A Genome-Wide Association Study Identifies Candidate SNPs and Genes Associated with Body Weight in the Northern Snakehead (Channa argus) Using a 50K SNP Array

Body weight is the principal economic trait in snakehead aquaculture, yet the genetic architecture of growth in the northern snakehead (Channa argus) remains largely unexplored. We performed a genome-wide association study (GWAS) for body weight in 205 cultured C. argus genotyped with a 50K SNP array. After quality control, 47,123 autosomal SNPs were tested under a univariate linear mixed model in GEMMA that accounted for genomic relatedness. One SNP on chromosome 7 (Chr07:1,329,732) exceeded the Bonferroni genome-wide threshold, and 14 SNPs reached a suggestive threshold, forming two candidate clusters on Chr07 and Chr24. Annotating candidate intervals (±100 kb) against the C. argus genome assembly yielded 93 candidate genes. Hypergeometric enrichment identified 44 Gene Ontology (GO) terms and 4 KEGG pathways, dominated by endolysosomal lumen, serine-type endopeptidase activity, collagen/extracellular-matrix catabolism, bone resorption, and the apoptosis, lysosome, Phagocytosis and antigen-processing pathways. The single genome-wide significant SNP fell in an intron of a collagen alpha-1(II) chain gene (COL2A1/zgc:113232), consistent with the collagen/extracellular-matrix enrichment signal; other plausible growth-related candidates included CTSS, S100A4, PYGM, DLAT, MSX2 and ZNRF3. The functional signal was largely driven by a tandem protease/cathepsin gene cluster on Chr07, indicating a regional rather than a genome-wide pathway effect. The lead SNP genotype was associated with a ~240 g (≈30%) difference in body weight, and this effect was reproduced in an independent cohort of 200 fish. These findings provide the first GWAS-based candidate loci for body weight in C. argus and a promising marker for future marker-assisted breeding, though validation to date is limited to a single additional cohort from the same broodstock source; broader multi-population testing will need needed before routine application.