A genome-wide association study in catfish reveals the presence of functional hubs of related genes within QTLs for columnaris disease resistance

Abstract

BackgroundColumnaris causes severe mortalities among many different wild and cultured freshwater fish species, but understanding of host resistance is lacking. Catfish, the primary aquaculture species in the United States, serves as a great model for the analysis of host resistance against columnaris disease. Channel catfish in general is highly resistant to the disease while blue catfish is highly susceptible. F2 generation of hybrids can be produced where phenotypes and genotypes are segregating, providing a useful system for QTL analysis. To identify genes associated with columnaris resistance, we performed a genome-wide association study (GWAS) using the catfish 250 K SNP array with 340 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).ResultsA genomic region on linkage group 7 was found to be significantly associated with columnaris resistance. Within this region, five have known functions in immunity, including pik3r3b, cyld-like, adcyap1r1, adcyap1r1-like, and mast2. In addition, 3 additional suggestively associated QTL regions were identified on linkage groups 7, 12, and 14. The resistant genotypes on the QTLs of linkage groups 7 and 12 were found to be homozygous with both alleles being derived from channel catfish. The paralogs of the candidate genes in the suggestively associated QTL of linkage group 12 were found on the QTLs of linkage group 7. Many candidate genes on the four associated regions are involved in PI3K pathway that is known to be required by many bacteria for efficient entry into the host.ConclusionThe 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.

Genome-Wide Association Study for Identifying Loci that Affect Fillet Yield, Carcass, and Body Weight Traits in Rainbow Trout (Oncorhynchus mykiss)

“…Several genome-wide association studies (GWAS) that match genetic variants, with or without pedigree records, with the observed phenotype have identified significant loci associated with economically important traits in livestock (Kadarmideen, 2014; Sharma et al, 2015). The aquaculture research community is following this trend, and interesting examples are available for growth and disease resistance traits in Atlantic Salmon (e.g., Correa et al, 2015; Gutierrez et al, 2015), rainbow trout (e.g., Kocmarek et al, 2015; Liu et al, 2015b; Palti et al, 2015b), and catfish (e.g., Geng et al, 2015). …”

Development of a 690 K SNP array in catfish and its application for genetic mapping and validation of the reference genome sequence

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Development of a goosegrass (Eleusine indica) draft genome and application to weed science research

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