Development of a Sex-Specific Marker for the Chinese Hooksnout Carp Opsariichthys bidens Günther, 1873 Based on Whole-Genome Resequencing and Bulked Segregant Analysis

Sex-specific markers are important basic tools for the sex-controlled breeding of farmed fish. Here, we aimed to develop a rapid yet accurate, cost-effective method for determining the genetic sex of the Chinese hooksnout carp (<i>Opsariichthys bidens</i>), a freshwater fish. Using whole-genome resequencing technology, along with bulked segregant analysis (BSA) and chromosome quotient (CQ) methods, sex-specific regions were screened, and corresponding primers were designed to validate the screening results. A total of 45 sex-specific regions were successfully screened through BSA sequencing and CQ analysis, and 50 pairs of primers were designed for use in the screening verification. The Mar28 primer pair showed stable sex specificity in multiple populations of <i>O. bidens</i>, accurately distinguishing male from female individuals. This primer pair amplified two bands (509 and 814 bp) in males, but only one band (509 bp) in females. The genetic sex identification method established here provides a theoretical basis for studying the mechanism of sex determination in <i>O. bidens</i>, has implications for the monosex culture and molecular breeding of <i>O. bidens</i>, and has significant scientific and practical value.