Comparative study of candidate sex determination regions in snakeheads (Channa argus and C. maculata) and development of novel sex markers

Belonging to the Channidae family, Channa argus and C. maculata are the main cultured snakehead species in China and have important economic value. Both species show distinct sexual dimorphism in growth, with males growing much faster than females. Therefore, the production of all males will majorly improve the efficiency of aquaculture. However, the sex-determination (SD) mechanism of snakeheads remains unclear. Herein, we used whole-genome resequencing data of C. maculata and C. argus to analyse sex-linked genomic regions in these two species. By using GWAS and Pool-seq analysis methods, their potential SD regions were refined to fewer than 200 kb, containing two protein-coding genes (rnf144a and id2) without known sex-related function. The gene content on the sex chromosomes of the two snakehead species was basically consistent, and gonadal transcriptome analysis results showed that the mRNA expression level of id2 in the testis was significantly lower than that in the ovary in both species, whereas rnf144a showed inconsistent expression trends in the two species. Moreover, we assembled the male reference genomes and identified a 4–5 kb male-specific noncoding fragment for both species, allowing us to design universal sex-specific markers for C. argus, C. maculata, and their hybrids (C. maculata ♀ × C. argus ♂). Our findings will facilitate the understanding of the molecular basis of the SD mechanism in snakeheads, and further promote their all-male breeding progress in the industry.