Genome resequencing reveals an XX/XY sex determination system and male-specific markers in Glyptosternum maculatum

Glyptosternum maculatum is an endangered cold-water fish endemic to Xizang, with pronounced sexual dimorphism in growth. Here, we combined whole-genome resequencing, pool-seq, population genomic analyses, and targeted marker validation to characterize its genetic sex determination system. We identified linkage group LG01 as the candidate sex chromosome and localized a sex-determining region spanning 2.7–2.8 Mb that showed strong differentiation between males and females. Within this region, 195 male-specific SNPs and 20 male-specific indels were identified, and 53 sex-linked markers were developed. Targeted sequencing of 29 males and 26 females showed that 93.1% of males were heterozygous and 96.2% of females were homozygous across the marker set. The locus LG01:27,671,222 showed complete genotype-phenotype concordance in the validation set. These findings support an XX/XY sex determination system and provide molecular tools for sex identification, conservation, and future breeding applications.