A rapid and reliable method for genetic sex identification in sea cucumber, Apostichopus japonicus

Identification of sex-specific markers has important implications for genetic breeding and sex control breeding in aquaculture. Sea cucumber (Apostichopus japonicus) is one of the most important mariculture species in China. Although a substantial difference in immunocompetence has been observed between male and female sea cucumbers, the sex-specific marker remains unclear. Moreover, there is no reliable method for genetic sex identification in sea cucumbers. In this study, we first applied a 2b-RAD-seq method and identified two male-specific 2b-RAD-tags. This includes a 313 bp male-specific fragment that was mapped to scaffold MRZV01000576.1 of the male genome of A. japonicus. Several genes associated with the centromere, such as tesin-a-like gene, centromere-associated gene, reverse transcriptase gene, were also annotated within this scaffold. By designing three different sex-specific primers, we characterized genetic sex of sea cucumbers in different culture populations and the wild population. Using a fast and low-cost alkaline lysis method for DNA extraction, a reliable PCR amplification-mediated genetic sex identification method was developed. Hence, the sex-specific markers provide a solid basis to reveal the sex determination mechanism and the origin of sex-determining regions in sea cucumber. Furthermore, this study will improve the efficiency of genetic and sex control breeding in sea cucumbers.