Identification of sex-linked markers and genes in Portuguese oyster (Magallana angulata)

The Portuguese oyster ( Magallana angulata ) is a valuable aquaculture species with sexual dimorphism in growth and nutritional traits, making it a promising candidate for sex-controlled breeding. However, the genetic mechanisms underlying its sex determination remain poorly understood. This study represents the first population-level investigation to identify sex-linked genetic markers and candidate genes in M. angulata using genome-wide association studies (GWAS) and transcriptomic analysis. A total of 1,613 sex-associated SNPs were identified, primarily located on Chr. 9 (7.99 Mb–10.51Mb). SNP annotation revealed 57 genes around these sex-associated SNPs. Transcriptomic analysis identified 8,635 differentially expressed genes (DEGs) between male and female gonads, of which 12 overlapped with GWAS-identified genes. Among these, four genes ( 5-HTR , ADPKD1-a , SCP , and SLC28A3 ) exhibited strong sex-specific genetic differentiation, with 5-HTR showing the most pronounced association. Further population genetic analysis revealed higher genetic diversity and heterozygosity of 5-HTR in males. Six sex-associated haplotypes based on SNPs within 5-HTR were constructed and validated in an independent population, although with reduced significance, suggesting both continuity and variation in sex determination mechanisms across populations. These findings provide a critical foundation for understanding the genetic basis of sex determination and advancing sex-controlled breeding strategies in M. angulata.