Objective The Channa argus is an important freshwater economic fish in China. In recent years, due to environmental impacts and breeding methods, the genetic resources have gradually deteriorated. This study aims to investigate the genetic basis of growth traits in C. argus using genome-wide association studies (GWAS) to provide a basis for the conservation of genetic resources and the selection of superior breeds in C. argus.

Methods A total of 405 individuals of C. argus were subjected to reduced-representation genome sequencing using the Illumina Nova (PE150) platform and SuperGBS technology. The GWAS analysis was performed using the efficient mixed model of the EMMAX software to identify SNPs significantly associated with growth traits. Sequences within 50 kb upstream and downstream of the significant loci were scanned to identify potential candidate genes. The biological functions of the candidate genes were annotated based on the NCBI database and literature search results, and candidate functional genes related to the target traits were screened.

Results After filtering the sequencing data, a total of 47 536 SNP loci were obtained. GWAS analysis identified three SNPs significantly associated with body mass traits: 2831060, 2830864, and 2830886. By scanning sequences within 50 kb upstream and downstream of the significant loci, seven candidate functional genes related to body mass in C. argus were annotated. In addition, six potential SNPs associated with total length traits were identified, and 17 potential candidate functional genes related to total length traits were annotated. Among these functional genes, seven were associated with both total length and body mass traits, namely irak3, tuba1a, hspa14, prl, rint1, helb and net1. These functional genes are mainly involved in biological processes such as growth metabolism, developmental regulation, cell proliferation, and immune regulation in C. argus.

Conclusion The identified SNPs and functional genes are significantly associated with body mass and total length traits in C. argus, providing important references for the mechanism analysis of growth traits, superior breed selection, and resource conservation in C. argus.