This Is AuburnElectronic Theses and Dissertations

Genome-wide association studies for columnaris resistance and morphology in hybrid catfish




Geng, Xin

Type of Degree



Fisheries and Allied Aquacultures


Catfish is the primary aquaculture species in the United States. Recently, the catfish industry in the USA has encountered unprecedented challenges due to increasing feed and energy costs, devastating diseases, and severe international competition. Therefore, prominent brood stocks should be developed with superior performance to profit aquaculture industry in the USA. However, little information is known about the genetic architecture controlling economically important traits, which hinders marker-assisted selection. In this project, we studied QTLs for two economically important traits. The first trait is columnaris disease resistance. Columnaris causes severe mortalities among many different wild and cultured freshwater fish species, and it is one of the major diseases threatening catfish production. The second trait is head size (head length, head width, and head depth). Skull morphology is fundamental to evolution and biological adaptation of species to its environments. With aquaculture fish species, head size is also important for economic reasons, because it has a direct impact on fillet yield. To identify genes associated with these economically important traits, columnaris resistance and head size, genome-wide association studies (GWAS) was performed 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). Backcross hybrid catfish serves as a great model for the QTL analysis, because backcross hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. The GWAS revealed four QTLs associated with columnaris resistance in catfish. Strikingly, the candidate genes may be arranged as functional hubs. The candidate genes within the associated QTLs on linkage groups 7 and 12 are not only co-localized, but also functionally related, with many of them being involved in the PI3K signal transduction pathway, suggesting its importance for columnaris resistance. Head size QTLs were mapped in catfish to genomic regions rich in genes involved in the small GTPase pathway on nine linkage groups. Comparative analysis revealed the conserved function of small GTPase pathway in controlling skull morphometric traits in different species.