Identification of male-specific DNA markers by whole genome re-sequencing in mandarin fish Siniperca chuatsi

Sex-specific markers are powerful tools for studying monosexual breeding programs and sex-determining genetic mechanisms in teleost fish. In this study, we performed whole-genome re-sequencing on 12 male and 12 female specimens of Siniperca chuatsi and screened 85 candidate Y chromosome-specific fragments through bioinformatics analyses. Subsequently, six sex-specific markers were identified to distinguish the genetic sex of S. chuatsi with high accuracy. Three of these markers were further developed as co-dominant markers that could discriminate XX females, XY males, and YY super-males based on different amplicon lengths generated for different sexes. Importantly, three sex-related genes ( GnRHr , Amhy , and Amh ), known to be involved in sex determination and differentiation, were annotated using BLAST for these sex-specific markers. Therefore, using a male heterogametic (XX/XY) system, we confirmed that genetic mechanisms govern sex determination in mandarin fish. This study has great practical significance for sex control breeding and theoretical importance in elucidating the sex determination mechanism in S. chuatsi . • We successfully isolated six Y-chromosome fragments with the application of genome re-sequencing approach in mandarin fish. • Three co-dominant sex markers were developed and represented a concordance rate of 100% between genotypic and phenotypic sex. • Three potential master sex determining genes were identified through annotation in the reference genome of S. chuatsi .