Screening and characterization of sex-specific markers for the hybrid (Megalobrama amblycephala ♀ × Ancherythroculter nigrocauda ♂) based on 2b-RAD and transcriptome sequencing

Abstract

Sex-specific molecular markers provide significant molecular basis for sex control breeding biotechnologies to produce mono-sex fish population in aquaculture breeding programs. “Xianfeng No. 2”, a new hybrid of Megalobrama amblycephala (M. amblycephala) (♀) × Ancherythroculter nigrocauda (A. nigrocauda) (♂), with the females growing faster than males, is one of an important aquaculture fish species in China. In order to avoid genetic contamination impact on the ecological environment, maintain gene purity and improve the economic value, it is greatly important to cultivate all-female strains. In this study, artificially induced gynogenesis was performed in the hybrid females and it was found that all progenies were females. Then, we used 2b-RAD-seq to screen the sex-specific markers of the hybrid species. Nine male-specific tags were firstly identified by the sequencing, and then two male-specific tags were screened and successfully validated by PCR amplification in both hybrid and paternal A. nigrocauda populations. Furthermore, one male-specific molecular marker ref57660–1 (326 bp) was validated by RNA-seq and quantitative interpretation from the gene expression level, which indicated the reliability of the marker. Together with the results of all females from gynogenesis population and the identified male-specific markers, it is suggested that this hybrid species is female homogametic (XX) with sex determination mechanism being XX/XY type. The identified sex-specific markers are of great value to improve the efficiency of all-male/all-female breeding practices for this hybird species as well as for paternal A. nigrocauda.