Screening and characterization of sex-specific markers by 2b-RAD sequencing in zig-zag eel (Mastacembelus armatus) with implication of XY sex determination system

Identification of sex-specific markers and revealing of the sex determination system have important implications for sex control breeding in aquaculture. The zig-zag eel (Mastacembelus armatus) mainly occurs in the Yangtze River and the Pearl River in China. An apparent sexual dimorphism in growth is observed, however, the sex determination mechanism is still unclear to date. In this study, two male-specific 2b-RAD tags and two SNPs were identified by 2b-RAD sequencing and verified by PCR amplification. Two female specific deletions with 281 bp and 4938 bp and a male-specific deletion with 156 bp were identified by sequence comparison between X-specific and Y-specific sequences obtained by genome walking from two 2b-RAD tags. Two sets of primers including Y-specific and XY-shared primers were designed based on these identified deletion regions to distinguish the genetic sex of zig-zag eel. The specificity of these primers was confirmed in 81 offspring of one F1 family. Furthermore, two male-specific SNP primers, which specifically amplify one band only in the males, were also designed. These data indicate that zig-zag eel possesses a male heterogametic XY sex determination system. The sex-specific markers presented here will have the potential to play an important role on the production of all-male populations of zig-zag eel for aquaculture in the future.