Screening and characterization of X chromosome-specific markers in mandarin fish (Siniperca chuatsi)

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The mandarin fish (Siniperca chuatsi) is an important aquaculture fish. All-male mandarin fish culture has the advantages of higher profits, more uniform size and lower energy consumption of gonadal development. However, the lack of accurate sex-specific markers has hampered the all-male breeding of this species. Herein, we successfully adopted a next generation sequencing strategy to identify potential X chromosome-specific sequences in mandarin fish. First of all, we performed genome sequencing of three YY super-males, and then align the reads to XX genome to identified candidate X chromosome-specific regions. A total of 49 candidate X chromosome-specific contigs were identified with length ranging from 448 to 1189 bp. After PCR validation, four pairs of primers derived from two X chromosome-specific contigs, Ma-XB1, Ma-XB2, Ma-XC1, Ma-XC2, could successfully produce X chromosome-specific bands of 935 bp, 1105 bp, 850 bp and 1146 bp, respectively, with no band amplified in six YY super-males. In conclusion, based on YY genome sequencing and PCR validation, four X chromosome-specific markers were developed, which would promote the development of all-male breeding of mandarin fish.