Understanding the genetic architecture underlying growth variation is central to improving aquaculture species through genomic selection. Here, we performed a genome-wide association study (GWAS) on 303 individuals from a G2 breeding population of channel catfish (Ictalurus punctatus) using whole-genome resequencing data. After stringent quality control, 5.64 million high-confidence single nucleotide polymorphisms (SNPs) were retained for association analyses of two key growth traits—monthly weight gain (MWG) and body depth (BH). We identified 15 and 28 loci significantly associated with MWG and BH, respectively, with the majority concentrated on chromosome 20. Two SNPs (Chr20:14,657,971 and Chr20:14,658,012) located in exon 9 of the rrp44 gene were significantly associated with both traits. Functional annotation and enrichment analyses revealed that the rrp44 gene, encoding an exoribonuclease subunit of the RNA exosome complex, participates in mitotic spindle regulation and post-transcriptional RNA decay, processes critical for cellular growth and metabolic homeostasis. We propose that rrp44 may influence growth through the modulation of feeding rhythm and circadian regulation, providing a potential molecular basis for growth heterogeneity in channel catfish. These findings enrich our understanding of growth-related genomic variation and offer valuable molecular markers for precision breeding and genetic improvement of catfish.
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