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.

Genomic selection (GS) is increasingly applied in breeding programs of major aquaculture species, enabling improved prediction accuracy and genetic gain compared to pedigree-based approaches. Koi Herpesvirus disease (KHVD) is notifiable by the World Organization for Animal Health and the European Union, causing major economic losses to carp production. GS has potential to breed carp with improved resistance to KHVD, thereby contributing to disease control. In the current study, Restriction-site Associated DNA sequencing (RAD-seq) was applied on a population of 1,425 common carp juveniles which had been challenged with Koi herpes virus, followed by sampling of survivors and mortalities. GS was tested on a wide range of scenarios by varying both SNP densities and the genetic relationships between training and validation sets. The accuracy of correctly identifying KHVD resistant animals using GS was between 8 and 18% higher than pedigree best linear unbiased predictor (pBLUP) depending on the tested scenario. Furthermore, minor decreases in prediction accuracy were observed with decreased SNP density. However, the genetic relationship between the training and validation sets was a key factor in the efficacy of genomic prediction of KHVD resistance in carp, with substantially lower prediction accuracy when the relationships between the training and validation sets did not contain close relatives.

Significant mortalities associated with emerging viral diseases are challenging the economy of common carp aquaculture. As such, there is an increased need to disentangle how infected fish cope with progressive disease pathology and lose the ability for homeostatic maintenance of key physiological parameters. A natural carp edema virus (CEV) infection outbreak at a carp fish farm provided an opportunity to examine diseased and healthy carp in the same storage pond, thereby contributing to our better understanding of CEV disease pathophysiology. The disease status of fish was determined using PCR-based virus identification combined with analysis of gill pathology. Compared with healthy control carp, the blood chemistry profile of CEV-infected fish revealed major disruptions in electrolyte and acid-base balance (i.e., hyponatraemia, hypochloraemia, hyperphosphatemia, elevated pH, base excess, and anion gap and decreased partial dissolved carbon dioxide). In addition, we recorded hyperproteinaemia, hyperalbuminaemia, hypotonic dehydration, endogenous hyperammonaemia, and decreased lactate along with increased creatinine, alkaline phosphatase, alanine aminotransferase, and aspartate aminotransferase. Red blood cell associated hematology variables were also elevated. The multivariate pattern of responses for blood chemistry variables (driven by sodium, pH, partial dissolved carbon dioxide, ammonia, and albumin in the principal component analysis) clearly discriminated between CEV-infected and control carp. To conclude, we show that CEV infection in carp exerts complex adverse effects and results in severe metabolic disturbance due to the impaired gill respiratory and excretory functioning.

This work describes the first confirmed cases of carp oedema virus disease (CEVD) in Slovakia and the Czech Republic and the phylogenetic analysis of Czech and Slovak carp oedema virus (CEV) isolates. Four cases of disease outbreak in the Czech Republic are described, the oldest dating from mid‐May 2013 and one case from Slovakia dating from May 2019. In all cases, virus presence was confirmed using nested PCR. PCR products were sequenced and compared with 357‐bp nucleotide sequences encoding the CEV P4a protein in GenBank. In four cases of disease outbreak (three common carp breeding facilities and one koi garden pond), CEV detected belonged to genogroup I. In one case (koi garden pond), fish were confirmed as infected with CEV from genogroup II. This work complements data on CEV occurrence in European countries and contributes to a better understanding of the pathways leading to transmission of the virus throughout Europe.

Common carp (Cyprinus carpio) is one of the most economically valuable freshwater fish worldwide. The majority of global production of common carp is destined for human consumption, but members of its ornamental variety, koi carp, are also raised for decorative purposes. According to annual statistics of FAO (Food and Agriculture Organization of the United Nations), fishery and aquaculture production of common carp accounted for more than 7.5% of the global freshwater fish production in 2018. More specifically, more than 4.3 million tons of carp were caught or bred in 2018 with a steady yearly increase (FAO, 2020). The importance of common carp is even greater in Europe, where it accounted for over 30% of the freshwater fish production in 2018 (FAO, 2020). Historically, chronicles depict domestication of common carp in China centuries before domestication in Europe, but it is possible that the domestication occurred independently in both places (Balon, 1995; Vilizzi, 2012). Viral diseases are one of the most relevant causes of a decrease in aquaculture production, either through significant reduction of their growth rate or by direct mortalities of the host fish. Among numerous carp viral diseases, three diseases seem to be most important as they cause extensive damage to carp aquaculture. Carp edema virus (CEV) together with cyprinid herpesvirus 3 (koi herpesvirus, CyHV-3, KHV) and carp sprivivirus (spring viraemia of carp virus, SVCV) are infectious viruses causing disease and major losses in common carp populations and carp varieties around the world. Out of these three, only SVCV affects a broad number of the Cyprinidae family members, causing spring viraemia of carp (SVC) (Hoole et al., 2001).

13Genomic selection (GS) is increasingly applied in breeding programmes of major aquaculture 14 species, enabling improved prediction accuracy and genetic gain compared to pedigree-based 15 approaches. Koi Herpesvirus disease (KHVD) is notifiable by the World Organisation for 16Animal Health and the European Union, causing major economic losses to carp production. 17Genomic selection has potential to breed carp with improved resistance to KHVD, thereby 18 contributing to disease control. In the current study, Restriction-site Associated DNA 19 sequencing (RAD-seq) was applied on a population of 1,425 common carp juveniles which 20 had been challenged with Koi herpes virus, followed by sampling of survivors and mortalities. 21Genomic selection (GS) was tested on a wide range of scenarios by varying both SNP densities 22 lower prediction accuracy when the relationships between the training and validation sets did 29 not contain close relatives. 30 31

Koi herpesvirus disease (KHVD) is currently the most serious threat to global carp farming. Prevention is a sensible strategy for tackling this disease and improved genetic resistance of carp strains is a desirable breeding goal. To study the potential for multitrait selection, the objective of the current study was to estimate the genetic correlations between KHVD resistance and production traits in Amur mirror carp. A total of 1500 fingerlings from four factorial crosses of five dams and ten sires were challenged with Koi herpesvirus (KHV). Juvenile growth-related traits were collected on the same individuals before the challenge test. Production traits were measured on siblings of the challenged population at different life stages (yearling to market size). The estimated heritability for resistance to KHVD was 0.43 ± 0.08 on the observed scale and 0.72 ± 0.13 on the underlying liability scale. Most genetic correlations between KHVD resistance and important production traits were insignificant, showing that selection for improved production traits would not increase susceptibility to KHV and vice versa. However, resistance to KHVD was negatively correlated with Fulton's condition factor (FC) after the second overwintering and relative head length (RHL), relative body height (RBH) and relative body width (RBW) from the second growing season to the market size, with a more prolonged body shape of Amur mirror carp (genes from Amur wild Please note that this is an author-produced PDF of an article accepted for publication following peer review. The definitive publisher-authenticated version is available on the publisher Web site.scaly carp, Cyprinus rubrofuscus) being associated with higher KHVD resistance. Intermediate favorable genetic correlations between KHVD resistance and log-log residuals of headless carcass yield (0.37 ± 0.14) and fillet yield (0.44 ± 0.13) at market size suggested that selection for improved yields of edible body parts might indirectly lead to a slight improvement in KHVD resistance and vice versa. Highlights► Heritability for Koi herpesvirus disease (KHVD) resistance was high. ► Most genetic correlations between KHVD resistance and important production traits were insignificant. ► KHVD resistance was significantly genetically correlated to body shape traits and slaughter yields.

The population of brown trout (Salmo trutta fario) in continental Europe is on the decline, with infectious diseases confirmed as one of the causative factors. However, no data on the epizootiological situation of wild fish in the Czech Republic are currently available. In this study, brown trout (n = 260) from eight rivers were examined for the presence of viral and parasitical pathogens. Salmonid alphavirus-2, infectious pancreatic necrosis virus, piscine novirhabdovirus (VHSV) and salmonid novirhabdovirus (IHNV) were not detected using PCR. Cell culturing showed no viruses as well, and serological analysis of 110 sera did not detect any specific antibodies against VHSV or IHNV. Fish from two rivers were positive for the presence of piscine orthoreovirus-3 (PRV-3), subtype PRV-3b. However, none of the PRV-3-positive fish showed gross pathologies typically associated with PRV infections. By far the most widespread pathogen was Tetracapsuloides bryosalmonae which was confirmed in each of the examined locations, with a prevalence of up to 65% and 100%, as established by immunohistochemistry and PCR, respectively. Furthermore, up to 43.8% of fish showed signs of proliferative kidney disease caused by T. bryosalmonae, suggesting that this parasite is a main health challenge for brown trout in the Czech Republic.