Heritability and mechanisms of n-3 long chain polyunsaturated fatty acid deposition in the flesh of Atlantic salmon

Molecular Regulation of Biosynthesis of Long Chain Polyunsaturated Fatty Acids in Atlantic Salmon

Salmon is a rich source of health-promoting omega-3 long chain polyunsaturated fatty acids (n-3 LC-PUFA), such as eicosapentaenoic acid (EPA, 20:5n-3) and docosahexaenoic acid (DHA, 22:6n-3). The LC-PUFA biosynthetic pathway in Atlantic salmon is one of the most studied compared to other teleosts. This has largely been due to the massive replacement of LC-PUFA-rich ingredients in aquafeeds with terrestrial plant oils devoid of these essential fatty acids (EFA) which ultimately pushed dietary content towards the minimal requirement of EFA. The practice would also reduce tissue content of n-3 LC-PUFA compromising the nutritional value of salmon to the human consumer. These necessitated detailed studies of endogenous biosynthetic capability as a contributor to these EFA. This review seeks to provide a comprehensive and concise overview of the current knowledge about the molecular genetics of PUFA biosynthesis in Atlantic salmon, highlighting the enzymology and nutritional regulation as well as transcriptional control networks. Furthermore, we discuss the impact of genome duplication on the complexity of salmon LC-PUFA pathway and highlight probable implications on endogenous biosynthetic capabilities. Finally, we have also compiled and made available a large RNAseq dataset from 316 salmon liver samples together with an R-script visualization resource to aid in explorative and hypothesis-driven research into salmon lipid metabolism.

Nutritional programming by maternal diet alters offspring lipid metabolism in a marine teleost

Nutritional programming - the association between the early nutritional environment and long-term consequences for an animal - is an emerging area of research in fish biology. Previous studies reported correlations between maternal provisioning of essential fatty acids to eggs and the whole-body fatty acid composition of larvae reared under uniform conditions for red drum, Sciaenops ocellatus. This study aimed to further investigate the nutritional stimulus and the consequences of nutritional programming by feeding adult red drum several distinct diets and rearing larvae under uniform conditions until 21 days post-hatching when larval lipid and fatty acid compositions were assessed. Different maternal diets produced eggs with distinctive lipid and fatty acid compositions, and despite receiving the same larval diet for almost 3 weeks, larvae showed differences in total fatty acid accumulation and in retention of highly unsaturated fatty acids (HUFA). Specifically, larvae reared from a maternal diet of shrimp generally showed elevated levels of fatty acids in the initial steps of the n-3 and n-6 HUFA biosynthetic pathways and reduced levels of fatty acid products of the same pathways, especially in triglyceride. Furthermore, the variations in larval fatty acid accumulation induced by maternal diet varied among females. Lipid metabolism altered by parental diet may have consequences for larval physiological processes and behavioral performance, which may ultimately influence larval survival.

Raman and near Infrared Spectroscopy for Quantification of Fatty Acids in Muscle Tissue-A Salmon Case Study

The aim of the present study was to critically evaluate the potential of using NIR and Raman spectroscopy for prediction of fatty acid features and single fatty acids in salmon muscle. The study was based on 618 homogenized salmon muscle samples acquired from Atlantic salmon representing a one year-class nucleus, fed the same high fish oil feed. NIR and Raman spectra were used to make regression models for fatty acid features and single fatty acids measured by gas chromatography. The predictive performance of both NIR and Raman was good for most fatty acids, with R2 above 0.6. Overall, Raman performed marginally better than NIR, and since the Raman models generally required fewer components than respective NIR models to reach high and optimal performance, Raman is likely more robust for measuring fatty acids compared to NIR. The fatty acids of the salmon samples co-varied to a large extent, a feature that was exacerbated by the overlapping peaks in NIR and Raman spectra. Thus, the fatty acid related variation of the spectroscopic data of the present study can be explained by only a few independent principal components. For the Raman spectra, this variation was dominated by functional groups originating from long-chain polyunsaturated FAs like EPA and DHA. By exploring the independent EPA and DHA Raman models, spectral signatures similar to the respective pure fatty acids could be seen. This proves the potential of Raman spectroscopy for single fatty acid prediction in muscle tissue.

Fatty Acid Composition and Contents of Fish of Genus Salvelinus from Natural Ecosystems and Aquaculture

Fatty acids (FA) of muscle tissue of Salvelinus species and its forms, S. alpinus, S. boganidae, S. drjagini, and S. fontinalis, from six Russian lakes and two aquacultures, were analyzed. Considerable variations in FA compositions and contents were found, including contents of eicosapentaenoic and docosahexaenoic acids (EPA and DHA), which are important indicators of fish nutritive value for humans. As found, contents of EPA+DHA (mg·g⁻¹ wet weight) in muscle tissue of Salvelinus species and forms varied more than tenfold. These differences were supposed to be primarily determined by phylogenetic factors, rather than ecological factors, including food. Two species, S. boganidae and S. drjagini, had the highest EPA+DHA contents in their biomass and thereby could be recommended as promising species for aquaculture to obtain production with especially high nutritive value. Basing on revealed differences in FA composition of wild and farmed fish, levels of 15-17-BFA (branched fatty acids), 18:2NMI (non-methylene interrupted), 20:2NMI, 20:4n-3, and 22:4n-3 fatty acids were recommended for verifying trade label information of fish products on shelves, as the biomarkers to differentiate wild and farmed charr.

Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Background

In response to major challenges regarding the supply and sustainability of marine ingredients in aquafeeds, the aquaculture industry has made a large-scale shift toward plant-based substitutions for fish oil and fish meal. But, this also led to lower levels of healthful n−3 long-chain polyunsaturated fatty acids (PUFAs)—especially eicosapentaenoic (EPA) and docosahexaenoic (DHA) acids—in flesh. One potential solution is to select fish with better abilities to retain or synthesise PUFAs, to increase the efficiency of aquaculture and promote the production of healthier fish products. To this end, we aimed i) to estimate the genetic variability in fatty acid (FA) composition in visceral fat quantified by Raman spectroscopy, with respect to both individual FAs and groups under a feeding regime with limited n-3 PUFAs; ii) to study the genetic and phenotypic correlations between FAs and processing yields- and fat-related traits; iii) to detect QTLs associated with FA composition and identify candidate genes; and iv) to assess the efficiency of genomic selection compared to pedigree-based BLUP selection.

Results

Proportions of the various FAs in fish were indirectly estimated using Raman scattering spectroscopy. Fish were genotyped using the 57 K SNP Axiom™ Trout Genotyping Array. Following quality control, the final analysis contained 29,652 SNPs from 1382 fish. Heritability estimates for traits ranged from 0.03 ± 0.03 (n-3 PUFAs) to 0.24 ± 0.05 (n-6 PUFAs), confirming the potential for genomic selection. n-3 PUFAs are positively correlated to a decrease in fat deposition in the fillet and in the viscera but negatively correlated to body weight. This highlights the potential interest to combine selection on FA and against fat deposition to improve nutritional merit of aquaculture products. Several QTLs were identified for FA composition, containing multiple candidate genes with indirect links to FA metabolism. In particular, one region on Omy1 was associated with n-6 PUFAs, monounsaturated FAs, linoleic acid, and EPA, while a region on Omy7 had effects on n-6 PUFAs, EPA, and linoleic acid. When we compared the effectiveness of breeding programmes based on genomic selection (using a reference population of 1000 individuals related to selection candidates) or on pedigree-based selection, we found that the former yielded increases in selection accuracy of 12 to 120% depending on the FA trait.

Conclusion

This study reveals the polygenic genetic architecture for FA composition in rainbow trout and confirms that genomic selection has potential to improve EPA and DHA proportions in aquaculture species.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08062-7.

Genetic Analysis of the Fatty Acid Profile in Gilthead Seabream (Sparus aurata L.)

Simple Summary

Humans require essential fatty acids in their diet and marine fish are a source of them, especially omega3 fatty acids that present high benefits on diverse vascular diseases and the immune system. Breeding programs in gilthead seabream usually include growth as the first criterion in the selection process of the fish. However, that could lead to fish with a higher fillet fat content and a fatty acid profile with a lower polyunsaturated fatty acids percentage. Fillet fat content and its fatty acids profile have been revealed as heritable traits. Therefore, further studies to go deeper in the selection process are advisable.

Abstract

The gilthead seabream is one of the most valuable species in the Mediterranean basin both for fisheries and aquaculture. Marine fish, such as gilthead seabream, are a source of n3 polyunsaturated fatty acids, highly appreciated for human food owing to their benefits on the cardiovascular and immune systems. The aim of the present study was to estimate heritability for fatty acid (FA) profile in fillet gilthead seabream to be considered as a strategy of a selective breeding program. Total of 399 fish, from a broodstock Mediterranean Sea, were analysed for growth, flesh composition and FA profile. Heritabilities for growth traits, and flesh composition (fat, protein, and moisture content) were medium. Heritability was moderate for 14:0, 16:0 and 18:1n9 and for sum of monounsaturated FA and n6/n3 ratio, and it was low for 20:1n11 and 22:6n3 and the ratio unsaturated/saturated FA. Breeding programs in gilthead seabream usually include growth as the first criterion in the selection process of the fish. However, other quality traits, such as fillet fat content and its fatty acids profile should be considered, since they are very important traits for the consumer, from a nutritional point of view and the benefits for the health.

Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines

Within the context of a growing aquaculture production coupled with a plateau of the production in the main components of aquafeeds (fish oil and fishmeal), recent studies have typically focused on replacing these feedstuffs with terrestrial plant ingredients for cultured carnivorous aquatic species, such as rainbow trout (Oncorhynchus mykiss). Substitution rates without adverse effects have, however, reached their limit. One potential way forward would be to take advantage of the genetic variability that exists in the salmonid population. However, to date, little is known about the underlying molecular mechanisms responsible for this genetic variability. The aim of the present research was to understand why some genotypes are better able to utilize plant-based diets devoid of marine resources. In this regard, three isogenic lines of rainbow trout (R23h, AB1h, and A22h), with similar growth when fed marine resources-based diets and which differ greatly in their responses to a plant-based diet, were fed with either a complete plant-based diet (V diet) or a marine resources-based diet (M diet) since first-feeding. Fish traits and the hepatic transcriptome of these three genotypes were compared after 5 months of feeding. First, differences in the ability to grow with the V diet observed amongst genotypes was not due to higher feed intake, but instead due to differences in feed efficiency. The comparison of transcriptome profiles revealed 575 (R23h vs. AB1h), 1,770 (R23h vs. A22h), and 2,973 (AB1h vs. A22h) probes differentially expressed amongst the three genotypes when fed the V diet. Interestingly, R23h and AB1h fish, which were the least affected by the V diet, exhibited the highest growth. These results demonstrate that these fish were able to maintain a high level of energy production and protein synthesis. Moreover, these genotypes were also able to activate pathways linked to lipid and cholesterol metabolisms, such as the biosynthesis of long-chain polyunsaturated fatty acids. Finally, as previously, immunity seems to also play an important role in the ability of fish to use the V diet, and further studies are needed to understand the mechanisms by which immunity interacts with growth.

Modulation of hepatic miRNA expression in Atlantic salmon (Salmo salar) by family background and dietary fatty acid composition

This study finds significant differences in hepatic fatty acid composition between four groups of Atlantic salmon (Salmo salar) consisting of offspring from families selected for high and low capacities to express the delta 6 desaturase isomer b and fed diets with 10% or 75% fish oil. The results demonstrated that hepatic lipid metabolism was affected by experimental conditions (diet/family). The fatty acid composition in the four groups mirrored the differences in dietary composition, but it was also associated with the family groups. Small RNA sequencing followed by RT-qPCR identified 12 differentially expressed microRNAs (DE miRNAs), with expression associated with family groups (miR-146 family members, miR-200b, miR-214, miR-221, miR-125, miR-135, miR-137, miR_nov_1), diets (miR-203, miR-462) or both conditions. All the conserved DE miRNAs have been reported as associated with lipid metabolism in other vertebrates. In silico predictions revealed 37 lipid metabolism pathway genes, including desaturases, transcription factors and key enzymes in the synthesis pathways as putative targets (e.g., srebp-1 and 2, Δ6fad_b and c, hmdh, elovl4 and 5b, cdc42). RT-qPCR analysis of selected target genes showed expression changes that were associated with diet and with family groups (d5fad, d6fad_a, srebp-1). There was a reciprocal difference in the abundance of ssa-miR-203a-3p and srebp-1 in one group comparison, whereas other predicted targets did not reveal any evidence of being negatively regulated by degradation. More experimental studies are needed to validate and fully understand the predicted interactions and how the DE miRNAs may participate in the regulation of hepatic lipid metabolism.

Comparison of Fatty Acid Contents in Major Lipid Classes of Seven Salmonid Species from Siberian Arctic Lakes

Long-chain omega-3 polyunsaturated fatty acids (LC-PUFA) essential for human nutrition are mostly obtained from wild-caught fish. To sustain the LC-PUFA supply from natural populations, one needs to know how environmental and intrinsic factors affect fish fatty acid (FA) profiles and contents. We studied seven Salmoniformes species from two arctic lakes. We aimed to estimate differences in the FA composition of total lipids and two major lipid classes, polar lipids (PL) and triacylglycerols (TAG), among the species and to evaluate LC-PUFA contents corresponding to PL and TAG in muscles. Fatty acid profiles of PL and TAG in all species were characterized by the prevalence of omega-3 LC-PUFA and C16-C18 monoenoic FA, respectively. Fish with similar feeding spectra were identified similarly in multivariate analyses of total lipids, TAG and PL, due to differences in levels of mostly the same FA. Thus, the suitability of both TAG and total lipids for the identification of the feeding spectra of fish was confirmed. All species had similar content of LC-PUFA esterified as PL, 1.9–3.5 mg g⁻¹, while the content of the TAG form strongly varied, from 0.9 to 9.8 mg g⁻¹. The LC-PUFA-rich fish species accumulated these valuable compounds predominately in the TAG form.

Interaction between dietary fatty acids and genotype on immune response in Atlantic salmon (Salmo salar) after vaccination: A transcriptome study

A pivotal matter to aquaculture is the sourcing of sustainable resources as ingredients to aquafeeds. Levels of plant delivered oils as source of fatty acids (FA) in aquafeeds have reached around 70% resulting in reduced levels of long-chain omega-3 polyunsaturated fatty acids (LC n-3 PUFA), such as eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), in salmon fillet composition. EPA and DHA can modulate inflammation and immune response, so it is crucial to understand how fish immune response is affected by low LC n-3 PUFA diet and if this diet can have a detrimental effect on vaccine response. Atlantic salmon (Salmo salar) can produce EPA/DHA from α-linolenic acid (ALA) and this endogenous capacity can be explored to develop families with higher tolerance to low LC n-3 PUFA diets. Here we analyze innate and adaptive immune response in Atlantic salmon to a commercial vaccine after being fed low levels of EPA and DHA, and we also compare three strains of salmon selected by their endogenous capacity of synthesizing LC- n-3 PUFA. A total of 2,890 differentially expressed genes (DEGs) were identified (p-value adjusted < 0.1) when comparing vaccinated fish against control non-vaccinated. Gene ontology (GO) and KEGG analysis with 442 up/downregulated genes revealed that most DEGs were both related to immune response as well as part of important immune related pathways, as "Toll-like receptor" and "Cytokine-Cytokine interaction". Adaptive response was also addressed by measuring antigen specific IgM, and titers were significantly higher than in the pre-immune fish at 62 days post-immunization. However, diet and strain had no/little effect on vaccine-specific IgM or innate immune responses. Atlantic salmon therefore display robustness in its response to vaccination even when feed low levels of LC n-3 PUFA.

Effect of plant-based diets with varying ratios of ω6 to ω3 fatty acids on growth performance, tissue composition, fatty acid biosynthesis and lipid-related gene expression in Atlantic salmon (Salmo salar)

Little is known about how variation in omega-6 to omega-3 (ω6:ω3) fatty acid (FA) ratios affects lipid metabolism and eicosanoid synthesis in salmon, and the potential underlying molecular mechanisms. The current study examined the impact of five plant-based diets (12-week exposure) with varying ω6:ω3 (0.3-2.7) on the growth, tissue lipid composition (muscle and liver), and hepatic transcript expression of lipid metabolism and eicosanoid synthesis-related genes in Atlantic salmon. Growth performance and organ indices were not affected by dietary ω6:ω3. The liver and muscle FA composition was highly reflective of the diet (ω6:ω3 of 0.2-0.8 and 0.3-1.9, respectively) and suggested elongation and desaturation of the ω3 and ω6 precursors 18:3ω3 and 18:2ω6. Furthermore, proportions of ω6 and ω3 PUFA in both tissues showed significant positive correlations with dietary inclusion (% of diet) of soy and linseed oils, respectively. Compound-specific stable isotope analysis (CSIA) further demonstrated that liver long-chain polyunsaturated fatty acid (LC-PUFA) synthesis (specifically 20:5ω3 and 20:4ω6) was largely driven by dietary 18:3ω3 and 18:2ω6, even when 20:5ω3 and 22:6ω3 were supplied at levels above minimum requirements. In addition, significant positive and negative correlations were identified between the transcript expression of LC-PUFA synthesis-related genes and liver ω6 and ω3 LC-PUFA, respectively, further supporting FA biosynthesis. Liver ω3 LC-PUFA also correlated negatively with the eicosanoid synthesis-related transcripts pgds and cox1. This is the first study to use CSIA, hepatic transcriptome, and tissue lipid composition analyses concurrently to demonstrate the impact of plant-based diets with varying ω6:ω3 on farmed Atlantic salmon.

Individual differences in EPA and DHA content of Atlantic salmon are associated with gene expression of key metabolic processes

The aim of this study was to explore how individual differences in content of the omega-3 fatty acids EPA and DHA in skeletal muscle of slaughter-sized Atlantic salmon, are associated with expression of genes involved in key metabolic processes. All experimental fish were fed the same diet throughout life and fasted for 14 days prior to slaughter. Still, there were relatively large individual variations in EPA and DHA content of skeletal muscle. Higher DHA content was concurrent with increased expression of genes of the glycolytic pathway and the production of pyruvate and lactate, whereas EPA was associated with increased expression of pentose phosphate pathway and glycogen breakdown genes. Furthermore, EPA, but not DHA, was associated with expression of genes involved in insulin signaling. Expression of genes specific for skeletal muscle function were positively associated with both EPA and DHA. EPA and DHA were also associated with expression of genes related to eicosanoid and resolvin production. EPA was negatively associated with expression of genes involved in lipid catabolism. Thus, a possible reason why some individuals have a higher level of EPA in the skeletal muscle is that they deposit - rather than oxidize - EPA for energy.

Genetic effects of fatty acid composition in muscle of Atlantic salmon

BACKGROUND

The replacement of fish oil (FO) and fishmeal with plant ingredients in the diet of farmed Atlantic salmon has resulted in reduced levels of the health-promoting long-chain polyunsaturated omega-3 fatty acids (n-3 LC-PUFA) eicosapentaenoic (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) in their filets. Previous studies showed the potential of selective breeding to increase n-3 LC-PUFA levels in salmon tissues, but knowledge on the genetic parameters for individual muscle fatty acids (FA) and their relationships with other traits is still lacking. Thus, we estimated genetic parameters for muscle content of individual FA, and their relationships with lipid deposition traits, muscle pigmentation, sea lice and pancreas disease in slaughter-sized Atlantic salmon. Our aim was to evaluate the selection potential for increased n-3 LC-PUFA content and provide insight into FA metabolism in Atlantic salmon muscle.

RESULTS

Among the n-3 PUFA, proportional contents of alpha-linolenic acid (ALA; 18:3n-3) and DHA had the highest heritability (0.26) and EPA the lowest (0.09). Genetic correlations of EPA and DHA proportions with muscle fat differed considerably, 0.60 and 0.01, respectively. The genetic correlation of DHA proportion with visceral fat was positive and high (0.61), whereas that of EPA proportion with lice density was negative. FA that are in close proximity along the bioconversion pathway showed positive correlations with each other, whereas the start (ALA) and end-point (DHA) of the pathway were negatively correlated (- 0.28), indicating active bioconversion of ALA to DHA in the muscle of fish fed high FO-diet.

CONCLUSIONS

Since contents of individual FA in salmon muscle show additive genetic variation, changing FA composition by selective breeding is possible. Taken together, our results show that the heritabilities of individual n-3 LC-PUFA and their genetic correlations with other traits vary, which indicates that they play different roles in muscle lipid metabolism, and that proportional muscle contents of EPA and DHA are linked to body fat deposition. Thus, different selection strategies can be applied in order to increase the content of healthy omega-3 FAin the salmon muscle. We recommend selection for the proportion of EPA + DHA in the muscle because they are both essential FA and because such selection has no clear detrimental effects on other traits.

Mapping QTL for Omega-3 Content in Hybrid Saline Tilapia

Tilapia is one of most important foodfish species. The low omega-3 to omega-6 fatty acid ratio in freshwater tilapia meat is disadvantageous for human health. Increasing omega-3 content is an important task in breeding to increase the nutritional value of tilapia. However, conventional breeding to increase omega-3 content is difficult and slow. To accelerate the increase of omega-3 through marker-assisted selection (MAS), we conducted QTL mapping for fatty acid contents and profiles in a F₂ family of saline tilapia generated by crossing red tilapia and Mozambique tilapia. The total omega-3 content in F₂ hybrid tilapia was 2.5 ± 1.0 mg/g, higher than that (2.00 mg/g) in freshwater tilapia. Genotyping by sequencing (GBS) technology was used to discover and genotype SNP markers, and microsatellites were also genotyped. We constructed a linkage map with 784 markers (151 microsatellites and 633 SNPs). The linkage map was 2076.7 cM long and consisted of 22 linkage groups. Significant and suggestive QTL for total lipid content were mapped on six linkage groups (LG3, -4, -6, -8, -13, and -15) and explained 5.8-8.3% of the phenotypic variance. QTL for omega-3 fatty acids were located on four LGs (LG11, -18, -19, and -20) and explained 5.0 to 7.5% of the phenotypic variance. Our data suggest that the total lipid and omega-3 fatty acid content were determined by multiple genes in tilapia. The markers flanking the QTL for omega-3 fatty acids can be used in MAS to accelerate the genetic improvements of these traits in salt-tolerant tilapia.

The genetics of overwintering performance in two-year old common carp and its relation to performance until market size

Using farmed common carp, we investigated the genetic background of the second year overwintering performance and its relation to the performance during the third growing season and at market size. The experimental stock was established by partial factorial design with a series of 4 factorial matings of 5 dams and 10 sires each. The families were reared communally and pedigree was re-constructed with 93.6% success using 12 microsatellites on 2008 offspring. Three successive recordings (second autumn, third spring, and third autumn—market size) covering two periods (second overwintering, third growing season) were included. Body weight, Fulton’s condition factor and percent muscle fat content were recorded at all times and headless carcass yield and fillet yield were recorded at market size. Specific growth rate, absolute and relative fat change and overall survival were calculated for each period. Heritability estimates were significantly different from zero and almost all traits were moderately to highly heritable (h² = 0.36–1.00), except survival in both periods and fat change (both patterns) during overwintering (h² = 0.12–0.15). Genetic and phenotypic correlations imply that selection against weight loss and fat loss during overwintering is expected to lead to a better winter survival, together with a positive effect on growth in the third growing season. Interestingly, higher muscle fat content was genetically correlated to lower survival in the following period (r_g = -0.59; -0.53, respectively for winter and the third summer). On the other hand, higher muscle fat was also genetically linked to better slaughter yields. Moreover, selection for higher condition factor would lead to better performance during winter, growing season and at market size.

Successful selection of rainbow trout (Oncorhynchus mykiss) on their ability to grow with a diet completely devoid of fishmeal and fish oil, and correlated changes in nutritional traits

In the context of limited marine resources, the exponential growth of aquaculture requires the substitution of fish oil and fishmeal, the traditional components of fish feeds by terrestrial plant ingredients. High levels of such substitution are known to negatively impact fish performance such as growth and survival in rainbow trout (Oncorhynchus mykiss) as in other salmonids. In this respect, genetic selection is a key enabler for improving those performances and hence for the further sustainable development of aquaculture. We selected a rainbow trout line over three generations for its ability to survive and grow on a 100% plant-based diet devoid of both fish oil and fishmeal (V diet) from the very first meal. In the present study, we compared the control line and the selected line after 3 generations of selection, both fed either the V diet or a marine resources-based diet (M diet). The objective of the study was to assess the efficiency of selection and the consequences on various correlated nutritional traits: feed intake, feed efficiency, digestibility, composition of whole fish, nutrient retention and fatty acid (FA) profile. We demonstrated that the genetic variability present in our rainbow trout population can be selected to improve survival and growth. The major result of the study is that after only three generations of selection, selected fish fed the V diet grew at the same rate as the control line fed the M diet, whilst the relative reduction of body weight was 36.8% before the selection. This enhanced performance on the V diet seems to be mostly linked to a higher feed intake for the selected fish.

The genetic architecture of growth and fillet traits in farmed Atlantic salmon (Salmo salar)

BACKGROUND

Performance and quality traits such as harvest weight, fillet weight and flesh color are of economic importance to the Atlantic salmon aquaculture industry. The genetic factors underlying these traits are of scientific and commercial interest. However, such traits are typically polygenic in nature, with the number and size of QTL likely to vary between studies and populations. The aim of this study was to investigate the genetic basis of several growth and fillet traits measured at harvest in a large farmed salmon population by using SNP markers. Due to the marked heterochiasmy in salmonids, an efficient two-stage mapping approach was applied whereby QTL were detected using a sire-based linkage analysis, a sparse SNP marker map and exploiting low rates of recombination, while a subsequent dam-based analysis focused on the significant chromosomes with a denser map to confirm QTL and estimate their position.

RESULTS

The harvest traits all showed significant heritability, ranging from 0.05 for fillet yield up to 0.53 for the weight traits. In the sire-based analysis, 1695 offspring with trait records and their 20 sires were successfully genotyped for the SNPs on the sparse map. Chromosomes 13, 18, 19 and 20 were shown to harbor genome-wide significant QTL affecting several growth-related traits. The QTL on chr. 13, 18 and 20 were detected in the dam-based analysis using 512 offspring from 10 dams and explained approximately 6-7 % of the within-family variation in these traits.

CONCLUSIONS

We have detected several QTL affecting economically important complex traits in a commercial salmon population. Overall, the results suggest that the traits are relatively polygenic and that QTL tend to be pleiotropic (affecting the weight of several components of the harvested fish). Comparison of QTL regions across studies suggests that harvest trait QTL tend to be relatively population-specific. Therefore, the application of marker or genomic selection for improvement in these traits is likely to be most effective when the discovery population is closely related to the selection candidates (e.g. within-family genomic selection).

Light-dependent transcriptional events during resting egg hatching of the rotifer Brachionus manjavacas

Rotifer resting eggs often have to endure harsh environmental conditions during the diapause phase. They are stimulated by light to hatch. In order to study the hatching mechanism, we observed resting eggs and measured their transcriptional expression under different light exposure periods (total darkness, and after 30 min, and 4h light). By using differential-display reverse transcription PCR (DDRT-PCR), we isolated 80 genes that displayed different expression patterns in response to the three light treatments: 20 genes were expressed in total darkness, 40 different genes were differentially expressed under 30 min light, and 20 further genes were expressed after 4h of light. The resting eggs showed no phenotypic differences in embryonic development during the 4h illumination period. In general, the expression patterns of the analyzed genes in resting eggs were differentially modulated by light exposure time. In total darkness, resting eggs mainly expressed genes encoding cell defense and homeostasis functions. In the 30 min illumination group, we found enriched expression of genes encoding fatty acid metabolism-related components, including Acyl-CoA dehydrogenase (ACAD). Genes encoding cellular and embryonic developmental functions were highly observed in the 30 min-illuminated group but were not observed in the 4h-illuminated group. Real-time RT-PCR revealed that several transcripts such as encoding V-type H(+)-translocating pyrophosphatase (V-PPase) and Meckelin had prolonged expression levels when exposed to light for 4h. In the 4h illuminated group, the RecQ protein-like 5 (RECQL5) gene was enriched. This RECQL5 gene may be expressed to protect the developing embryo from continuous light exposure. The data presented in this study indicate that DDRT-PCR-aided gene screening can be helpful to isolate candidate genes involved in the hatching process.

Nutritional quality of salmon products available from major retailers in the UK: content and composition of n-3 long-chain PUFA

In the present study, salmon products available from UK retailers were analysed to determine the levels of n-3 long-chain PUFA (LC-PUFA), a key determinant of nutritional quality. There was a wide variation in the proportions and absolute contents of EPA and DHA in the products. Relatively high contents of 18 : 1n-9, 18 : 2n-6 and 18 : 3n-3, characteristic of vegetable oils (VO), were found in several farmed salmon products, which also had generally lower proportions of EPA and DHA. In contrast, farmed salmon products with higher levels of 16 : 0 and 22 : 1, characteristic of fish oil (FO), had higher proportions of EPA and DHA. Therefore, there was a clear correlation between the levels of VO and FO in feeds and the proportions of n-3 LC-PUFA in products. Although wild salmon products were characterised by higher proportions of n-3 LC-PUFA (20-40%) compared with farmed fish (9-26%), they contained lower total lipid contents (1-6% compared with 7-17% in farmed salmon products). As a result, farmed salmon products invariably had higher levels of n-3 LC-PUFA in absolute terms (g/100 g fillet) and, therefore, delivered a higher 'dose' of EPA and DHA per portion. Overall, despite the finite and limiting supply of FO and increasing use of VO, farmed salmon continue to be an excellent source of and delivery system for n-3 LC-PUFA to consumers.

Microarray analysis of hepatic gene expression in juvenile Japanese flounder Paralichthys olivaceus fed diets supplemented with fish or vegetable oils

Gene expression profiling was performed in Japanese flounder Paralichthys olivaceus fed diets supplemented with fish oil (FO), linseed oil (LO), or olive oil (OO) for 6 weeks. The LO and OO groups showed significantly retarded growth, lower feed intake, lower protein efficiency ratio, and lower hepatosomatic index (P < 0.05). Liver fatty acid composition reflected the dietary fatty acid composition. Microarray analysis revealed that dietary n - 3 highly unsaturated fatty acid (HUFA) deficiency affected 169 transcripts. In the LO group, 57 genes were up-regulated and 38 genes were down-regulated, whereas in the OO group nine genes were up-regulated and 87 genes were down-regulated. Analysis of the functional annotations suggested that dietary n - 3 HUFA affected genes involved in signal transduction (23.2 %), cellular processes (21.1 %), metabolism (including glucose, lipid, and nucleobase; 15.5 %), transport (11.3 %), regulation of transcription (10.5 %), and immune response (4.2 %). Several genes encoding serine/threonine kinases such as protein kinase C and calmodulin-dependent kinase and nuclear hormone receptors such as vitamin D receptor, retinoic acid receptor, and receptors for cytokines (bone morphogenic protein and transforming growth factor β) were affected. Among 169 transcripts, 22 genes were affected in both LO and OO groups. The present study identified several genes involved in n - 3 HUFA deficiency-sensitive pathways, which will be useful for selective breeding of flounder strains able to adapt to n - 3 HUFA deficiency.

Changes in tissue lipid and fatty acid composition of farmed rainbow trout in response to dietary camelina oil as a replacement of fish oil

Camelina oil (CO) replaced 50 and 100 % of fish oil (FO) in diets for farmed rainbow trout (initial weight 44 ± 3 g fish(-1)). The oilseed is particularly unique due to its high lipid content (40 %) and high amount of 18:3n-3 (α-linolenic acid, ALA) (30 %). Replacing 100 % of fish oil with camelina oil did not negatively affect growth of rainbow trout after a 12-week feeding trial (FO = 168 ± 32 g fish(-1); CO = 184 ± 35 g fish(-1)). Lipid and fatty acid profiles of muscle, viscera and skin were significantly affected by the addition of CO after 12 weeks of feeding. However, final 22:6n-3 [docosahexaenoic acid (DHA)] and 20:5n-3 [eicosapentaenoic acid (EPA)] amounts (563 mg) in a 75 g fillet (1 serving) were enough to satisfy daily DHA and EPA requirements (250 mg) set by the World Health Organization. Other health benefits include lower SFA and higher MUFA in filets fed CO versus FO. Compound-specific stable isotope analysis (CSIA) confirmed that the δ(13)C isotopic signature of DHA in CO fed trout shifted significantly compared to DHA in FO fed trout. The shift in DHA δ(13)C indicates mixing of a terrestrial isotopic signature compared to the isotopic signature of DHA in fish oil-fed tissue. These results suggest that ~27 % of DHA was synthesized from the terrestrial and isotopically lighter ALA in the CO diet rather than incorporation of DHA from fish meal in the CO diet. This was the first study to use CSIA in a feeding experiment to demonstrate synthesis of DHA in fish.

Metabolism and fatty acid profile in fat and lean rainbow trout lines fed with vegetable oil: effect of carbohydrates

The present study investigated the effect of dietary carbohydrates on metabolism, with special focus on fatty acid bioconversion and flesh lipid composition in two rainbow trout lines divergently selected for muscle lipid content and fed with vegetable oils. These lines were chosen based on previously demonstrated potential differences in LC-PUFA synthesis and carbohydrate utilization. Applying a factorial study design, juvenile trout from the lean (L) and the fat (F) line were fed vegetable oil based diets with or without gelatinised starch (17.1%) for 12 weeks. Blood, liver, muscle, intestine and adipose tissue were sampled after the last meal. Feed intake and growth was higher in the L line than the F line, irrespective of the diet. Moderate postprandial hyperglycemia, strong induction of hepatic glucokinase and repressed glucose-6-phosphatase transcripts confirmed the metabolic response of both lines to carbohydrate intake. Further at the transcriptional level, dietary carbohydrate in the presence of n-3 LC-PUFA deficient vegetable oils enhanced intestinal chylomicron assembly, disturbed hepatic lipid metabolism and importantly elicited a higher response of key desaturase and elongase enzymes in the liver and intestine that endorsed our hypothesis. PPARγ was identified as the factor mediating this dietary regulation of fatty acid bioconversion enzymes in the liver. However, these molecular changes were not sufficient to modify the fatty acid composition of muscle or liver. Concerning the genotype effect, there was no evidence of substantial genotypic difference in lipid metabolism, LC-PUFA synthesis and flesh fatty acid profile when fed with vegetable oils. The minor reduction in plasma glucose and triglyceride levels in the F line was linked to potentially higher glucose and lipid uptake in the muscle. Overall, these data emphasize the importance of dietary macro-nutrient interface in evolving fish nutrition strategies.

Fatty acid desaturase 2 (FADS2) insertion/deletion polymorphism impact on muscle fatty acid profile in European grayling (Thymallus thymallus)

An insertion (In)/deletion (Del) polymorphism in the fatty acid desaturase 2 (FADS2) gene, which codes for Δ6-desaturase, was for the first time observed in fish. The polymorphism is located in the seventh intron of FADS2 and the insertion consists of eleven repeats of CTGT (44 bp) with an allelic frequency, for the insertion, of 39 %. The polymorphism was associated with a modulation in Δ6-desaturase activity as significant effects on the ratio of EPA or DHA to their precursors were found (P< 0·001). A different distribution of SFA, MUFA and PUFA among the In/In, In/Del and Del/Del groups was also detected in fish fillet. The results suggest that genetic selection for this marker might improve the ability of European grayling to utilise dietary n-3 long-chain PUFA precursors, as Δ6-desaturase is the rate-limiting enzyme in the production of EPA and DHA from α-linolenic acid.

Selection for high muscle fat in rainbow trout induces potentially higher chylomicron synthesis and PUFA biosynthesis in the intestine

Two lines of rainbow trout divergently selected for muscle fat content, fat line (F) and lean line (L) were used to investigate the effect of genetic selection on digestion, intestinal nutrient transport and fatty acid bioconversion, in relation to dietary starch intake. This study involved a digestibility trial for 2 weeks using Cr(2)O(3) as inert marker, followed by a feeding trial for 4 weeks. For the entire duration, juvenile trout from the two lines were fed diets with or without gelatinized starch. Blood, pyloric ceca, midgut and hindgut were sampled at 24 h after the last meal. Transcripts of the proteins involved in nutrient transport and fatty acid bioconversion were abundant in the proximal intestine. GLUT2 transcripts were slightly higher in the F line ceca than in the L line. Dietary starch intake did not enhance the transcription of intestinal glucose transporters, SGLT1 and GLUT2; but it was associated with the higher expression of ApoA1 and PepT1 in the midgut. Significantly, the F line exhibited higher intestinal mRNA levels of MTP, ApoA4, Elovl2, Elovl5 and D6D than the L line, linked to chylomicron assembly and fatty acid bioconversion. Apparent digestibility coefficients of protein, lipid and starch were high in both lines, but not significantly different between them. In conclusion, we found a higher potential of chylomicron synthesis and fatty acid bioconversion in the intestine of F line, but no adaptive transcriptional response of glucose transporters to dietary starch and no genotypic differences in nutrient digestibility.

Effects of genotype and dietary fish oil replacement with vegetable oil on the intestinal transcriptome and proteome of Atlantic salmon (Salmo salar)

Background

Expansion of aquaculture requires alternative feeds and breeding strategies to reduce dependency on fish oil (FO) and better utilization of dietary vegetable oil (VO). Despite the central role of intestine in maintaining body homeostasis and health, its molecular response to replacement of dietary FO by VO has been little investigated. This study employed transcriptomic and proteomic analyses to study effects of dietary VO in two family groups of Atlantic salmon selected for flesh lipid content, 'Lean' or 'Fat'.

Results

Metabolism, particularly of lipid and energy, was the functional category most affected by diet. Important effects were also measured in ribosomal proteins and signalling. The long-chain polyunsaturated fatty acid (LC-PUFA) biosynthesis pathway, assessed by fatty acid composition and gene expression, was influenced by genotype. Intestinal tissue contents of docosahexaenoic acid were equivalent in Lean salmon fed either a FO or VO diet and expression of LC-PUFA biosynthesis genes was up-regulated in VO-fed fish in Fat salmon. Dietary VO increased lipogenesis in Lean fish, assessed by expression of FAS, while no effect was observed on β-oxidation although transcripts of the mitochondrial respiratory chain were down-regulated, suggesting less active energetic metabolism in fish fed VO. In contrast, dietary VO up-regulated genes and proteins involved in detoxification, antioxidant defence and apoptosis, which could be associated with higher levels of polycyclic aromatic hydrocarbons in this diet. Regarding genotype, the following pathways were identified as being differentially affected: proteasomal proteolysis, response to oxidative and cellular stress (xenobiotic and oxidant metabolism and heat shock proteins), apoptosis and structural proteins particularly associated with tissue contractile properties. Genotype effects were accentuated by dietary VO.

Conclusions

Intestinal metabolism was affected by diet and genotype. Lean fish may have higher responsiveness to low dietary n-3 LC-PUFA, up-regulating the biosynthetic pathway when fed dietary VO. As global aquaculture searches for alternative oils for feeds, this study alerts to the potential of VO introducing contaminants and demonstrates the detoxifying role of intestine. Finally, data indicate genotype-specific responses in the intestinal transcriptome and proteome to dietary VO, including possibly structural properties of the intestinal layer and defence against cellular stress, with Lean fish being more susceptible to diet-induced oxidative stress.

Hepatic transcriptome analysis of inter-family variability in flesh n-3 long-chain polyunsaturated fatty acid content in Atlantic salmon

Background

Genetic selection of Atlantic salmon families better adapted to alternative feed formulations containing high levels of vegetable ingredients has been suggested to ensure sustainable growth of aquaculture. The present study aimed to identify molecular pathways that could underlie phenotypic differences in flesh n-3 long-chain polyunsaturated fatty acid (LC-PUFA) levels when fish are fed vegetable oil diets. Liver transcriptome was analyzed and compared in four families presenting higher or lower n-3 LC-PUFA contents at two contrasting flesh total lipid levels.

Results

The main effect of n-3 LC-PUFA contents was in the expression of immune response genes (38% of all significantly affected genes), broadly implicated in the modulation of inflammatory processes and innate immune response. Although genetic evaluations of traits used in the breeding program revealed that the chosen families were not balanced for viral disease resistance, this did not fully explain the preponderance of immune response genes in the transcriptomic analysis. Employing stringent statistical analysis no lipid metabolism genes were detected as being significantly altered in liver when comparing families with high and low n-3 LC-PUFA flesh contents. However, relaxing the statistical analysis enabled identification of potentially relevant effects, further studied by RT-qPCR, in cholesterol biosynthesis, lipoprotein metabolism and lipid transport, as well as eicosanoid metabolism particularly affecting the lipoxygenase pathway. Total lipid level in flesh also showed an important effect on immune response and 8% of significantly affected genes related to lipid metabolism, including a fatty acyl elongase (elovl2), an acyl carrier protein and stearoyl-CoA desaturase.

Conclusions

Inter-family differences in n-3 LC-PUFA content could not be related to effects on lipid metabolism, including transcriptional modulation of the LC-PUFA biosynthesis pathway. An association was found between flesh adiposity and n-3 LC-PUFA in regulation of cholesterol biosynthesis, which was most likely explained by variation in tissue n-3 LC-PUFA levels regulating transcription of cholesterol metabolism genes through srebp2. A preponderance of immune response genes significantly affected by n-3 LC-PUFA contents could be potentially associated with disease resistance, possibly involving anti-inflammatory actions of tissue n-3 LC-PUFA through eicosanoid metabolism. This association may have been fortuitous, but it is important to clarify if this trait is included in future salmon breeding programmes.

Metabolic responses to high-fat diets rich in n-3 or n-6 long-chain polyunsaturated fatty acids in mice selected for either high body weight or leanness explain different health outcomes

Background

Increasing evidence suggests that diets high in polyunsaturated fatty acids (PUFA) confer health benefits by improving insulin sensitivity and lipid metabolism in liver, muscle and adipose tissue.

Methods

The present study investigates metabolic responses in two different lines of mice either selected for high body weight (DU6) leading to rapid obesity development, or selected for high treadmill performance (DUhTP) leading to a lean phenotype. At 29 days of age the mice were fed standard chow (7.2% fat, 25.7% protein), or a high-fat diet rich in n-3 PUFA (n-3 HFD, 27.7% fat, 19% protein) or a high-fat diet rich in n-6 PUFA (n-6 HFD, 27.7% fat, 18.6% protein) for 8 weeks. The aim of the study was to determine the effect of these PUFA-rich high-fat diets on the fatty acid profile and on the protein expression of key components of insulin signalling pathways.

Results

Plasma concentrations of leptin and insulin were higher in DU6 in comparison with DUhTP mice. The high-fat diets stimulated a strong increase in leptin levels and body fat only in DU6 mice. Muscle and liver fatty acid composition were clearly changed by dietary lipid composition. In both lines of mice n-3 HFD feeding significantly reduced the hepatic insulin receptor β protein concentration which may explain decreased insulin action in liver. In contrast, protein kinase C ζ expression increased strongly in abdominal fat of n-3 HFD fed DUhTP mice, indicating enhanced insulin sensitivity in adipose tissue.

Conclusions

A diet high in n-3 PUFA may facilitate a shift from fuel deposition in liver to fuel storage as fat in adipose tissue in mice. Tissue specific changes in insulin sensitivity may describe, at least in part, the health improving properties of dietary n-3 PUFA. However, important genotype-diet interactions may explain why such diets have little effect in some population groups.

Diet × genotype interactions in hepatic cholesterol and lipoprotein metabolism in Atlantic salmon (Salmo salar) in response to replacement of dietary fish oil with vegetable oil

The present study investigates the effects of genotype on responses to alternative feeds in Atlantic salmon. Microarray analysis of the liver transcriptome of two family groups, lean or fat, fed a diet containing either a fish oil (FO) or a vegetable oil (VO) blend indicated that pathways of cholesterol and lipoprotein metabolism might be differentially affected by the diet depending on the genetic background of the fish, and this was further investigated by real-time quantitative PCR, plasma and lipoprotein biochemical analysis. Results indicate a reduction in VLDL and LDL levels, with no changes in HDL, when FO is replaced by VO in the lean family group, whereas in fat fish fed FO, levels of apoB-containing lipoproteins were low and comparable with those fed VO in both family groups. Significantly lower levels of plasma TAG and LDL-TAG were measured in the fat group that was independent of diet, whereas plasma cholesterol was significantly higher in fish fed the FO diet in both groups. Hepatic expression of genes involved in cholesterol homeostasis, β-oxidation and lipoprotein metabolism showed relatively subtle changes. A significantly lower expression of genes considered anti-atherogenic in mammals (ATP-binding cassette transporter A1, apoAI, scavenger receptor class B type 1, lipoprotein lipase (LPL)b (TC67836) and LPLc (TC84899)) was found in lean fish, compared with fat fish, when fed VO. Furthermore, the lean family group appeared to show a greater response to diet composition in the cholesterol biosynthesis pathway, mediated by sterol-responsive element-binding protein 2. Finally, the presence of three different transcripts for LPL, with differential patterns of nutritional regulation, was demonstrated.

Genotype-specific responses in Atlantic salmon (Salmo salar) subject to dietary fish oil replacement by vegetable oil: a liver transcriptomic analysis

Background

Expansion of aquaculture is seriously limited by reductions in fish oil (FO) supply for aquafeeds. Terrestrial alternatives such as vegetable oils (VO) have been investigated and recently a strategy combining genetic selection with changes in diet formulations has been proposed to meet growing demands for aquaculture products. This study investigates the influence of genotype on transcriptomic responses to sustainable feeds in Atlantic salmon.

Results

A microarray analysis was performed to investigate the liver transcriptome of two family groups selected according to their estimated breeding values (EBVs) for flesh lipid content, 'Lean' or 'Fat', fed diets containing either FO or a VO blend. Diet principally affected metabolism genes, mainly of lipid and carbohydrate, followed by immune response genes. Genotype had a much lower impact on metabolism-related genes and affected mostly signalling pathways. Replacement of dietary FO by VO caused an up-regulation of long-chain polyunsaturated fatty acid biosynthesis, but there was a clear genotype effect as fatty acyl elongase (elovl2) was only up-regulated and desaturases (Δ5 fad and Δ6 fad) showed a higher magnitude of response in Lean fish, which was reflected in liver fatty acid composition. Fatty acid synthase (FAS) was also up-regulated by VO and the effect was independent of genotype. Genetic background of the fish clearly affected regulation of lipid metabolism, as PPARα and PPARβ were down-regulated by the VO diet only in Lean fish, while in Fat salmon SREBP-1 expression was up-regulated by VO. In addition, all three genes had a lower expression in the Lean family group than in the Fat, when fed VO. Differences in muscle adiposity between family groups may have been caused by higher levels of hepatic fatty acid and glycerophospholipid synthesis in the Fat fish, as indicated by the expression of FAS, 1-acyl-sn-glycerol-3-phosphate acyltransferase and lipid phosphate phosphohydrolase 2.

Conclusions

This study has identified metabolic pathways and key regulators that may respond differently to alternative plant-based feeds depending on genotype. Further studies are required but data suggest that it will be possible to identify families better adapted to alternative diet formulations that might be appropriate for future genetic selection programmes.