Genomic and transcriptomic analysis of genes involved in disease resistance against enteric septicemia of catfish (ESC) in catfish

Abstract

Catfish is the leading aquaculture species in the United States, accounting for over 50% of all U.S. aquaculture production. In recent years, catfish industry has been facing numerous challenges, including increased costs of feed and fuel, international competition, and infectious diseases. Among infectious diseases, enteric septicemia of catfish (ESC), caused by the bacterium Edwardsiella ictaluri, resulted in the most significant losses. Sustainable and effective prevention/control strategies of ESC have been elusive, and improved understanding of the underlying molecular mechanism could help develop broodstocks with enhanced ESC resistance. For the first part of my dissertation work, I conducted a genome-wide association study (GWAS) to map quantitative trait loci (QTL) for ESC disease resistance using the first-generation backcrosses. Channel catfish and blue catfish exhibit great contrast in ESC resistance, with channel catfish being highly susceptible and blue catfish being very resistant. The interspecific backcrosses provide an ideal system for the identification of QTL, because both disease resistance gene and trait are segregating in this population. Two significant QTL on LG1 and LG23 were identified as revealed by a mixed linear model and family-based association test. Examination of the resistance alleles indicated their origin from blue catfish. The significantly associated markers should be useful for marker-assisted introgression to develop catfish breeds with ESC resistance. Candidate genes were also investigated, suggesting the importance of involved pathways of phagocytosis and T-cell activation in ESC resistance. The second part of my dissertation work focused on post-transcriptional regulation of the transcriptome, specifically the regulation of alternative splicing (AS) after infection with E. ictaluri. AS can generate more than one transcript from a single pre-mRNA in eukaryotes, playing crucial roles in gene regulation. My questions were if E. ictaluri infection affected alternative splicing, and if so, what genes were affected? What was the mode of alternative splicing catfish adopted to cope with E. ictaluri infection? I utilized genomic information and RNA-Seq datasets to characterize AS profiles and their induced changes after bacterial infection with E. ictaluri in channel catfish. A total of 27,476 AS events from 9,694 genes were identified in channel catfish. AS was observed to be greatly induced by E. ictaluri infection. Intriguingly, genes involved in RNA binding and RNA splicing themselves were significantly enriched in differentially alternatively spliced (DAS) genes after infection. These results will help in understanding the molecular mechanisms underlying ESC resistance and host responses to E. ictaluri in catfish.