Genetic mapping of Koi herpesvirus resistance (KHVR) in Mirror carp (Cyprinus carpio) revealed genes and molecular mechanisms of disease resistance

Koi herpesvirus is a double-stranded DNA virus that causes fatal disease and mortality in koi and common carp (Cyprinus carpio) of all ages. Koi herpesvirus disease has been added to the list of notifiable diseases of the World Organisation for Animal Health. The genetic basis of fish resistance to Koi herpesvirus remains little understood, and thus, it cannot be used in genetic breeding programs to produce high-resistance carp strains. Dissection of the molecular mechanism of resistance could help prevent or reduce losses due to Koi herpesvirus disease. Common carp is a widely distributed species cultured all around the world. Its allotetraploidy and high economic and environmental value have attracted a great deal of interest in its genetics and genomics. Here, we use both QTL mapping and GWAS in Mirror carp subjected to Koi herpesvirus infection to detect potential loci and genes related to resistance to this virus. Many immune-related genes were identified around the significant QTLs or SNPs, including tnfa, hif1a, galectin-8, rootletin, and palladin. GO and KEGG analyses were performed based on the union of the candidates. Of particular interest were the Herpes simplex infection pathway and mTOR signaling pathway, which play potential roles in the immune response. Using publicly available transcriptome data from Koi herpesvirus infected carp, the expression patterns of candidate genes were obtained, and the results indicated potential roles of homoeolog functional divergence in immune response in the allotetraploid common carp. Overall, our study of the genetic architecture of carp Koi herpesvirus resistance provides many valuable candidate genes, which could be considered in the marker-assisted selection of common carp strains with high resistance to Koi herpesvirus.