Characterization of rrp44 gene in channel catfish (Ictalurus punctatus): Molecular cloning, tissue distribution, and single nucleotide polymorphisms (SNPs) association analysis with growth traits

• DOI: 10.1016/j.aqrep.2023.101613
• Publication Date: 2023-05-31T01:33:23Z
• Authors: Hongyan Liu; Wenping Zhang; Minghua Wang; Siqi Xu; Liqiang Zhong; Wenji Bian; Shiyong Zhang; Xiaohui Chen
• Keywords: 0303 health sciences; 03 medical and health sciences; Aquaculture. Fisheries. Angling; Rrp44/Dis3; SH1-691; Gene clone; Channel catfish; Growth traits; SNPs

Understanding the genetic basis for variations in growth-associated traits in channel catfish (Ictalurus punctatus) has important implications for the catfish breeding industry. Rrp44/Dis3, an RNase II family protein, is the exosome catalytic subunit. Through GWAS significant marker-trait associations were found between the rrp44 gene and growth traits.In this study, we investigated the rrp44 gene in channel catfish through molecular cloning and genomics methods, to explore its potential role in growth. We obtained the full-length coding sequence (2853 bp) of the rrp44 gene, encoding 951 amino acids. Multiple sequence alignments and synteny comparisons confirmed that rrp44 paralogs were widespread in fish genomes (Atlantic cod, Japanese medaka, southern platyfish, channel catfish, Atlantic salmon and zebrafish. Phylogenetic analyses showed that the phylogenetic tree of fish can be divided into four clades (Siluriformes, Cypriniformes, Salmoniformes and Perciformes). In fish, Pangasianodon hypophthalmus, Silurus meridionalis and Ictalurus punctatus have close kinship, in agreement with their traditional taxonomic status. Quantitative real-time PCR demonstrated that rrp44 had the highest expression in the kidneys, and the lowest expression in the spleen. A target-seq strategy was used to screen and genotype single nucleotide polymorphisms (SNPs) of the rrp44 gene. SNP genotypes and diplotypes of the rrp44 gene and their associations with growth traits were also examined. The results revealed 78 SNPs in the rrp44 gene, of which seven (rs2, rs5, rs6, rs13, rs17, rs19 and rs20) were associated with body weight. The masses of fish with the rs2 CC and rs13 GC genotypes were 6.97 % and 5.49 % higher than the group average mass, respectively. Furthermore, rs20 caused a mutation in the RNB domain of Rrp44 (serine to glutamine substitution), and fish carrying one or two copies of the adenine mutant allele of rs20 had significantly higher body mass than GG individuals (P < 0.005). Furthermore, two haploid combinations were associated with body mass. Our research provides necessary support and new insights to aid in channel catfish molecular marker-assisted breeding.