an excellent model for studying sexual maturation due to its diverse life history strategies and ecological and economic importance. However, a comprehensive transcriptional investigation of reproductive tissues that captures dynamic changes across individuals, tissues, and developmental stages has been lacking. Furthermore, while long non-coding RNAs (lncRNAs) play crucial roles in maturation, their functions in salmon maturation remain largely unexplored. Method: The broodstock is a first-generation hatchery stock composed of a mixture of northern Baltic Sea lineages and maintained by the Natural Resources Institute Finland (LUKE). Eggs were fertilized and raised in controlled conditions at the University of Helsinki research animal facility. We used Atlantic salmon from two age cohorts that were raised in common garden hatchery conditions, with an annual cycle of natural water temperature and light corresponding to the location in southern Finland. The fish represent a mix of Baltic Sea lineages from Finnish rivers. 1-year-old individuals used in this study were raised in the fish facilities at the Viikki campus of the University of Helsinki, and the 4-year-old individuals used were reared in larger experimental facilities at Lammi Biological Station (University of Helsinki). Maturation status was determined based on the presence or absence of milt release. Tissue samples including pituitary and gonads were flash-frozen in liquid nitrogen and stored at -80°C until RNA extraction. Results: Our results showed key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. We identified high-confidence newly characterized coding genes and lncRNA from intergenic regions, many exhibiting tissue-specific expression. Gene co-expression network analysis (WGCNA) revealed tissue-specific gene network modules linked to key biological functions. Discovery of new copies of known genes associated with the regulation of gonadal and pituitary functions. Discovery of new copies of known genes associated with the regulation of gonadal and pituitary functions. Conclusions: Our findings significantly improve the Atlantic salmon transcriptome assembly and further our understanding of the molecular mechanisms underlying sexual maturation and potential maturation age determining mechanisms. Our findings highlight key regulatory pathways and novel molecular players involved in sexual maturation, particularly in the testis. Importantly, our study highlights the regulatory potential of lncRNAs in governing key aspects of maturation and, potentially, the variation within. Our findings build a solid framework for future discoveries of the role of previously uncharacterized genes and lncRNAs in mediating evolution in maturation age.