Genome-wide sequencing to identify a sex-specific marker in Spotted longbarbel catfish Hemibagrus guttatus

Sex-specific markers are crucial molecular tools for identifying the genetic sex and enhancing the economic value of fish, and server as an important foundation for understanding sex determination mechanisms. Hemibagrus guttatus is a rare freshwater fish known for its delicate flavor and high nutritional value. Due to overfishing, wild populations have been severely impacted, and artificial breeding techniques are still underdeveloped. Cultivating more egg‑producing females is beneficial for expanding aquaculture scale and promoting species conservation. However, the long‑term lack of effective sex identification methods has hindered both the efficiency of artificial breeding and research on the sex determination of H. guttatus . In this study, whole‑genome resequencing was performed on 20 males and 20 females, generating a total of 224.77 Gb of male data and 259.82 Gb of female data. Through comparative genomic analysis between male and female, 40 candidate male‑specific sequences were identified. After further PCR validation, a male‑specific marker was successfully developed and named HG46M2. Subsequently, the marker was applied to identify the genetic sex in three additional H. guttatus populations. Moreover, the genetic sex of the population feed with Limnodilus spp . was identified by HG46M2 marker and determined the sex reversal from male to female in breeding. This study provides a rapid and effective method for determining the genetic sex of H. guttatus . The sex‑specific marker developed here will contribute to improving the efficiency of artificial breeding, facilitate sex‑controlled breeding programs, and holds great significance for research on sex determination and conservation efforts for H. guttatus . • First time to report the sex-specific indel marker in Hemibagrus guttatus. • The sex-specific indel maker was applied to identify the genetic sex of the population. • In the industry, we found a high proportion of sex-reversal individuals in Hemibagrus guttatus after feeding with Limnodilus spp .