Structural Variation Analysis in the samd3/elf3 Intergenic Region of the Barred knifejaw (Oplegnathus fasciatus) and the Development of Molecular Marker for Efficient Sex Identification

Abstract

The fish species Oplegnathus fasciatus exhibits an X₁X₁X₂X₂/X₁X₂Y sex determination mechanism. This species holds considerable economic value and displays pronounced sexual dimorphism in growth. Therefore, the development of a rapid and accurate method for sex identification is critical to enhancing breeding efficiency and maximizing production value. Using third-generation PacBio whole-genome sequencing, we identified a homologous region in the samd3/elf3 intergenic region of the X and Y chromosomes of O. fasciatus. Analysis of the whole-genome sequence revealed a large DNA insertion marker fragment within this region. Using specifically designed primers, two bands of 390 bp and 1008 bp were successfully amplified in males, whereas only a single 390 bp band was detected in females. This marker can be easily distinguished by agarose gel electrophoresis, greatly enhancing the efficiency and accuracy of sex identification. This study not only expands the molecular marker system for sex identification of O. fasciatus but also offers a valuable methodological reference for sex identification in other economically important fish species. These findings have significant implications for germplasm improvement and efficient selection in aquaculture.