Genomic selection for survival under naturally occurring Saprolegnia oomycete infection in farmed European whitefish Coregonus lavaretus.

Saprolegnia oomycete infection causes serious economic losses and reduces fish health in aquaculture. Genomic selection based on thousands of DNA markers is a powerful tool to improve fish traits in selective breeding programs. Our goal was to develop a single nucleotide polymorphism (SNP) marker panel and to test its use in genomic selection for improved survival against Saprolegnia infection in European whitefish Coregonus lavaretus, the second most important farmed fish species in Finland. We used a double digest restriction site associated DNA (ddRAD) genotyping by sequencing method to produce a SNP panel, and we tested it analyzing data from a cohort of 1,335 fish, which were measured at different times for mortality to Saprolegnia oomycete infection and weight traits. We calculated the genetic relationship matrix (GRM) from the genome-wide genetic data, integrating it in multivariate mixed models used for the estimation of variance components and genomic breeding values (GEBVs), and to carry out Genome-Wide Association Studies for the presence of quantitative trait loci (QTL) affecting the phenotypes in analysis. We identified one major QTL on chromosome 6 affecting mortality to Saprolegnia infection, explaining 7.7% to 51.3% of genetic variance, and a QTL for weight on chromosome 4, explaining 1.8% to 5.4% of genetic variance. Heritability for mortality was 0.20 to 0.43 on the liability scale, and heritability for weight was 0.44 to 0.53. The QTL for mortality showed an additive allelic effect. We tested whether integrating the QTL for mortality as a fixed factor, together with a new GRM calculated excluding the QTL from the genetic data, would improve the accuracy estimation of GEBVs. This test was done through a cross-validation approach, which indicated that the inclusion of the QTL increased the mean accuracy of the GEBVs by 0.28 points, from 0.33 to 0.61, relative to the use of full GRM only. The area under the curve of the receiver-operator curve for mortality increased from 0.58 to 0.67 when the QTL was included in the model. The inclusion of the QTL as a fixed effect in the model increased the correlation between the GEBVs of early mortality with the late mortality, compared to a model that did not include the QTL. These results validate the usability of the produced SNP panel for genomic selection in European whitefish and highlight the opportunity for modeling QTLs in genomic evaluation of mortality due to Saprolegnia infection.

Saprolegnia infection causes serious economic losses and reduces fish health in aquaculture. We created a novel set of genetic markers to use in the selective breeding of European whitefish to reduce mortality due to the fungus. Using genetic markers, we estimated how much different fish traits are determined by genetic variation, and thus what potential traits have to be selected. We observed that resistance to infection was controlled by both a genetic variant with a major effect on mortality and by many other variants with a small effect distributed across the genome. We tested whether we could increase the precision of genomic breeding values used in the selective breeding by explicitly adding the major genetic variant to the analysis, and we observed an increase in precision in our results. We conclude that directly including information about the major genetic variant increases the precision of our predictions, rather than assuming that all genetic variants each explain a small amount of the genetic variation.

Improvement in feed efficiency and reduction in nutrient loading from rainbow trout farms: the role of selective breeding.

Resource efficiency, the ratio of inputs to outputs, is essential for both the economic and environmental performance of any sector of food production. This study quantified the advancement in the feed conversion ratio (FCR) and reduction in nutrient loading from rainbow trout farming in Finland and the degree to which genetic improvements made by a national breeding program have contributed to this advancement. The study combined two datasets. One included annual records on farm-level performance of commercial rainbow trout farms from 1980 onwards, and the other included individuals across eight generations of the national breeding program. The data from the commercial farms showed that from 1980 onwards, the farm-level feed conversion ratio improved by 53.4%, and the specific nitrogen and phosphorus loading from the farms decreased by over 70%. Hence, to produce 1 kg of fish today, only half of the feed is needed compared to the 1980s. The first generation of the breeding program was established in 1992. The FCR was not directly selected for, and hence, the genetic improvement in the FCR is a correlated genetic change in response to the selection for growth and body composition. Since 1992, the estimated genetic improvement in the FCR has been 1.74% per generation, resulting in a cumulative genetic improvement of 11.6% in eight generations. Genetic improvement in the FCR is estimated to be 32.6% of the total improvement in the FCR observed at farms, implying that genetic improvement is a significant contributor to resource efficiency. The use of genetically improved rainbow trout, instead of the base population of fish, reduces feed costs by 18.3% and total production costs by 7.8% at commercial farms (by -0.266€ per kg of ungutted fish). For phosphorus and nitrogen, it can be assumed that the use of fish material with an improved FCR also leads to 18.3% less nitrogen and phosphorus flowing into an aquatic environment. Such improvements in resource efficiency are win-wins for both industry and the environment-the same amount of seafood can be produced with significantly reduced amounts of raw materials and reduced environmental impact.

Resource efficiency, the ratio of inputs to outputs, is essential for both the economic and environmental performance of aquaculture. The data from commercial rainbow trout farms showed that from 1980 onwards, the farm-level feed conversion ratio (FCR) improved by 53.4%, and the specific nitrogen and phosphorus loading from the farms decreased by over 70%. Hence, to produce 1 kg of fish today, only half of the feed is needed compared to the 1980s. Selective breeding is a major contributor to this improvement, and it has resulted in an estimated genetic gain of 1.74% per generation in the FCR. The use of genetically improved rainbow trout, instead of a base population of fish, reduces feed costs and nutrient loading by 18.3% and total production costs by 7.8% at commercial farms. Such improvements in resource efficiency are win­wins for both industry and the environment­the same amount of seafood can be produced with significantly reduced amounts of raw materials and reduced environmental impact.

Susceptibility of rainbow trout to three different genogroups of infectious pancreatic necrosis virus.

Infectious pancreatic necrosis (IPN) is a globally distributed viral disease that is highly prevalent in rainbow trout Oncorhynchus mykiss farms in Finland. Seven genogroups (1-7) of infectious pancreatic necrosis virus (IPNV) exist, of which genogroup 5 (serotype Sp) is generally considered to be the most virulent in European salmonid farming. In Finland, 3 genogroups (2, 5 and 6) have been detected. Genogroup 2 is the most widespread and to date is the only genogroup associated with clinical disease in field observations. A bath challenge model infection trial was conducted to investigate the potential pathogenicity of the existing Finnish IPNV genogroups on IPNV-negative rainbow trout fry. Three Finnish IPNV isolates, a positive control (a Norwegian genogroup 5 isolate previously associated with high virulence in Atlantic salmon Salmo salar) and a negative control were used, and mortality was recorded daily for 8 wk. The Finnish IPNV genogroup 5 isolate caused the highest cumulative mortality, and the genogroup 2 isolate also caused elevated mortalities. The genogroup 6 isolate caused only low mortality, and the positive control treatment showed negligible mortality. Fish exposed to the Finnish genogroup 2 and 5 isolates had IPN-associated lesions, while no lesions were noted in the other treatment groups. These results indicate that Finnish IPNV genogroup 5 is potentially the most virulent IPNV genogroup for Finnish rainbow trout. Interestingly, the Norwegian IPNV genogroup 5 isolate caused only a subclinical IPN infection, providing further evidence for a host species-dependent, virus isolate-related difference in virulence in IPNV genogroup 5. The results also support the continuation of legislative disease control of IPNV genogroup 5 in Finnish inland waters.

Thermal sensitivity of growth indicates heritable variation in 1-year-old rainbow trout (Oncorhynchus mykiss).

BACKGROUND: Rainbow trout is an important aquaculture species, which has a worldwide distribution across various production environments. The diverse locations of trout farms involve remarkable variation in environmental factors such as water temperature, which is of major importance for the performance of fish. Thus, robust fish that could thrive under different and suboptimal thermal conditions is a desirable goal for trout breeding. Using a split-family experimental design (40 full-/half-sib groups) for a rainbow trout population derived from the Finnish national breeding program, we studied how two different rearing temperatures (14 and 20 °C) affect feed intake, growth rate and feed conversion ratio in 1-year-old fish. Furthermore, we quantified the additive genetic (co-)variation for daily growth coefficient (DGC) and its thermal sensitivity (TS), defined as the slope of the growth reaction norm between the two temperatures. RESULTS: The fish showed consistently lower feed intake, faster growth and better feed conversion ratio at the lower temperature. Heritability of TS of DGC was moderate ([Formula: see text]). The co-heritability parameter derived from selection index theory, which describes the heritable variance of TS, was negative when the intercept was placed at the lower temperature (-0.28). This resulted in moderate accuracy of selection. At the higher temperature, co-heritability of TS was positive (0.20). The genetic correlation between DGC and its TS was strongly negative (-0.64) when the intercept was at the lower temperature and positive (0.38) but not significantly different from zero at the higher temperature. CONCLUSIONS: The considerable amount of genetic variation in TS of growth indicates a potential for selection response and thus for targeted genetic improvement in TS. The negative genetic correlation between DGC and its TS suggests that selection for high growth rate at the lower temperature will result in more temperature-sensitive fish. Instead, the correlated response of TS is less pronounced if the selection for a higher DGC occurred at the higher temperature. It seems possible to control the correlated genetic change of TS while selecting for fast growth across environments, especially if measurements from both environments are available and breeding values for reaction norm slope are directly included in the selection index.