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Inulin affects nutrition and metabolism in many animals. Although inulin is widely used in the diet of teleosts, its mechanism of action is unknown. Here, we investigated the effect of inulin (2 %) on the intestinal microbiome and metabolism in rainbow trout (Oncorhynchus mykiss) selected for growth and survival when fed a 100 % plant-based diet (suave) and a control line (temoin). Metabolic responses to the two factors (line and inulin) in liver, intestine, muscle and adipose were tissue-specific, with line and interaction between the two factors influencing overall expression in liver. In the intestine, inulin and line and in muscle, line influenced the expression of metabolic genes. Microbiota between the mucus and digestive contents was significantly different, with genera from Proteobacteria being more abundant in the mucus, whereas genera from the Firmicutes and Planctomycetes being more abundant in contents. Effect of inulin and interaction between factors on the microbiome was evident in contents. The significant taxa of control and inulin-fed groups differed greatly with Streptococcus and Weissella being significantly abundant in the inulin-fed group. There was a general trend showing higher levels of all SCFA in temoin group with propionic acid levels being significantly higher. An operational taxonomic unit (OTU) belonging to the Ruminococcaceae was significantly abundant in suave. The tissue-specific correlations between OTU and gene expression may indicate the link between microbiome and metabolism. Together, these results suggest that line and inulin impact the gene expression in a tissue-specific manner, possibly driven by specific OTUs enriched in inulin-fed groups and suave. [ABSTRACT FROM AUTHOR]

Background: Selective breeding is a promising solution to reduce the vulnerability of fish farms to heat waves, which are predicted to increase in intensity and frequency. However, limited information about the genetic architecture of acute hyperthermia resistance in fish is available. Two batches of sibs from a rainbow trout commercial line were produced: the first (N = 1382) was phenotyped for acute hyperthermia resistance at nine months of age and the second (N = 1506) was phenotyped for main production traits (growth, body length, muscle fat content and carcass yield) at 20 months of age. Fish were genotyped on a 57 K single nucleotide polymorphism (SNP) array and their genotypes were imputed to high-density based on the parent's genotypes from a 665 K SNP array. Results: The heritability estimate of resistance to acute hyperthermia was 0.29 ± 0.05, confirming the potential of selective breeding for this trait. Since genetic correlations of acute hyperthermia resistance with the main production traits near harvest age were all close to zero, selecting for acute hyperthermia resistance should not impact the main production traits, and vice-versa. A genome-wide association study revealed that resistance to acute hyperthermia is a highly polygenic trait, with six quantitative trait loci (QTL) detected, but explaining less than 5% of the genetic variance. Two of these QTL, including the most significant one, may explain differences in acute hyperthermia resistance across INRAE isogenic lines of rainbow trout. Differences in mean acute hyperthermia resistance phenotypes between homozygotes at the most significant SNP was 69% of the phenotypic standard deviation, showing promising potential for marker-assisted selection. We identified 89 candidate genes within the QTL regions, among which the most convincing functional candidates are dnajc7, hsp70b, nkiras2, cdk12, phb, fkbp10, ddx5, cygb1, enpp7, pdhx and acly. Conclusions: This study provides valuable insight into the genetic architecture of acute hyperthermia resistance in juvenile rainbow trout. We show that the selection potential for this trait is substantial and selection for this trait should not be too detrimental to improvement of other traits of interest. Identified functional candidate genes provide new knowledge on the physiological mechanisms involved in acute hyperthermia resistance, such as protein chaperoning, oxidative stress response, homeostasis maintenance and cell survival. [ABSTRACT FROM AUTHOR]

Single nucleotide polymorphism (SNP) arrays, also named « SNP chips », enable very large numbers of individuals to be genotyped at a targeted set of thousands of genome-wide identified markers. We used preexisting variant datasets from USDA, a French commercial line and 30X-coverage whole genome sequencing of INRAE isogenic lines to develop an Affymetrix 665 K SNP array (HD chip) for rainbow trout. In total, we identified 32,372,492 SNPs that were polymorphic in the USDA or INRAE databases. A subset of identified SNPs were selected for inclusion on the chip, prioritizing SNPs whose flanking sequence uniquely aligned to the Swanson reference genome, with homogenous repartition over the genome and the highest Minimum Allele Frequency in both USDA and French databases. Of the 664,531 SNPs which passed the Affymetrix quality filters and were manufactured on the HD chip, 65.3% and 60.9% passed filtering metrics and were polymorphic in two other distinct French commercial populations in which, respectively, 288 and 175 sampled fish were genotyped. Only 576,118 SNPs mapped uniquely on both Swanson and Arlee reference genomes, and 12,071 SNPs did not map at all on the Arlee reference genome. Among those 576,118 SNPs, 38,948 SNPs were kept from the commercially available medium-density 57 K SNP chip. We demonstrate the utility of the HD chip by describing the high rates of linkage disequilibrium at 2–10 kb in the rainbow trout genome in comparison to the linkage disequilibrium observed at 50–100 kb which are usual distances between markers of the medium-density chip. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Phenotypic plasticity is a key component of the ability of organisms to respond to changing environmental conditions. In this study, we aimed to study the establishment of DNA methylation marks in response to an environmental stress in rainbow trout and to assess whether these marks depend on the genetic background. The environmental stress chosen here was temperature, a known induction factor of epigenetic marks in fish. To disentangle the role of epigenetic mechanisms such as DNA methylation in generating phenotypic variations, nine rainbow trout isogenic lines with no genetic variability within a line were used. For each line, half of the eggs were incubated at standard temperature (11°C) and the other half at high temperature (16°C), from eyed-stage to hatching. In order to gain a first insight into the establishment of DNA methylation marks in response to an early temperature regime (control 11°C vs. heated 16°C), we have studied the expression of 8 dnmt3 (DNA methyltransferase) genes, potentially involved in de novo methylation, and analysed global DNA methylation in the different rainbow trout isogenic lines using LUMA (LUminometric Methylation Assay). Finally, finer investigation of genome-wide methylation patterns was performed using EpiRADseq, a reduced-representation library approach based on the ddRADseq (Double Digest Restriction Associated DNA) protocol, for six rainbow trout isogenic lines. We have demonstrated that thermal history during embryonic development alters patterns of DNA methylation, but to a greater or lesser extent depending on the genetic background. [ABSTRACT FROM AUTHOR]

One of the top priorities of the aquaculture industry is the genetic improvement of economically important traits in fish, such as those related to processing and quality. However, the accuracy of genetic evaluations has been hindered by a lack of data on such traits from a sufficiently large population of animals. The objectives of this study were thus threefold: (i) to estimate genetic parameters of growth-, yield-, and quality-related traits in rainbow trout (Oncorhynchus mykiss) using three different phenotyping technologies [invasive and non-invasive: microwave-based, digital image analysis, and magnetic resonance imaging (MRI)], (ii) to detect quantitative trait loci (QTLs) associated with these traits, and (iii) to identify candidate genes present within these QTL regions. Our study collected data from 1,379 fish on growth, yield-related traits (body weight, condition coefficient, head yield, carcass yield, headless gutted carcass yield), and quality-related traits (total fat, percentage of fat in subcutaneous adipose tissue, percentage of fat in flesh, flesh colour); genotypic data were then obtained for all fish using the 57K SNP Axiom® Trout Genotyping array. Heritability estimates for most of the 14 traits examined were moderate to strong, varying from 0.12 to 0.67. Most traits were clearly polygenic, but our genome-wide association studies (GWASs) identified two genomic regions on chromosome 8 that explained up to 10% of the genetic variance (cumulative effects of two QTLs) for several traits (weight, condition coefficient, subcutaneous and total fat content, carcass and headless gutted carcass yields). For flesh colour traits, six QTLs explained 1–4% of the genetic variance. Within these regions, we identified several genes (htr1 , gnpat , ephx1 , bcmo1 , and cyp2x) that have been implicated in adipogenesis or carotenoid metabolism, and thus represent good candidates for further functional validation. Finally, of the three techniques used for phenotyping, MRI demonstrated particular promise for measurements of fat content and distribution, while the digital image analysis-based approach was very useful in quantifying colour-related traits. This work provides new insights that may aid the development of commercial breeding programmes in rainbow trout, specifically with regard to the genetic improvement of yield and flesh-quality traits as well as the use of invasive and/or non-invasive technologies to predict such traits. [ABSTRACT FROM AUTHOR]

Fillet yield, the proportion of edible fillet relative to body weight, is a major trait to improve in fish sold processed, as it has a direct impact on profitability and can simultaneously decrease the environmental impact of producing a given amount of fillet. However, it is difficult to improve by selective breeding, because it cannot be measured on live breeding candidates, its phenotypic variation is low, and, as a ratio, it is not normally distributed and a same change in fillet yield can be the result of different changes in fillet weight and body weight. Residual headless gutted carcass weight (rHGCW) is heritable and highly genetically correlated to Fillet% in rainbow trout, and can be predicted by the ratio of abdominal wall thickness to depth of the peritoneal cavity (E8/E23), measured on live fish by ultrasound tomography. We selected broodstock based on rHGCW, measured on sibs of the selection candidates, on ultrasound measurements (E8/E23) measured on the selection candidates, or a combination of both. Seven broodstock groups were selected: fish with 15% highest (rHGCW+) or lowest (rHGCW−) EBV for rHGCW, with 15% highest (E8/E23+) or lowest (E8/E23−) EBV for E8/E23, with both rHGCW+ and E8/E23+ (Both+) or rHGCW− and E8/E23− (Both−), or with close to zero EBVs for both traits (Mid). Seven corresponding groups of offspring were produced and reared communally. At harvest size (1.5 kg mean weight), 1,561 trout were slaughtered, measured for the traits of interest, and pedigreed with DNA fingerprinting. Offspring from groups Both+, rHGCW+ and E8/E23+ had a higher EBV for rHGCW than the control group, while down-selected groups had a lower EBV. Looking at the phenotypic mean for Fillet% (correlated response), up-selected fish had more fillet than down-selected fish. The highest difference was between Both+ (69.36%) and Both− (68.20%), a 1.16% units difference in fillet percentage. The change in Fillet% was explained by an opposite change in Viscera%, while Head% remained stable. Selection using sib information on rHGCW was on average more efficient than selection using the candidates' own E8/E23 phenotypes, and downward selection (decreasing Fillet%) was more efficient than upward selection. [ABSTRACT FROM AUTHOR]

To meet the growing demand of fish feed for aquaculture, an increasing proportion of marine ingredients are being replaced by blends of plant products. However, the total replacement of marine ingredients in salmonid diets impairs fish performance. This is particularly true during the early fry stage and this stage is therefore considered of particular importance. In rainbow trout (RBT), the existence of a genetic variability to survive and grow with plant-based diets devoid of marine ingredients has now been proved, but the mechanisms behind are little studied especially at early stage. To investigate these, we analysed the whole transcriptome of three isogenic lines of RBT fry, which have similar growth when fed a marine resources-based diet (M diet) but which highly differ in their responses to a plant-based diet (V diet). Analysis of transcriptomes profiles revealed 1740, 1834 and 246 probes differentially expressed among the three genotypes when fed the V diet. The use of these lines led to the discovery of potential molecular markers linked to plant-based diet utilisation, some of them belonging to new pathways, never described before. An important number of genes was related to immunity, but further investigations are needed to better understand the difference between the genotypes in their immune status response to V diet exposure. Finally, differences in expression of genes related to feed intake and sensory perception among genotypes suggested that the mechanisms underlying the differences in growth on plant-based diet are closely linked to diet acceptance. Research on plants components affecting feed intake should be thus further explored. [ABSTRACT FROM AUTHOR]

When compared with fish meal and fish oil, plant ingredients differ not only in their protein content and amino acid and fatty acid profiles but are also devoid of cholesterol, the major component of cell membrane and precursor of several bioactive compounds. Based on these nutritional characteristics, plant-based diets can affect fish physiology and cholesterol metabolism. To investigate the mechanisms underlying cholesterol homeostasis, rainbow trout were fed from 1 g body wt for 6 mo with a totally plant-based diet (V), a marine diet (M), and a marine-restricted diet (MR), with feed intake adjusted to that of the V group. The expression of genes involved in cholesterol synthesis, esterification, excretion, bile acid synthesis, and cholesterol efflux was measured in liver. Results showed that genes involved in cholesterol synthesis were upregulated in trout fed the V diet, whereas expression of genes related to bile acid synthesis (cyp7a1) and cholesterol elimination (abcg8) were reduced. Feeding trout the V diet also enhanced the expression of srebp-2 while reducing that of lxrα and miR-223. Overall, these data suggested that rainbow trout coped with the altered nutritional characteristics and absence of dietary cholesterol supply by increasing cholesterol synthesis and limiting cholesterol efflux through molecular mechanisms involving at least srebp-2, lxrα, and miR-223. However, plasma and body cholesterol levels in trout fed the V diet were lower than in fish fed the M diet, raising the question of the role of cholesterol in the negative effect of plant-based diet on growt [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Background: The achievement of sustainable feeding practices in aquaculture by reducing the reliance on wild-captured fish, via replacement of fish-based feed with plant-based feed, is impeded by the poor growth response seen in fish fed high levels of plant ingredients. Our recent strategy to nutritionally program rainbow trout by early short-term exposure to a plant-based (V) diet versus a control fish-based (M) diet at the first-feeding fry stage when the trout fry start to consume exogenous feed, resulted in remarkable improvements in feed intake, growth and feed utilization when the same fish were challenged with the diet V (V-challenge) at the juvenile stage, several months following initial exposure. We employed microarray expression analysis at the first-feeding and juvenile stages to deduce the mechanisms associated with the nutritional programming of plant-based feed acceptance in trout. Results: Transcriptomic analysis was performed on rainbow trout whole fry after 3 weeks exposure to either diet V or diet M at the first feeding stage (3-week), and in the whole brain and liver of juvenile trout after a 25 day V-challenge, using a rainbow trout custom oligonucleotide microarray. Overall, 1787 (3-week + Brain) and 924 (3-week + Liver) mRNA probes were affected by the early-feeding exposure. Gene ontology and pathway analysis of the corresponding genes revealed that nutritional programming affects pathways of sensory perception, synaptic transmission, cognitive processes and neuroendocrine peptides in the brain; whereas in the liver, pathways mediating intermediary metabolism, xenobiotic metabolism, proteolysis, and cytoskeletal regulation of cell cycle are affected. These results suggest that the nutritionally programmed enhanced acceptance of a plant-based feed in rainbow trout is driven by probable acquisition of flavour and feed preferences, and reduced sensitivity to changes in hepatic metabolic and stress pathways. Conclusions: This study outlines the molecular mechanisms in trout brain and liver that accompany the nutritional programming of plant-based diet acceptance in trout, reinforces the notion of the first-feeding stage in oviparous fish as a critical window for nutritional programming, and provides support for utilizing this strategy to achieve improvements in sustainability of feeding practices in aquaculture. [ABSTRACT FROM AUTHOR]

Terrestrial plant resources are increasingly used as substitutes for fish meal and fish oil in fish feed in order to reduce the reliance of aquaculture on marine fishery resources. Although many studies have been conducted to assess the effects of such nutritional transition, no whole breeding cycles of fish fed diets free from marine resources has been reported to date. We therefore studied the reproductive performance of trout after a complete cycle of breeding while consuming a diet totally devoid of marine ingredients and thus of n-3 long chain polyunsaturated fatty acids (n-3 LC-PUFAs) that play a major role in the formation of ova. Two groups of female rainbow trout were fed from first feeding either a commercial diet (C, marine and plant ingredients), or a 100% plant-based diet (V, blend of plant proteins and vegetable oils). Livers, viscera, carcasses and ova were sampled at spawning and analyzed for lipids and fatty acids. Although the V-diet was devoid of n-3 LC-PUFAs, significant amounts of EPA and DHA were found in livers and ova, demonstrating efficient bioconversion of linolenic acid and selective orientation towards the ova. Some ova were fertilized to assess the reproductive performance and offspring survival. We observed for the first time that trout fed a 100% plant-based diet over a 3-year breeding cycle were able to produce ova and viable alevins, although the ova were smaller. The survival of offspring from V-fed females was lower (-22%) at first spawning, but not at the second. Our study showed that, in addition to being able to grow on a plant-based diet, rainbow trout reared entirely on such a diet can successfully produce ova in which neo-synthesized n-3 LC-PUFAs are accumulated, leading to viable offspring. However, further adjustment of the feed formula is still needed to optimize reproductive performance. [ABSTRACT FROM AUTHOR]

The study of inter-individual variability of personality in fish is a growing field of interest but the genetic basis of this complex trait is still poorly investigated due to the difficulty in controlling fish genetic origin and life history. When available, isogenic lines that allow performing independent tests on different individuals having identical genotype constitute a very relevant experimental material to disentangle the genetic and environmental components of behavioural individuality. We took advantage of heterozygous isogenic lines to investigate the personality in rainbow trout through the analysis of their reactions to different experimental situations. To this end, seven to ten rainbow trout isogenic lines were screened for their spatial exploratory behaviour, their flight response toward a stressor and their risk taking behaviour. Results showed that some lines seemed less sensitive to new events or environmental changes and could be defined as low responsive, while others were very sensitive and defined as high responsive. The use of isogenic lines highlighted the importance of genetic factors, in combination with life history, in the expression of personality in domesticated fish. [ABSTRACT FROM AUTHOR]

Sustainable aquaculture, which entails proportional replacement of fish-based feed sources by plant-based ingredients, is impeded by the poor growth response frequently seen in fish fed high levels of plant ingredients. This study explores the potential to improve, by means of early nutritional exposure, the growth of fish fed plant-based feed. Rainbow trout swim-up fry were fed for 3 weeks either a plant-based diet (diet V, V-fish) or a diet containing fishmeal and fish oil as protein and fat source (diet M, M-fish). After this 3-wk nutritional history period, all V- or M-fish received diet M for a 7-month intermediate growth phase. Both groups were then challenged by feeding diet V for 25 days during which voluntary feed intake, growth, and nutrient utilisation were monitored (V-challenge). Three isogenic rainbow trout lines were used for evaluating possible family effects. The results of the V-challenge showed a 42% higher growth rate (P = 0.002) and 30% higher feed intake (P = 0.005) in fish of nutritional history V compared to M (averaged over the three families). Besides the effects on feed intake, V-fish utilized diet V more efficiently than M-fish, as reflected by the on average 18% higher feed efficiency (P = 0.003). We noted a significant family effect for the above parameters (P<0.001), but the nutritional history effect was consistent for all three families (no interaction effect, P>0.05). In summary, our study shows that an early short-term exposure of rainbow trout fry to a plant-based diet improves acceptance and utilization of the same diet when given at later life stages. This positive response is encouraging as a potential strategy to improve the use of plant-based feed in fish, of interest in the field of fish farming and animal nutrition in general. Future work needs to determine the persistency of this positive early feeding effect and the underlying mechanisms. [ABSTRACT FROM AUTHOR]

Abstract: This study examined the genetic variability and genotype×diet interactions during early growth (initial mean body weight 1.2g) among seven heterozygous clones of rainbow trout, Oncorhynchus mykiss. The clones were hand-fed a diet containing either fishmeal or plant proteins during a 49-day trial divided into two periods (P1, 26days, and P2, 23days). Weight, variation of weight within clone, feed intake, feed efficiency and mortality were calculated for both periods. There was a highly significant effect of diet and of clone for all traits at both periods, except for feed efficiency and mortality at P1. Highly significant interactions between diet and clone were also recorded for all these traits, except for mortality at P1. The occurrence of genotype×diet interactions when feeding juvenile rainbow trout with an all plant-protein diet indicates that a highly performing genotype on a fishmeal diet may perform poorly when fed a plant-protein diet. Interactions were found for the two major determinants of growth, i.e. feed intake and feed efficiency, showing that the dietary response differs according to the genotype. Monitoring of the within-clone variability of weight showed that a plant-based diet is likely to enhance the overall phenotypic variance in a population, whatever its initial genetic variability. [Copyright &y& Elsevier]

The article discusses a study which examines the impact of sexual maturation on heritability calculation among rainbow trout (Oncorhynchus mykiss). In the study, body weight was recorded and gonads weight was used to calculate the gonado-somatic index (GSI) to identify matured males. The study concludes that sexual maturation greatly affects the genetic variability of weight without taking into account the effects in quantitative genetics models.

Background: Selective breeding is a relatively recent practice in aquaculture species compared to terrestrial livestock. Nevertheless, the genetic variability of farmed salmonid lines, which have been selected for several generations, should be assessed. Indeed, a significant decrease in genetic variability due to high selection intensity could have occurred, potentially jeopardizing the long-term genetic progress as well as the adaptive capacities of populations facing change(s) in the environment. Thus, it is important to evaluate the impact of selection practices on genetic diversity to limit future inbreeding. The current study presents an analysis of genetic diversity within and between six French rainbow trout (Oncorhynchus mykiss) experimental or commercial lines based on a medium-density single nucleotide polymorphism (SNP) chip and various molecular genetic indicators: fixation index (FST), linkage disequilibrium (LD), effective population size (Ne) and inbreeding coefficient derived from runs of homozygosity (ROH). Results: Our results showed a moderate level of genetic differentiation between selected lines (FST ranging from 0.08 to 0.15). LD declined rapidly over the first 100 kb, but then remained quite high at long distances, leading to low estimates of Ne in the last generation ranging from 24 to 68 depending on the line and methodology considered. These results were consistent with inbreeding estimates that varied from 10.0% in an unselected experimental line to 19.5% in a commercial line, and which are clearly higher than corresponding estimates in ruminants or pigs. In addition, strong variations in LD and inbreeding were observed along the genome that may be due to differences in local rates of recombination or due to key genes that tended to have fixed favorable alleles for domestication or production. Conclusions: This is the first report on ROH for any aquaculture species. Inbreeding appeared to be moderate to high in the six French rainbow trout lines, due to founder effects at the start of the breeding programs, but also likely to sweepstakes reproductive success in addition to selection for the selected lines. Efficient management of inbreeding is a major goal in breeding programs to ensure that populations can adapt to future breeding objectives and SNP information can be used to manage the rate at which inbreeding builds up in the fish genome. [ABSTRACT FROM AUTHOR]

To expand the availability of marketable eyed eggs, a common practice in rainbow trout aquaculture is to store eyed eggs at low temperatures (2–4 °C) for periods of up to 2–3 weeks. Early exposure to environmental stimuli such as temperature can impact fish physiology, growth, metabolism, and nutrition at mid- or long-term questioning about the potential effects of such breeder practice. This study aimed to test the impact of incubating eyed eggs at low temperatures (3 °C instead of 12 °C) for 15 days on resistance to later stresses using two experimental rainbow trout lines divergent for fat content. Plasma parameters (i.e. cortisol, glucose, lactate, and chloride ions) have been measured after an acute confinement challenge. For the hyperthermia challenge, time at the loss of equilibrium was compared between lines and incubation temperatures. Our results showed that deformities rate and early survival were not affected by cold temperature storage. Furthermore, plasma parameters measured after the confinement were not impacted by temperature. The two lines differently responded to the hyperthermia challenges with the fat line showing significantly higher resistance to temperature elevation. These findings suggest that the incubation temperature did not impair the responses to stress at the juvenile stage, indicating that the practice of cold storage of eyed eggs does not appear to be detrimental to subsequent rearing. • Stress response was evaluated in juvenile rainbow trout of two divergent experimental lines incubated at cold temperature. • Deformities rate and early survival were not affected by cold temperature incubation. • Plasmatic parameters measured after a confinement challenge were not influenced by the incubation temperature. • Incubation temperature did not affect the time of equilibrium loss in a hyperthermia challenge. • The two experimental lines responded differently to hyperthermia challenges. [ABSTRACT FROM AUTHOR]

Accurately measuring individual feed intake is required to include feed efficiency (FE) as an objective in commercial breeding programs. Phenotyping individual feed intake through direct measurements remains complex in fish reared in groups. One way to overcome this challenge is to find proxies for estimating FE. This study aimed to investigate the correlations between fish FE and potential predictive criteria in rainbow trout Oncorhynchus mykiss. As predictive criteria, we considered the variations of body weight assessed as thermal growth coefficients (TGC) and the feeding behaviour assessed as the number of feed demands over a period and the proportion of the demands made before noon. Feed intake was assessed over three different periods in ten isogenic lines allowing a recording for each of the ten genotypes while keeping fish in groups. The protocol consisted of two successive feed deprivation and refeeding phases after initial basal growth periods. Correlations were then calculated between FE, measured either as feed conversion ratio (FCR) or residual feed intake (RFI), and the different indirect criteria. We found positive phenotypic correlations between FCR and RFI over the feed intake measurement periods (r ⩾ 0.79, P < 0.001). Assessment of the relationship between FE traits (FCR and RFI) calculated over the three measurement periods and TGC revealed no significant association. Regarding feeding behaviour, significant differences in the daily profile of feed demands and their numbers were found among the ten isogenic lines. RFI calculated from the first feed intake measurement period and feeding behaviour, assessed as the number of feed demands were positively correlated (r = 0.42–0.49, P ⩽ 0.022). Nevertheless, such correlations were not established for the two other measurement periods following feed deprivation. While we demonstrated that the weight variations during feed deprivation are not a good proxy for FE (FCR or RFI) in rainbow trout, we also highlighted the interest in exploring more the relationships between FE and feeding behaviour in fish. • Feed efficiency was assessed through FCR and RFI in rainbow trout isogenic lines. • Weight and feeding behaviour were followed over starvation and refeeding periods. • Feeding behaviour traits differed among the ten isogenic lines. • There is no association between feed efficiency and thermal growth coefficients. • Correlation was found between RFI and feed demands but not constant over time. [ABSTRACT FROM AUTHOR]

Abstract For the sustainable development of aquaculture, vegetable ingredients have been used to replace the traditional ingredients fishmeal and fish oil in aquafeeds. On the other hand, selective breeding has also been implemented at research level to obtain strains that are adapted to feeding on the plant-based diet. To better understand the underlying mechanisms prompting the adaptation to plant-based diets in fish, we investigated the hepatic expression of several microRNAs (miRNAs) that are involved in the post-transcriptional regulation of cholesterol and lipid metabolism at 8 h and 16 h after the last meal in two lines of rainbow trout: one selected for better adaptation to plant-based diets and the corresponding control line. Both groups were fed either a fishmeal and fish oil based diet or a 100% plant-based diet. Results showed that the expression of miR-33a in liver was greatly elevated in trout fed the plant-based diet, while the expression of miR-122 and miR-128 was much higher in the selected line at 8 h after the last meal regardless of the diet. Furthermore, our results indicated that some genes involved in immune processes (caspase 6 apoptosis-related cysteine peptidase like 2, casp6l2) and cAMP signal transduction (phosphodiesterase 4B cAMP-specific a, pde4ba) were also potentially regulated by miRNAs. They were newly identified as putative direct targets of miRNAs and affected in trout fed the plant-based diet. Though further investigations are still needed to establish a valid relationship between miRNAs and their target genes, our study found miR-33a, miR-122 and miR-128 as potential candidates for further study and provided new perspectives to understand the role of miRNAs in the selective breeding for adaptation to the plant-based diets. Highlights • Hepatic expression of miR-33a is enhanced in trout fed plant-based diet • Selection of trout for better adaptation to plant-based diet influences the hepatic expression of miR-122 and miR-128 • Expression of caspase 6 apoptosis-related cysteine peptidase like 2, casp6l2 is potentially directly inhibited by miR-33a • cyp27a , pde4ba and roraa are newly identified as genes regulated by plant-based diet in trout [ABSTRACT FROM AUTHOR]

Marker-based parentage assignment provides the opportunity to investigate factors of efficiency for mixed-family designs and factorial mating. In such designs, family size is both uncontrolled and small, which may be thought to limit the accuracy of estimated breeding values (EBVs). The objective of this work was to estimate the accuracy of EBVs of growth and quality traits in a large factorial mating design and in commercial breeding conditions. An expected six hundred full-sib families of rainbow trout Oncorhynchus mykiss (2042 fish in total) were produced by ten factorial matings of six dams with ten sires. Fish were phenotyped for body weight, carcass yield, fillet yield, fillet fat content and fillet colour, and family information was recovered using microsatellite markers. The accuracy of EBVs was estimated using or removing individual performance to mimic combined family selection (with individual phenotype) or sib selection (without individual phenotype). The traits investigated had medium to high heritability (0.17–0.58). High to very high accuracy (0.630–0.817) was estimated for combined family selection. The accuracy of sib selection (not using individual phenotype) was 18–22% lower (0.542–0.638), but remained in the upper range reported for such traits. This level of accuracy was higher than those reported in conventional breeding programs using separate family rearing. This was true even for families with a very low number of full-sibs. Individual EBV accuracy was more closely linked to the total number of full- and half-sibs of each fish than to its number of full-sibs. We hypothesize that this was due to the factorial mating, which led to a high number of the genetic ties between sibs. These results highlight the possibility of introducing precise estimated breeding values for quality traits into combined or sib selection in breeding programs when using mixed families from factorial designs and marker-based parentage assignment in aquaculture species. [ABSTRACT FROM AUTHOR]

Abstract: Selection to improve processing yields relies on sib selection, in which live candidates are ranked according to their family breeding value. This approach limits genetic progress, as it only exploits genetic variability between families and not within them. Indirect criteria measured on live candidates could overcome this limitation. The present study (1) proposes a procedure to identify indirect criteria to predict processing yields in rainbow trout (head, carcass and fillet yields), (2) estimates genetic parameters of these indirect criteria, and (3) predicts relative genetic gains in processing yields using full-sib selection or indirect individual selection on those indirect criteria. DNA-pedigreed all-female rainbow trout Oncorhynchus mykiss (n =2029, 1631.0±355.6g) from 600 families produced from 100 sires and 60 dams were characterized by external and internal non-lethal morphological measures using digital pictures and real time ultrasound tomography. Nineteen landmarks were recorded on the digital pictures to define the outline of the body, head and lateral line. Their coordinates were used to calculate different lengths, heights and areas. Five different internal thicknesses were measured by ultrasound tomography. In the first phase of this study, processing yields were predicted using multiple linear regressions including both external and internal morphometric variables. In a second phase, the heritability of the predicted values and their genetic correlations with real processing yields were estimated using animal models. Predicted yields exhibited intermediate heritabilities (0.25–0.28) that were half the value of heritabilities for real processing yields (0.47–0.55), but had high genetic correlations with these real yields (0.87–0.90). The relative efficiency of indirect selection (IS) on these indirect criteria was compared to theoretical mass selection (MS) or sib selection (FS) with different family sizes (10 or 100) and two different selection pressures (10% or 40%). At the same selection pressure (10%, with 100 sibs per family %), full-sib selection created genetic progress 49.6% to 60.5% higher than indirect selection according to the processing yield targeted. However, when sib-selection pressure was limited to a more realistic between family selection pressure (40% and 10 sibs per family), indirect selection with 10% selection pressure was 21.9% to 32.7% more efficient than sib selection. [Copyright &y& Elsevier]

Abstract: Genetic parameters of production traits (growth, carcass yield, fillet yield) and bony tissues (head and vertebral axis) were estimated for large all-female rainbow trout Oncorhynchus mykiss reared in freshwater. Genetic parameters were estimated using REML at 16months of age (1636g) on 1962 DNA-assigned progenies from a partial factorial mating design with 60 dams and 100 sex-reversed sires. Most traits presented medium to high heritability (0.37 to 0.54). A high genetic correlation (rA =0.97) was found between fillet yield and headless gutted carcass yield (or HGCarc%). Due to its higher heritability and high genetic correlation with fillet yield, selection on HGCarc% should result in a 50% increase in selection efficiency on fillet yield by reducing operator-linked variability at filleting. However, strong negative genetic correlations were estimated between body weight or fillet yield and bony tissue development as head yield or the head and vertebral column yield (−0.48 to −0.57). Ten generations of selection on body weight (or fillet yield) are, therefore, predicted to decrease the relative head development by 25 to 30% for slaughtering at constant age. As it is impossible to disentangle this result from a correlation that is only mathematically determined, this result needs further investigations. If yields are corrected according to their allometric relationship with body weight, only selection for fillet yield will decrease the proportion of bony tissues for a slaughtering at a constant body weight. Whatever the final objective of selection (to increase body weight or to shorten the production cycle at constant body weight), it is concluded that at least selection on fillet yield will affect the relative head and the vertebral axis development and that selection on growth may affect bony tissue development. These results are discussed in relation to the past results from livestock breeding, resource energy allocation theory and a future improvement of robustness by selection. [Copyright &y& Elsevier]

Abstract: In the last years, the increase of aquaculture production has led to the evolution of feed composition with an increasing substitution of fish meal and fish oil with terrestrial plant products. In the meantime, selective breeding of fish has been widely developed. The ability to grow on plant-based diets has recently been proven to be genetically variable, pointing out the interest to increase knowledge on the potential consequences of substitution of fish meal and fish oil on current breeding programs. Moreover, heritabilities of major production traits other than growth also need to be estimated in this new environment. Experimental rainbow trouts (about 3000) were derived from a factorial mating design (25 sires and 10 dams), separated in two batches and fed two experimental diets since the first meal. The marine diet (M) was based on fish meal (FM) and fish oil (FO), while the substitution rate by plant products was total in the plant-based (PB) diet (free of FM and FO). We estimated heritabilities under both diets and genotype by diet interactions for body weight, fork length, condition factor, TGC (thermal-unit growth coefficient) and processing yields: viscera yield, carcass yield, filet yield and head yield. Due to the reduced growth of fish fed the plant-based diet, the estimation of genetic parameters was done on fish from both dietary treatments measured at the same age and also on fish measured at the same weight assuming that family rankings could evolve with further growth. Survival rates were high and did not depend on the diet. At 343days, the body weight of the M batch (440.2g±11.3) was twice that of the PB batch (216.0g±12.6). After 465days, the PB batch reached 407.4g±17.1. Whatever the comparison (at same age or same weight), there were significant diet-induced differences for processing traits except for head yield (P =0.80, same age) and filet yield (P =0.82, same weight). The main findings are the high heritabilities observed in fish fed the plant-based diet for body weight (0.69±0.13), TGC (0.65±0.12) and the generally low, though significant, genotype by diet interactions for final body weight, fork length, carcass yield, viscera yield, head yield and filet yield between fish fed source-contrasted diets. Estimates of genetic correlation between diets were the lowest for early weight (0.67±0.12) and indicate differential abilities for initial growth between M and PB diets. [Copyright &y& Elsevier]

Fillet yield (i.e. the proportion of edible muscle in a fish) is a key economic trait for species sold as fillets. Its genetic improvement is complicated by several of its characteristics 1) it is a ratio trait, 2) its numerator (fillet weight) and denominator (body weight) are strongly correlated (correlations in the range 0.89–0.99), 3) it offers little phenotypic variation and 4) it cannot be measured on alive breeding candidates. In a former study, we showed that it could be improved by selection, especially with three selection indices, fillet yield, residual fillet weight and a ratio-specific linear index. However, it is well known that the heritability of ratio traits does not permit a reliable prediction of genetic gains. As predictability of genetic gains is a key requirement to define breeding programs, we investigated how genetic gains in fillet yield could be predicted by the genetic parameters of fillet yield, of residual fillet weight and of the component traits of the linear index. To this end, we compared simulated genetic gains with those estimated by classical prediction methods. This was done using real sets of genetic parameters obtained in nine populations of rainbow trout, European sea bass, gilthead sea bream and common carp. We show that the genetic parameters of fillet yield cannot be used to reliably predict genetic gains in fillet yield. Conversely, selection index theory using a linear index, combining either fillet weight and body weight or fillet weight and waste weight, provides almost perfect prediction of gains. Still, it is highly sensitive to the precision of the genetic and phenotypic correlations estimates, which should not be rounded to less than three decimals for fillet weight and body weight, while two decimals are appropriate for fillet weight and waste weight. A simple, reasonably precise alternative to the linear index is the use of residual fillet weight (the residual of the regression of fillet weight on body weight) as a surrogate for fillet yield. • Genetic parameters of fillet yield are not predictive of genetic gain. • Selection index theory enables efficient prediction of genetic gain in fillet yield. • Genetic parameters of residual fillet weight are reasonably predictive. • We provide recommendations for efficient prediction of genetic gains in fillet yield. • Current published literature mostly does not comply with these recommendations. [ABSTRACT FROM AUTHOR]

Selection to improve processing yields relies on sib selection, in which live candidates are ranked according to their family breeding value. This approach limits genetic progress, as it only exploits genetic variability between families and not within them. Indirect criteria measured on live candidates could overcome this limitation. The present study (1) proposes a procedure to identify indirect criteria to predict processing yields in rainbow trout (head, carcass and fillet yields), (2) estimates genetic parameters of these indirect criteria, and (3) predicts relative genetic gains in processing yields using full-sib selection or indirect individual selection on those indirect criteria. DNA-pedigreed all-female rainbow trout Oncorhynchus mykiss ( n = 2029, 1631.0 ± 355.6 g) from 600 families produced from 100 sires and 60 dams were characterized by external and internal non-lethal morphological measures using digital pictures and real time ultrasound tomography. Nineteen landmarks were recorded on the digital pictures to define the outline of the body, head and lateral line. Their coordinates were used to calculate different lengths, heights and areas. Five different internal thicknesses were measured by ultrasound tomography. In the first phase of this study, processing yields were predicted using multiple linear regressions including both external and internal morphometric variables. In a second phase, the heritability of the predicted values and their genetic correlations with real processing yields were estimated using animal models. Predicted yields exhibited intermediate heritabilities (0.25–0.28) that were half the value of heritabilities for real processing yields (0.47–0.55), but had high genetic correlations with these real yields (0.87–0.90). The relative efficiency of indirect selection (IS) on these indirect criteria was compared to theoretical mass selection (MS) or sib selection (FS) with different family sizes (10 or 100) and two different selection pressures (10% or 40%). At the same selection pressure (10%, with 100 sibs per family %), full-sib selection created genetic progress 49.6% to 60.5% higher than indirect selection according to the processing yield targeted. However, when sib-selection pressure was limited to a more realistic between family selection pressure (40% and 10 sibs per family), indirect selection with 10% selection pressure was 21.9% to 32.7% more efficient than sib selection. [ABSTRACT FROM AUTHOR]