Abstract
BackgroundA complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. Atlantic salmon belongs to the family Salmonidae of fishes and represents a species of great commercial value. Although the species is assumed to be male heterogametic with XY sex determination, the precise genetic basis of sexual development remains unclear. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability. This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. In this study, we have used a 220 K SNP panel developed for Atlantic salmon to identify the chromosomes explaining the highest proportion of the genetic variance for sex as well as candidate regions and genes associated to sexual development in this species.ResultsResults from regional heritability analysis showed that the chromosomes explaining the highest proportion of variance in these populations were Ssa02 (heritability = 0.42, SE = 0.12) and Ssa21 (heritability = 0.26, SE = 0.11). After pruning by linkage disequilibrium, genome-wide association analyses revealed 114 SNPs that were significantly associated with sex, being Ssa02 the chromosome containing a greatest number of regions. Close examination of the candidate regions evidenced important genes related to sex in other species of Class Actinopterygii, including SDY, genes from family SOX, RSPO1, ESR1, U2AF2A, LMO7, GNRH-R, DND and FIGLA.ConclusionsThe combined results from regional heritability analysis and genome-wide association have provided new advances in the knowledge of the genetic regulation of sex determination in Atlantic salmon, supporting that Ssa02 is the candidate chromosome for sex in this species and suggesting an alternative population lineage in Spanish wild populations according to the results from Ssa21.
Highlights
A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development
Genome-wide association analysis Results derived from genome-wide association studies (GWAS) after pruning the single nucleotide polymorphism (SNP) for linkage disequilibrium (LD) and after applying false discovery rate (FDR) multitest correction at 5% level (Log10 (P) > 3.8), revealed 114 SNPs significantly associated with sex (Fig. 2, Table 2)
Our findings revealed sex-related genes in our candidate regions that had been previously identified in other species of the class Actinopterygii, including important maleness related genes such as sexually dimorphic on the Y-chromosome (SDY) and genes from the sex-determining region Y (SRY)-type high mobility group box (SOX) family
Summary
A complete understanding of the genetic basis for sexual determination and differentiation is necessary in order to implement efficient breeding schemes at early stages of development. The complexity is likely associated to the relatively recent salmonid specific whole genome duplication that may be responsible for certain genome instability This instability together with the capacity of the sex-determining gene to move across the genome as reported by previous studies, may explain that sexual development genes are not circumscribed to the same chromosomes in all members of the species. Sexual development is a multistep process involving sex determination (SD), initiation, gonadal differentiation and maintenance This process comprises a great diversity of strategies that can be controlled by a variety of genetic and/or environmental mechanisms [1,2,3]. Gaining control over SD enables to develop appropriate breeding schemes in early stages of development when sex external secondary characteristics are not yet differentiated [4, 5]. Atlantic salmon (Salmo salar) represents one of the most important farmed fish species in the world, with a global annual production achieving 2.5 million tonnes that entails an economic value of $15.4 billion (USD) [7]
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