Identification of the sex-linked region of Siniperca scherzeri and development of sex-specific markers

Spotted mandarin fish Siniperca scherzeri, as a significant freshwater aquaculture species in China, displays pronounced sexual dimorphism. Adult female S. scherzeri typically weigh over 10–30 % more than their male counterparts. Nonetheless, the external morphological differences between females and males are not readily noticeable, especially during the juvenile stage, with challenging to precisely distinguish and confirm their morphological sex using traditional methods. Moreover, the genetic mechanisms underlying sex determination in S. scherzeri are unclear. Hence, it is crucial to investigate the genetic basis of sex in S. scherzeri in-depth and develop corresponding molecular markers. Such advancements are essential for the future implementation of sex-controlled breeding program. In this study, whole-genome resequencing was conducted on 50 S. scherzeri (25 males and 25 females), followed by a genome-wide association analysis (GWAS) integrated with an Fst analysis. For the first time, chromosome 14 was identified as the sex chromosome in S. scherzeri and a 0.44 Mb region (19.34 Mb–19.78 Mb) was confirmed as the sex-linked region. Within this region, 19 SNPs and 4 InDels related to gender dimorphic were screened. From these, two InDels were selected to develop one male-specific marker and one female-specific marker, both achieving a 100 % accuracy rate in sex identification. Furthermore, the developed sex markers and sex-linked SNPs confirmed that S. scherzeri exhibits an XX/XY male heterogametic reproductive system. These findings provide significant propositions and essential tools for elucidating the molecular mechanisms of sex determination and differentiation in S. scherzeri, and for developing sex-controlled breeding programs as well.