A Genome-Wide Association Study Identifies Candidate SNPs and Genes Associated with Body Weight in the Northern...

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 be needed before routine application.