Screening and characterization of sex-specific markers developed by a simple NGS method in mandarin fish (Siniperca chuatsi)

Sex-specific markers are the prerequisite for interpreting the mechanisms of sex determination and sex control breeding in fish. Here, we provided a simple next generation sequencing strategy to identify potential sex-specific sequences in mandarin fish (Siniperca chuatsi) that is a greatly important freshwater fish in China. Through genome assembly, reads mapping, sequencing depth and coverage analysis of sequenced genomes of three males and three females, we identified 212 potential male-specific sequences. After two rounds of verification, a total of eight primer pairs were identified as potential candidate markers to be able to distinguish the genetic sex of mandarin fish. Subsequently, the best three markers were further tested in another four different farmed populations of mandarin fish, and the authenticity was 100%. Moreover, based on these markers, eight neomales were demonstrated to be genetic females and about 1: 1 sex ratio was observed in 215 juvenile offspring from two full-sib families. Notably, a duplicate of anti-Müllerian hormone, a gene participating in sex determination process in fish, was identified from the verified male-specific sequences. Overall, this study provided a simple and effective next generation sequencing method to identify sex-specific sequences and the male-specific molecular markers suggested an XY sex determination system in mandarin fish.