Abstract
Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male fish carry a single copy of the male specific region, consistent with an XX/XY or male heterogametric sex system. Haplotype analysis revealed deep divergence between the putatively ancestral locus on chromosome 2, compared with loci on chromosomes 3 and 6. Haplotypes in fish carrying either the chromosome 3 or 6 loci were nearly indistinguishable, indicating a founding event that occurred following the speciation event that defined Salmo salar from other salmonids. These findings highlight the evolutionarily fluid state of sex determination systems in salmonids, and resolve to the sequence level differences in animals with divergent sex lineages.
Highlights
The genetic and environment factors that contribute to sexual determination are of fundamental biological interest, both from an evolutionary perspective and within an aquacultural production context
To measure genome diversity and characterise sex determination loci in Tasmanian Atlantic salmon (TAS), we performed whole genome sequencing (WGS) of 20 fish selected from a range of year classes and families
To assess the relative level of diversity in comparison to other farmed salmon populations, public WGS datasets were obtained from North American (NA) and European (EU) derived strains of Atlantic salmon cultured in Chile[12]
Summary
The genetic and environment factors that contribute to sexual determination are of fundamental biological interest, both from an evolutionary perspective and within an aquacultural production context. In this study we characterise the number, location and evolutionary history of sex determination loci in Atlantic salmon. Tasmania is outside the natural range of the species, and the study population originates from North American wild stocks[9,10] To commence their genetic characterisation, we performed whole genome sequencing of 20 animals and compared www.nature.com/scientificreports/. To characterise the evolutionary history of each SD locus, genome sequence from animals with known sex lineage were used for read mapping and variant detection. This defined the boundary of the male specific region and confirmed males carry a single copy consistent with male heterogameity. We identify the likely ancestral sex determination locus, and two descendent lineages of which one has likely been founded after the speciation event that defines Atlantic salmon
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