Cyprinids are the most highly produced group of fishes globally, with common carp being one of the most valuable species of the group. Koi herpesvirus (KHV) infections can result in high levels of mortality, causing major economic losses, and is listed as a notifiable disease by the World Organization for Animal Health. Selective breeding for host resistance has the potential to reduce morbidity and losses due to KHV. Therefore, improving knowledge about host resistance and methods of incorporating genomic data into breeding for resistance may contribute to a decrease in economic losses in carp farming. In the current study, a population of 1,425 carp juveniles, originating from a factorial cross between 40 sires and 20 dams was challenged with KHV. Mortalities and survivors were recorded and sampled for genotyping by sequencing using Restriction Site-Associated DNA sequencing (RADseq). Genome-wide association analyses were performed to investigate the genetic architecture of resistance to KHV. A genome-wide significant QTL affecting resistance to KHV was identified on linkage group 44, explaining approximately 7% of the additive genetic variance. Pooled whole genome resequencing of a subset of resistant (n = 60) and susceptible animals (n = 60) was performed to characterize QTL regions, including identification of putative candidate genes and functional annotation of associated polymorphisms. The TRIM25 gene was identified as a promising positional and functional candidate within the QTL region of LG 44, and a putative premature stop mutation in this gene was discovered.

The Roslin Institute Royal School of Veterinary Studies University of Edinburgh Easter Bush Midlothian EH25 9RG Scotland United Kingdom

The Roslin Institute Royal School of Veterinary Studies University of Edinburgh Easter Bush Midlothian EH25 9RG Scotland United Kingdom Department of Animal Breeding and Genetics Swedish University of Agricultural Sciences Box 7090 750 07 Uppsala Sweden

University of South Bohemia in Ceske Budejovice Faculty of Fisheries and Protection of Waters South Bohemian Research Centre of Aquaculture and Biodiversity of Hydrocenoses Zatisi 728 2 389 25 Vodnany Czech Republic

Veterinary Research Institute Hudcova 70 Brno 62100 Czech Republic

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