Candidate genes for ESC Disease Resistance of Catfish as Revealed by a Genome Wide Association Study

Enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the leading disease problem for the catfish industry. It causes tens of millions of dollars of economic losses each year. Channel catfish (Ictalurus punctatus) is generally susceptible to the disease while blue catfish (Ictalurus furcatus) is generally resistant. Therefore, the hybrid catfish is a great model system to study ESC resistance because of the strong phenotypic contrast between channel catfish and blue catfish. In this study, 499 individuals of the fourth generation of backcross progenies of hybrid catfish were used to conduct genome wide association study (GWAS) for ESC resistance. A genomic region on linkage group 1 was found significantly associated with ESC disease resistance. Within this region, 14 genes have known functions in immunity, including wwp1,inhba, fzd8, klf6, nck1, agtr1, racgap1, nlrp12, trpc1, acbd5a, apbb1ip, myo3a, stat2, nlrc3. Among the 14 genes, 8 genes or their paralogs were found differently expressed between ESC resistance and sensitive catfish by RNA-seq analysis of previous study. The genes within the significant QTL on LG1 were known to be related to immune functions, such as phagocytosis, defense response, stimulus response, T cell differentiation, B cell differentiation, macrophage development, antigen processing and presentation. In addition to the significant QTL, two suggestively associated QTL regions were identified on linkage group 12 and 16. It appears that the identified QTLs are limited to specific families of F4 fish, consistent with the segregation of the genomic regions derived from the original blue catfish parent.