Genetic/Genomic basis of sex determination in fish of aquaculture interest

Sex determination (SD) systems in teleosts display remarkable variability and remain only partially understood, both due to the extremely high number of species (around 30,000) and because research efforts have traditionally prioritized aquaculture-relevant fishes. In aquaculture, monosex populations are often preferred because they exhibit traits of economic importance, such as higher growth rates. The family Mugilidae, a group of fish of major ecological and economic importance, represents an excellent model to investigate SD mechanisms and their potential applications. Among them, Mugil cephalus is particularly relevant due the commercial value of female ovaries used for bottarga production. This PhD thesis, articulated in two studies, aimed to characterize the genetic factors underlying SD in different Mugilidae species through a genomic-based approach, which is more accessible compared to the environmental component. Taken together, the two studies provide a complementary perspective that combines intraspecific and interspecific levels analysis, offering a broader view of SD variability in this family. In the first study, published in a peer-reviewed journal, a new high-quality reference genome was assembled for Mugil cephalus, and whole-genome resequencing was performed on males and females from two Mediterranean populations. The analysis confirmed the fshr variants, previously associated with an XX/XY systems, partially explain SD in the Tyrrhenian population. In contrast, in the Aegean population, variants at this locus does not appear to be associated with SD. Additionally, an intronic variant in the sestd1 gene was identified, consistent with a ZZ/ZW system, suggesting the coexistence of multiple mechanisms and a potential contribution of both geographic and environmental factors. In the second study not yet published, it is reported the first chromosome-level genome assembly for two species of the genus Chelon, namely Chelon auratus and Chelon ramada. Comparative analyses between male and female genomes of the two species revealed inter- and intraspecific genetic variants, highlighting two shared SD gene candidates consistent with an XX/XY system, together with additional species-specific signals in both species. These findings support the hypothesis of a polygenic basis of SD in this genus. Overall, this thesis advances our current knowledge of the genetic mechanisms and variability of SD in Mugilidae, a family still poorly investigated from this perspective, providing novel insights into the evolution of SD in teleosts. Beyond their relevance for SD, the genomic resources generated here constitute a valuable foundation for future studies on diversity, adaptation and evolutionary biology in Mugilidae. At the same time, the identification of SD markers offers practical application for stock management and the development of more sustainable aquaculture practices, including marker-assisted selection and the production of monosex populations for farming purposes.