Sex-specific markers developed by 2b-RAD and genome sequencing reveal an XX/XY sex-determination system in mud carp (Cirrhinus molitorella)

Sex-specific markers are a powerful tool for studying sex-determination mechanisms and sex-control breeding in aquaculture. Mud carp (Cirrhinus molitorella) is one of the most important edible fishes in South China and Southeast Asia, and its processed products, such as tinned foods, have a high market value. The age of first maturation for mud carp is often three years. However, the sex-determination mechanism of mud carp is still unclear, which has affected its genetic breeding and culture industrial development. In this study, we identified sex-specific markers by 2b-RAD and genome sequencing in mud carp. The whole genome of a male mud carp was sequenced, and the total size of the draft genome was 1078.7 Mb. Nine males and nine females were subjected to 2b-RAD sequencing, and 12 male-specific scaffolds were isolated. Primers were designed based on these male scaffolds, and five male-specific markers from five scaffolds successfully discriminated males from females in the broodstock populations with 100% accuracy. Furthermore, five male-specific SNPs were identified and verified by Sanger sequencing, and all of them showed female homogamety and male heterogamety. These results indicate that mud carp has a male-heterogametic XX/XY sex-determination system. To the best of our knowledge, this is the first report of practical sex-specific markers in this species. Our results will contribute to elucidating the genetic basis of sex determination and improving the efficiency of genetic breeding in mud carp.