GWAS and Transcriptome Analysis Reveal Male Heterogametic Sex-Specific Markers and Candidate Genes in Darkbarbel Catfish (pelteobagrus Vachelli)

The darkbarbel catfish (Pelteobagrus vachelli) is an economically important aquaculture species in Asia, characterized by sexual dimorphism in growth between females and males. All-male breeding holds significant potential for aquaculture, but the sex-determining mechanism in this species remains unknown, and no sex-specific markers are available to differentiate males from females during the juvenile stage. In this study, whole-genome resequencing was applied to 60 individuals to identify genetic loci associated with sex, and the resulting data were analyzed using genome-wide association studies (GWAS) and FST analyses. For the first time, a total of 1435 SNPs and 461 InDels were identified on chromosome 3 significantly associated with sex, with these markers concentrated within a 17.1 Mb region. Within this region, male individuals exhibit heterozygosity SNPs, whereas females are homozygous, confirming an XX/XY sex-determination system. Based on InDel variations, two sexspecific markers were successfully developed, which can identify male and female individuals. Additionally, 300 genes were identified within the sex-determining region on chromosome 3, and transcriptomic data validated four potential candidate genes for sex determination, including sox11, hsf2, esr1, and pbk. Among these, sox11 and hsf2 may be involved in gonadal development as primary candidate sex-determining genes and may play critical roles in sex differentiation, thereby providing novel insights into the evolutionary mechanisms of sex chromosomes in this species. These findings present the first identification of a sex-linked marker in the darkbarbel catfish through whole-genome resequencing, offering valuable perspectives on the sex determination mechanism and the potential for all-male breeding in this species.