Mowi (Norway)

Improving feed efficiency (FE) is poised to become a primary focus of future aquaculture breeding programs, with ongoing research aiming to incorporate this trait to increase fish production, reduce feed costs and minimize environmental impact. Selection for improving FE requires a detailed understanding of its genetic parameters and association with growth traits under commercial conditions. However, scientific studies on FE at the individual level are missing in Atlantic salmon, likely due to the absence of accurate and efficient methods for measuring individual feed intake (IFI). Here we have used X-ray imaging on 700 salmon smolts, which have consumed feed containing radio-opaque beads, to phenotype the IFI at multiple time points. The study aims to I) train and validate a deep learning image based “YOLO-XBeads” model for accurate estimation of IFI from X-ray images, II) estimate the genetic parameters of IFI and different FE metrics such as feed conversion ratio (FCR), phenotypic residual feed intake (pRFI), genetic residual feed intake (gRFI), and growth traits such as Body weight (BW), average daily gain (ADG) and whole-body fat (WBF), and III) quantify the phenotypic and genetic relationships among these traits in Atlantic salmon. The YOLO-XBeads model performed well on X-ray images, with a high correlation to the true value (R 2 = 0.99) and mean absolute percentage error of 2.60–5.94 %. The time efficiency (two orders of magnitude faster than available software) of our model significantly reduces the analysis time, labour and cost compared to conventional image software and manual human counting. We found significant heritability estimates for IFI (0.20 ± 0.05–0.50 ± 0.07), ADG (0.44 ± 0.06–0.55 ± 0.06), BW (0.50 ± 0.06–0.55 ± 0.06), pRFI (0.11 ± 0.05–0.16 ± 0.07), gRFI (0.06 ± 0.03–0.18 ± 0.06), FCR (0.09 ± 0.04–0.23 ± 0.06) and WBF (0.62 ± 0.06), indicating potential for genetic improvement. Additionally, the strong genetic correlations (r g = 0.71 ± 0.07–0.96 ± 0.01) between different point estimates of the primary traits (IFI, ADG and BW) over time demonstrated the stability of these traits over the studied growth period. Averaging the FE and related traits over the whole growth period (50–300 g) of salmon showed variable r g between traits. The highest r g values (0.86 ± 0.05–0.99 ± 0.01) were observed among different FE metrics, indicating similar genetic regulation. Following this, a strong r g (0.95 ± 0.02) was found between IFI and ADG, indicating that ADG can explain a significant proportion of the genetic variation in IFI. However, we found low but significant genetic variation for pRFI and gRFI, which shows heritable variation remains after accounting for the relationships of BW and ADG with the IFI. In addition, WBF showed moderate r g (0.52 ± 0.09–0.64 ± 0.07) with IFI, BW and ADG traits. Conversely, FE metrics showed weak r g with ADG (0.00 ± 0.21–0.38 ± 0.17) as well as with WBF (−0.03 ± 0.18–0.21 ± 0.19), indicating little or no indirect genetic improvement in FE through selection for growth or WBF in freshwater smolts. Overall, the FE and related traits were found to be measurable and heritable at the individual level in Atlantic salmon smolts, signifying the potential for improving economic gain and minimizing environmental impact. However, further studies are needed at the sea phase. • X-ray imaging combined with the YOLO-XBeads model can serve as a scalable, fast, accurate and non-invasive method for assessing individual-level feed intake. • There is significant variability and heritability associated with feed efficiency in Atlantic salmon. • Little to no indirect genetic improvement in feed efficiency through selection for growth or body fat levels in freshwater smolts.

The interest in recirculating aquaculture systems (RAS) is growing due to their benefits such as increased productivity, better control over animal care, reduced environmental effects, and less water consumption. However, in some regions of the world, traditional aquaculture methods remain prevalent, and selective breeding has often been designed for performance within these systems. Therefore, it is important to evaluate how current fish populations fare in RAS to guide future breeding choices. In a commercial setting, we explore the genetic structure of growth characteristics, measure genotype-environment interactions (GxE) in salmon smolts, and examine genetic markers related to growth in freshwater lochs and RAS. Young salmon were raised together until they reached the parr stage, after which they were divided equally between freshwater net-pens and RAS. After an 8-week period, we sampled fish from each environment and genotyped them. Our findings revealed that fish reared in RAS were generally smaller in weight and length but exhibited a higher condition factor and uniformity. We found a notably smaller component of unexplained variance in the RAS, leading to higher heritability estimates. We observed a low GxE effect for length and condition factor, but significant re-ranking for whole-body weight, as well as noticeable differences in trait associations across environments. Specifically, a segment of chromosome 22 was found to be linked with the condition factor in the RAS population only. Results suggests that if the use of RAS continues to expand, the efficiency of existing commercial populations may not reach its full potential unless breeding programs specific to RAS are implemented.

Atlantic salmon (Salmo salar) is an important source of food globally; however, fillet color can significantly affect consumer purchasing, leading to potential food waste. Fish diets can be supplemented with astaxanthin to increase the organic pigment, carotenoid, responsible for flesh coloration; however, there is variation in the amount of overall fillet coloration in response to feeding astaxanthin. The uptake of this pigment is influenced by the environment and genetics and has been shown to be heritable. Therefore, we set out to determine the genomic associations of two separate year classes of farmed North American Atlantic salmon with measured Minolta Chroma Meter (lightness, redness, and yellowness) and SalmoFan phenotypic traits. Using ASReml-R genome-wide association, two genetic markers on chromosome 26 were significantly associated with almost all color traits, and these two markers explained between 6.0% and 12.5% of the variances. The genomic region on chromosome 26 was importantly found to be associated with the beta-carotene oxygenase 1 (bco1) gene, which is essential in the conversion of beta-carotenoids to vitamin A, implying that this gene may also play an important role in flesh coloration in North American Atlantic salmon. Additionally, there were several genomic regions significantly associated with color traits, in which the accompanying genes had functions in line with thermogenesis, immune function, and pathogenic responses. Understanding how environmental and genetic factors work together to affect fillet quality traits will help inform genetic improvement.

Feed efficiency is a highly desirable breeding goal trait as it can potentially reduce the relative economic cost of feed and concurrently reduce the environmental footprint of fish production. However, recording feed intake is a bottleneck in Atlantic salmon production. We recorded feed intake in 700 Atlantic salmon parr from 34 full sibling families using the X-ray method, where fish were fed feed containing radio-opaque beads and subsequently X-ray imaged one time after a full meal corresponding to the daily ration. In parallel, we cultured siblings from the same 35 families in duplicate family tanks of 25 individuals per tank and recorded the daily feed intake of each family at the tank level, which is known as the gold standard tank-based method. The heritability estimate for daily feed intake in Atlantic salmon using the X-ray method was significantly different from zero (0.19 ± 0.06) and was genetically correlated to growth-related traits (rg = 0.48–0.81). Daily feed intake at the family level with the X-ray method was highly genetically correlated to the daily feed intake traits using the tank-based feeding method at 0.78–0.82, depending on whether the comparison was made at a common time, common weight, or cumulative feed intake for the entire period. Whilst the X-ray method holds promise for research on the genetic background of feed intake and feed efficiency, more studies are needed to investigate the feasibility during the sea phase of Atlantic salmon production.

A controlled Saprolegnia parasitica infection model was used to challenge 1158 fish representing 105 pedigreed Atlantic salmon families to evaluate the possibility of selecting for Saprolegnia resistance in a commercial breeding programme. Fish were infected in five study tanks and observed for 40 days post‐infection for lesion score and survival. Survival analysis of the top 10 resistant and bottom 10 susceptible families indicated that the hazard of dying following Saprolegnia infection was 1509% higher in susceptible families. In all fish, a 10 g increase in weight correlated with a 7.8% increase in the hazard of dying while sex did not affect mortality. Resistance to Saprolegnia was estimated to have a heritability of 0.25, indicating that selection is possible. Genetic and phenotypic correlations indicated that the 11‐point scoring system, developed in this study to quantify Saprolegnia infection severity, had a high negative correlation with survival as days to mortality at ≥−0.922(±0.005), suggesting that the scoring method could help assess lesion development in studies where mortality is not the primary biological endpoint.

Salmon lice are ectoparasites that threaten wild and farmed salmonids. Artificial selection of salmon for resistance to the infectious copepodid lice stage currently relies on in vivo challenge trials on thousands of salmon a year. We challenged 5750 salmon with salmon lice (Lepeophtheirus salmonis) from two distinct farmed strains of salmon in two separate trials. We found that volatile organic compounds (VOC), 1-penten-3-ol, 1-octen-3-ol and 6-methyl-5-hepten-2-one in the mucus of the salmon host after salmon lice infection, were significantly associated with lice infection numbers across a range of water temperatures (5 °C, 10 °C, 17 °C). Some VOCs (benzene, 1-octen-3-ol and 3,5,5-trimethyl-2-hexene) were significantly different between lines divergently selected for salmon lice resistance. In a combined population assessment, selected VOCs varied between families in the range of 47- 59% indicating a genetic component and were positively correlated to the salmon hosts estimated breeding values 0.59–0.74. Mucosal VOC phenotypes could supplement current breeding practices and have the potential to be a more direct and ethical proxy for salmon lice resistance provided they can be measured prior to lice infestation.

Amoebic gill disease (AGD) is a parasitic disease caused by the amoeba Paramoeba perurans, which colonizes the gill tissues and causes distress for the host. AGD can cause high morbidity and mortalities in salmonid and non-salmonid fish species. To understand the genetic basis of AGD and improve health status of farmed A. salmon, a population of ~ 6,100 individuals belonging to 150 full-sib families was monitored for development of AGD in the sea of Ireland. The population was followed for two rounds of AGD infections, and fish were gill scored to identify severity of disease in first (N = 3,663) and the second (N = 3,511) infection with freshwater treatment after the first gill-scoring. A subset of this gill-scored population (N = 1,141) from 119 full-sib families were genotyped with 57,184 SNPs using custom-made Affymetrix SNP-chip. GWAS analyses were performed which resulted in five significantly associated SNP variants distributed over chromosome 1, 2 and 5. Three candidate genes; c4, tnxb and slc44a4 were found within QTL region of chromosome 2. The tnxb and c4 genes are known to be a part of innate immune system, and may play a role in resistance to AGD. The gain in prediction accuracy obtained by involving genomic information was 9–17% higher than using traditional pedigree information.