Identification of sex determination region and candidate genes in blotched snakehead (Channa maculata) through genome-wide association studies and transcriptome analysis

The blotched snakehead (Channa maculata) is an economically significant freshwater species in China, exhibiting pronounced sexual size dimorphism, with males displaying faster growth rates and larger body sizes. Monosex farming has the potential to significantly substantially enhance aquaculture efficiency for this species. In this study, we conducted whole-genome resequencing of 45 female and 50 male blotched snakehead individuals. Genome-wide association analysis (GWAS) was performed based on genome-wide SNPs and InDels, and combined with fixation index (Fst) analysis between male and female groups, which identified a candidate sex-determining region located on Chr.02: 34,288,075–34,351,554 (63.479 kb). Linkage disequilibrium analysis revealed that the sex-determining region has formed a haplotype block with a state of linkage disequilibrium. Within this region, we identified six InDels larger than 15 bp and developed two sex-specific markers capable of accurately identifying the genetic sex of blotched snakehead. Additionally, we performed transcriptome analyses of male and female gonads at 120, 150, and 180 days post-fertilization (dpf). Combined with the GWAS results, we identified candidate sex-determining genes, including five male-biased genes (EVM0022796, ITGB1BP1, RSAD2, CMPK2, and KIDINS220) and two female-biased genes (Sox11 and DNAJC30). This study enhances our understanding of the genetic basis of sex determination in blotched snakehead, providing novel insights into its genetic mechanisms. Our findings establish a solid scientific foundation for applications in monosex breeding and marker-assisted selection breeding programs in this species.