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

TL;DR

Researchers developed a genetic marker to quickly and accurately identify the sex of Chinese hooksnout carp using genome sequencing, aiding breeding and research.

Contribution

A novel sex-specific genetic marker (Mar28 primer pair) was developed for O. bidens using whole-genome resequencing and bulked segregant analysis.

Findings

The Mar28 primer pair reliably distinguishes males from females by amplifying two bands in males and one in females.

45 male-specific genomic regions were identified through BSA and CQ analysis.

The method is practical for monosex breeding and sex determination research in O. bidens.

Abstract

This study developed and validated a rapid, accurate, and cost-effective genetic sex identification method for the freshwater fish Opsariichthys bidens. Using whole-genome resequencing and the chromosome quotient approach, 45 male-specific genomic regions were identified. Among 50 designed primer pairs, the Mar28 primer pair consistently distinguished males from females across multiple populations, amplifying two bands in males and only one band in females. This marker provides a practical tool for monosex breeding and aids further research on sex determination in O. bidens.

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 (Opsariichthys bidens), 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 O. bidens, 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 O. bidens, has implications for the monosex culture and molecular breeding of O. bidens, and has significant scientific and practical value.

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