UNDERSTANDING THE EFFECTS OF STRAIN SELECTION AND HYBRIDIZATION OF CHANNEL CATFISH Ictalurus punctatus ON ENVIRONMENTAL GENE RESPONSE  

The United States catfish industry has long used selective breeding of channel catfish (Ictalurus punctatus) and hybridization to increase production yield. Many of these strains have been developed over the past 50 years to provide improved growth rate, disease resistance, increased feed conversion efficiency, and greater dress-out percentage. Additionally, the hybridization of I. punctatus with blue catfish (I. furcatus) has led to faster growth, easier harvest, more uniform size, and greater tolerance of low oxygen levels in crowded ponds. Increasing temperatures of aquaculture ponds with climate change is a growing concern for the Southeastern US catfish industry. To better understand how strain selection and hybridization of channel catfish can help the industry adjust to environmental pressures, we examined differential expression (DE) of gene transcripts from liver samples collected from two geographically distinct channel catfish strains and one hybrid catfish strain under simulated natural thermal regimes. To simulate normal daily pond fluctuations, we put fish of each group in two different treatments. The first, an ideal temperature range for optimal growth at 27-31°C, and the second at the upper range of acceptable growth temperatures of 32-36°C. These fish were kept in these treatments for six-weeks at the end of which survival and growth data were collected in addition to tissue samples. We mapped three biological replicates of each temperature treatment for all three catfish types (n=18) to the channel catfish genome using Tophat2 and estimated gene expression with HTSeq from the alignments. We removed genes with no expression from analysis and used EdgeR to find differentially expressed genes. We used GAGE to find significant gene ontology (GO) gene-sets and then used GO to examine the biological processes, cellular components, and molecular function of each fish group. Principle component analysis of mRNA libraries showed clear differences between hybrids and both strains of channel catfish at the 32-36°C temperature treatment. Southern channel catfish had greater amounts of up- and down-regulated DE transcripts than northern channel catfish. Hybrid catfish had lower amounts of up- and down-regulated DE transcripts compared to channel catfish of the same strain. Implications from our study may be beneficial for understanding how selection of catfish types can aid the industry in the face of climate change.