GWAS Analyses in Catfish Reveal the Functional Hubs of Related Genes within Major QTLs for Columnaris Disease Resistance

Catfish is the primary aquaculture species in the United States. Its production is threatened by serious disease problems. Columnaris disease is considered as the second most important disease affecting the catfish industry, but little is known about the genetic basis for columnaris resistance in catfish. In this study, we performed GWAS analyses using the catfish 250k SNP array with backcross progenies derived from crossing female channel catfish (Ictalurus punctatus) with male F1 hybrid catfish (female channel catfish I. punctatus × male blue catfish I. furcatus). A genomic region on chromosome 7 was found to be significantly associated with columnaris resistance. The resistant genotypes were homozygous with both alleles derived from channel catfish. The disease resistance QTL was narrowed down to a region of approximately 620 Kb. Within this region, 10 genes were identified, of which five have known functions in immunity including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, three additional suggestively associated QTL regions were identified on chromosomes 7, 12, and 14. Strikingly, the candidate genes may be arranged as functional hubs; the candidate genes within the four major QTLs are not only co-localized, but also functionally related with the PI3K signal transduction pathway that is known to be required by many bacteria for efficient entry into the host, suggesting its importance for columnaris resistance. These findings suggest that the candidate genes are arranged in “functional hubs” that may work in a coordinated fashion.