Identification of sex-determination regions and development of male-specific markers for topmouth culter (Culter alburnus)

The topmouth culter ( Culter alburnus ), a carnivorous freshwater species in the family Cyprinidae (order Cypriniformes), holds high economic value and displays marked sexual dimorphism in growth, where females exhibit accelerated growth relative to males. Therefore, the study of the sex determination mechanism in topmouth culter is of great significance for monosex breeding (such as all-male or all-female populations) and the conservation of germplasm resources. However, the genetic basis of sex determination of topmouth culter remains unknown. In this study, we performed whole-genome resequencing of female and male topmouth culter against a male reference genome to characterize sex determination and sex chromosomes. Genome-wide association studies (GWAS) showed that male-specific SNPs were significantly enriched on LG4, which was potential sex chromosome of the topmouth culter. Furthermore, potential male-specific sequences were identified on LG4 by screening for sequencing depth differences between males and females. With these sequences, male-specific molecular markers were screened and then validated in three different populations. None of reported sex-determination genes were annotated in these sex-biased regions on LG4. Our results indicated that the topmouth culter employed a male heterogametic (XX/XY) sex determination system. In summary, we successfully developed effective male-specific molecular markers for sex identification and characterized the genetic basis of sex determination in the topmouth culter. Our findings provide valuable genetic markers for sex-controlled breeding programs and lay a theoretical foundation for further exploration of the mechanisms underlying fish sex determination. • Topmouth culter was confirmed utilizing a male heterogametic (XX/XY) sex determination system. • LG4 was identified as potential sex chromosome harboring male-specific sequences. • Male-specific molecular markers were developed, enabling sex identification and advancing monosex breeding programs.