GWAS-Identified SNPs and Candidate Genes Influencing Sex in Loach (Misgurnus anguillicaudatus)

Loach (Misgurnus anguillicaudatus) is a small benthic fish favored by consumers in East Asia. Female loaches exhibit greater production value due to their larger size and higher meat yield. Therefore, controlling the sex of loach should be studied to implement an all-female breeding strategy. This study identified sex-related SNP markers and candidate genes in loach through GWAS. Genotyping male and female populations with WGRS revealed 84 SNPs labeled as associated with sex. Distinct SNP peaks appeared on Chr6 and Chr3, with over half of the sex-associated SNPs located on Chr6. Within these sex-associated regions, 15 key candidate genes related to sex and reproduction were identified, including hemgn and foxl2a. Among these genes, pik3cb on Chr3 and hhip, cntln, and pard3ba on Chr6 have multiple sex-associated haplotypes that can be utilized for subsequent monosex breeding. Notably, a highly male-linked SNP marker was identified on pard3ba, whose genotype is consistent with the male heterogamete (XX/XY). Through gene enrichment analysis and expression validation, signaling pathways such as TGF-β, FoxO, and mTOR were identified as being involved in sex regulation. This study provides molecular markers for sex-controlled breeding in loach, facilitating in-depth research into the mechanisms of sex regulation in loach.