New Insight for Genomic Structure of Xx/Xy Sexual Determining Type Cyprinidae Through Male-Specific Fragment Analysis

Abstract

Sex-specific markers are vitally important to further study the mechanism of sex determination and sex differences in species. For the lower phylogenetic vertebrates (such as fishes) without significant heteromorphic sex chromosomes at some developmental stages, it is important to study the genomic regions or sequences of sex difference between males and females for the elucidation of sex differentiation mechanism. This study developed an analysis process based on resequencing and the sex-specific markers applied to the main economically farmed fishes, silver carp (Hypophthalmichthys molitrix), bighead carp (Hypophthalmichthys nobilis) and blunt snout bream (Megalobrama amblycephala), all of which are based on XX/XY sex determination mechanism. Ten female and 10 male blunt breams were sequenced by NGS. As this process was applied to the genomes of these fishes and the results showed that 13 male specific fragments of H. molitrix, 11 male specific fragments of H. nobilis and 21 male specific fragments of M. amblycephala were screened. There were 3 conserved fragments across these three fishes. Three male-specific markers of M. amblycephala were verified by PCR, and one of them is very stable. By further analyzing this conserved region, a possible male-specific gene in this region was identified, which was conserved in other Cyprus species, so that it could be used for sex identification in application in Cyprus fish. This developed method could be used as a general way to find the male-specific fragments and screen the sex markers for the identification of male or female in the early stage of sex differentiation, which could be also applied for the study of sex determination mechanisms for unisexual reproduction and sex reversal.

Keywords: male-specific fragment, Next-generation sequencing, Cyprinidae, bighead carp, Megalobrama amblycephala