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1. New alternative ingredients and genetic selection are the next game changers in rainbow trout nutrition: a metabolomics appraisal

Author: Simon Roques, Catherine Deborde, Sandrine Skiba-Cassy, Françoise Médale, Mathilde Dupont-Nivet, Florence Lefevre, Jérome Bugeon, Laurent Labbé, Yann Marchand, Annick Moing, and Benoit Fauconneau
Subjects: Medicine, Science
Abstract: Abstract The formulation of sustainable fish feeds based on plant ingredients supplemented by alternative ingredients to plant (insect, micro-algae, yeast) and genetic selection of fish for plant-based diets were tested on rainbow trout in two separate experiments. Plant-based diets and corresponding diets supplemented with an ingredient mix: insect, micro-algae and yeast in Experiment A, and insect and yeast in Experiment B were compared to commercial-like diets. In experiment A, the mix-supplemented diet was successful in compensating the altered growth performance of fish fed their respective plant-based diet compared to those fed the commercial diet, by restoring feed conversion. In experiment B, the selected line demonstrated improved growth performances of fish fed mix-supplemented and plant-based diets compared to the non-selected line. Metabolomics demonstrated a plasma compositional stability in fish fed mix-supplemented and basal plant-based diets comprising an amino acid accumulation and a glucose depletion, compared to those fed commercial diets. The selected line fed mix-supplemented and commercial diets showed changes in inositol, ethanol and methanol compared to the non-selected line, suggesting an involvement of microbiota. Changes in plasma glycine-betaine content in fish fed the mix-supplemented diet suggest the ability of the selected line to adapt to alternative ingredients.
Published: 2023
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2. Genetic architecture of acute hyperthermia resistance in juvenile rainbow trout (Oncorhynchus mykiss) and genetic correlations with production traits

Author: Henri Lagarde, Delphine Lallias, Pierre Patrice, Audrey Dehaullon, Martin Prchal, Yoannah François, Jonathan D’Ambrosio, Emilien Segret, Ana Acin-Perez, Frederic Cachelou, Pierrick Haffray, Mathilde Dupont-Nivet, and Florence Phocas
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract 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.
Published: 2023
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3. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Author: Carole Blay, Pierrick Haffray, Jonathan D’Ambrosio, Enora Prado, Nicolas Dechamp, Virginie Nazabal, Jérôme Bugeon, Florian Enez, David Causeur, Christophe Eklouh-Molinier, Vincent Petit, Florence Phocas, Geneviève Corraze, and Mathilde Dupont-Nivet
Subjects: Fish, Genomic selection, QTL, GWAS, Fatty acid, Raman, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract: Abstract 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.
Published: 2021
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4. Realised genetic gains on growth, survival, feed conversion ratio and quality traits after ten generations of multi-trait selection in rainbow trout Oncorhynchus mykiss, fed a standard diet or a 'future' fish-free and soy-free diet

Author: Marc Vandeputte, Geneviève Corraze, Jérôme Doerflinger, Florian Enez, Frédéric Clota, Frédéric Terrier, Mathilde Horat, Laurence Larroquet, Vincent Petit, Pierrick Haffray, Sandrine Skiba-Cassy, and Mathilde Dupont-Nivet
Subjects: Selective breeding, Selection response, Rainbow trout, Genotype by feed interaction, Aquaculture. Fisheries. Angling, SH1-691
Abstract: There is limited scientific evidence on the real impact of selective breeding in aquaculture on the medium term, while the composition of aquafeeds is rapidly evolving towards plant-based raw materials. We compared a rainbow trout line selected in freshwater for fillet production (improved growth, carcass yield and fillet fat) for ten generations (G10) with an unselected control line from the same base population (G0). We crossed G10 and G0 neomales to the same G10 females, thus creating a Selected and a Control group expected to diverge by half the true difference between G0 and G10. Those were grown to 1.6 kg, and two feeds were compared across the two lines from 264 to 374 days post-hatching. One was a commercial standard, the second was a “future” feed devoid of fishmeal, fish oil and soy-based products, with microalgae as a source of docosahexaenoic acid (DHA). After doubling the difference between the Selected and the Control to estimate the true performance of G0, we saw that G10 was improved relative to G0 for body weight (+61%), feed conversion ratio (−17 to −20%), fillet fat (+28–53%) and carcass yield (+4.2%), but not for fillet yield. Survival was not affected by selection. Both feeds had a similar performance in terms of growth, but the future feed showed a higher FCR, probably due to a feed intake measurement issue. Fish had a good EPA+DHA content (>1.2 g/100 g wet weight) with both feeds, partly linked to endogenous synthesis of these fatty acids. There was little if any genotype by feed interaction. This study shows that selective breeding can produce fast growing, feed efficient and thus provide opportunity for more sustainable fish culture. We showed that highly nutritious fish can be produced with good growth performance without using any fish meal, fish oil or soy-based product.
Published: 2022
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5. Sources of variation of DNA methylation in rainbow trout: combined effects of temperature and genetic background

Author: Delphine Lallias, Maria Bernard, Céline Ciobotaru, Nicolas Dechamp, Laurent Labbé, Lionel Goardon, Jean-Michel Le Calvez, Marjorie Bideau, Alexandre Fricot, Audrey Prézelin, Mathieu Charles, Marco Moroldo, Xavier Cousin, Olivier Bouchez, Alain Roulet, Edwige Quillet, and Mathilde Dupont-Nivet
Subjects: temperature, epiradseq, dna methylation, dnmt3, rainbow trout, isogenic lines, Genetics, QH426-470
Abstract: 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.
Published: 2021
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6. Development of a High-Density 665 K SNP Array for Rainbow Trout Genome-Wide Genotyping

Author: Maria Bernard, Audrey Dehaullon, Guangtu Gao, Katy Paul, Henri Lagarde, Mathieu Charles, Martin Prchal, Jeanne Danon, Lydia Jaffrelo, Charles Poncet, Pierre Patrice, Pierrick Haffray, Edwige Quillet, Mathilde Dupont-Nivet, Yniv Palti, Delphine Lallias, and Florence Phocas
Subjects: SNP, single nucleotide polymorphism, sequence, high-density chip, linkage disequilibrium, rainbow trout, Genetics, QH426-470
Abstract: 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.
Published: 2022
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7. Why Do Some Rainbow Trout Genotypes Grow Better With a Complete Plant-Based Diet? Transcriptomic and Physiological Analyses on Three Isogenic Lines

Author: Thérèse Callet, Mathilde Dupont-Nivet, Morgane Danion, Christine Burel, Marianne Cluzeaud, Anne Surget, Pierre Aguirre, Thierry Kerneis, Laurent Labbé, Stephane Panserat, Edwige Quillet, Inge Geurden, Sandrine Skiba-Cassy, and Françoise Médale
Subjects: aquaculture, genetic variability, LC-PUFA, plant-based diet, salmonid, Physiology, QP1-981
Abstract: 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.
Published: 2021
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8. Why and How to Switch to Genomic Selection: Lessons From Plant and Animal Breeding Experience

Author: R2D2 Consortium, Aline Fugeray-Scarbel, Catherine Bastien, Mathilde Dupont-Nivet, and Stéphane Lemarié
Subjects: prediction accuracy, duration of breeding cycle, selection intensity, breeder’s equation, breeding organization, breeding program, Genetics, QH426-470
Abstract: The present study is a transversal analysis of the interest in genomic selection for plant and animal species. It focuses on the arguments that may convince breeders to switch to genomic selection. The arguments are classified into three different “bricks.” The first brick considers the addition of genotyping to improve the accuracy of the prediction of breeding values. The second consists of saving costs and/or shortening the breeding cycle by replacing all or a portion of the phenotyping effort with genotyping. The third concerns population management to improve the choice of parents to either optimize crossbreeding or maintain genetic diversity. We analyse the relevance of these different bricks for a wide range of animal and plant species and sought to explain the differences between species according to their biological specificities and the organization of breeding programs.
Published: 2021
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9. Genome-wide estimates of genetic diversity, inbreeding and effective size of experimental and commercial rainbow trout lines undergoing selective breeding

Author: Jonathan D’Ambrosio, Florence Phocas, Pierrick Haffray, Anastasia Bestin, Sophie Brard-Fudulea, Charles Poncet, Edwige Quillet, Nicolas Dechamp, Clémence Fraslin, Mathieu Charles, and Mathilde Dupont-Nivet
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract 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 (F ST), linkage disequilibrium (LD), effective population size (N e ) and inbreeding coefficient derived from runs of homozygosity (ROH). Results Our results showed a moderate level of genetic differentiation between selected lines (F ST 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 N e 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.
Published: 2019
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10. Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout, Oncorhynchus mykiss

Author: Carole Blay, Pierrick Haffray, Jérôme Bugeon, Jonathan D’Ambrosio, Nicolas Dechamp, Guylaine Collewet, Florian Enez, Vincent Petit, Xavier Cousin, Geneviève Corraze, Florence Phocas, and Mathilde Dupont-Nivet
Subjects: aquaculture, fat content, flesh colour, magnetic resonance imaging, Fatmeter, computer vision, Genetics, QH426-470
Abstract: 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.
Published: 2021
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11. First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements

Author: Marc Vandeputte, Jérôme Bugeon, Anastasia Bestin, Alexandre Desgranges, Jean-Michel Allamellou, Anne-Sophie Tyran, François Allal, Mathilde Dupont-Nivet, and Pierrick Haffray
Subjects: aquaculture, fillet yield, selective breeding, selection response, production efficiency, heritability, Genetics, QH426-470
Abstract: 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.
Published: 2019
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12. Regulation by Dietary Carbohydrates of Intermediary Metabolism in Liver and Muscle of Two Isogenic Lines of Rainbow Trout

Author: Xuerong Song, Lucie Marandel, Sandrine Skiba-Cassy, Geneviève Corraze, Mathilde Dupont-Nivet, Edwige Quillet, Inge Geurden, and Stephane Panserat
Subjects: glycolysis, gluconeogenesis, fatty acid metabolism, cholesterol metabolism, mitochondrial metabolism, genetic variability, Physiology, QP1-981
Abstract: Rainbow trout (Oncorhynchus mykiss) is recognized as a typical “glucose-intolerant” fish, and the limits of dietary carbohydrate utilization have been investigated for many years. In this study, the objective was to test the molecular effects of dietary carbohydrates on intermediary metabolism in two major metabolic tissues, liver and muscle. Another objective was also to study if the response to carbohydrate intake depended on the genetic background. We fed two isogenic lines of rainbow trout (named A22h and N38h) with high carbohydrate diet (carbohydrate, 22.9%) or low carbohydrate diet (carbohydrate, 3.6%) for 12 weeks. Carbohydrates were associated with higher feed utilization owned by the well-known protein-sparing effect, with better fish growth performance. However, atypical regulation of glycolysis and gluconeogenesis in liver and absence of hk and glut4 induction in muscle, were also observed. Regarding the effects of carbohydrates on other metabolism, we observed an increased, at a molecular level, of hepatic cholesterol biosynthesis, fatty acid oxidation and mitochondrial energy metabolism. Genetic variability (revealed by the differences between the two isogenic lines) was observed for some metabolic genes especially for those involved in the EPA and DHA biosynthetic capacity. Finally, our study demonstrates that dietary carbohydrate not only affect glucose metabolism but also strongly impact the lipid and energy metabolism in liver and muscle of trout.
Published: 2018
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13. Hepatic glucose metabolic responses to digestible dietary carbohydrates in two isogenic lines of rainbow trout

Author: Xuerong Song, Lucie Marandel, Mathilde Dupont-Nivet, Edwige Quillet, Inge Geurden, and Stephane Panserat
Subjects: Fish nutrition, Carnivorous, Genetics, Metabolism pathway, Gene expression, Science, Biology (General), QH301-705.5
Abstract: Rainbow trout (Oncorhynchus mykiss) was recognized as a typical ‘glucose-intolerant’ fish and poor dietary carbohydrate user. Our first objective was to test the effect of dietary carbohydrates themselves (without modification of dietary protein intake) on hepatic glucose gene expression (taking into account the paralogs). The second aim was to research if two isogenic trout lines had different responses to carbohydrate intake, showing one with a better use dietary carbohydrates. Thus, we used two isogenic lines of rainbow trout (named A32h and AB1h) fed with either a high carbohydrate diet or a low carbohydrate diet for 12 weeks. We analysed the zootechnical parameters, the plasma metabolites, the hepatic glucose metabolism at the molecular level and the hormonal-nutrient sensing pathway. Globally, dietary carbohydrate intake was associated with hyperglycaemia and down regulation of the energy sensor Ampk, but also with atypical regulation of glycolysis and gluconeogenesis in the liver. Indeed, the first steps of glycolysis and gluconeogenesis catalysed by the glucokinase and the phospenolpyruvate carboxykinase are regulated at the molecular level by dietary carbohydrates as expected (i.e. induction of the glycolytic gck and repression of the gluconeogenic pck); by contrast, and surprisingly, for two other key glycolytic enzymes (phosphofructokinase enzyme – pfkl and pyruvate kinase – pk) some of the paralogs (pfklb and pklr) are inhibited by carbohydrates whereas some of the genes coding gluconeogenic enzymes (the glucose-6-phosphatase enzyme g6pcb1b and g6pcb2a gene and the fructose1-6 biphosphatase paralog fbp1a) are induced. On the other hand, some differences for the zootechnical parameters and metabolic genes were also found between the two isogenic lines, confirming the existence of genetic polymorphisms for nutritional regulation of intermediary metabolism in rainbow trout. In conclusion, our study determines some new and unexpected molecular regulations of the glucose metabolism in rainbow trout which may partly lead to the poor utilization of dietary carbohydrates and it underlines the existence of differences in molecular regulation of glucose metabolism between two isogenic lines which provides arguments for future selection of rainbow trout.
Published: 2018
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14. Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry.

Author: Thérèse Callet, Mathilde Dupont-Nivet, Marianne Cluzeaud, Florence Jaffrezic, Denis Laloë, Thierry Kerneis, Laurent Labbé, Edwige Quillet, Inge Geurden, David Mazurais, Sandrine Skiba-Cassy, and Françoise Médale
Subjects: Medicine, Science
Abstract: 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.
Published: 2018
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15. Genetic variability of environmental sensitivity revealed by phenotypic variation in body weight and (its) correlations to physiological and behavioral traits.

Author: Delphine Lallias, Edwige Quillet, Marie-Laure Bégout, Benoit Aupérin, Hooi Ling Khaw, Sandie Millot, Claudiane Valotaire, Thierry Kernéis, Laurent Labbé, Patrick Prunet, and Mathilde Dupont-Nivet
Subjects: Medicine, Science
Abstract: Adaptive phenotypic plasticity is a key component of the ability of organisms to cope with changing environmental conditions. Fish have been shown to exhibit a substantial level of phenotypic plasticity in response to abiotic and biotic factors. In the present study, we investigate the link between environmental sensitivity assessed globally (revealed by phenotypic variation in body weight) and more targeted physiological and behavioral indicators that are generally used to assess the sensitivity of a fish to environmental stressors. We took advantage of original biological material, the rainbow trout isogenic lines, which allowed the disentangling of the genetic and environmental parts of the phenotypic variance. Ten lines were characterized for the changes of body weight variability (weight measurements taken every month during 18 months), the plasma cortisol response to confinement stress (3 challenges) and a set of selected behavioral indicators. This study unambiguously demonstrated the existence of genetic determinism of environmental sensitivity, with some lines being particularly sensitive to environmental fluctuations and others rather insensitive. Correlations between coefficient of variation (CV) for body weight and behavioral and physiological traits were observed. This confirmed that CV for body weight could be used as an indicator of environmental sensitivity. As the relationship between indicators (CV weight, risk-taking, exploration and cortisol) was shown to be likely depending on the nature and intensity of the stressor, the joint use of several indicators should help to investigate the biological complexity of environmental sensitivity.
Published: 2017
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16. 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.

Author: Thérèse Callet, Françoise Médale, Laurence Larroquet, Anne Surget, Pierre Aguirre, Thierry Kerneis, Laurent Labbé, Edwige Quillet, Inge Geurden, Sandrine Skiba-Cassy, and Mathilde Dupont-Nivet
Subjects: Medicine, Science
Abstract: 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.
Published: 2017
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17. Three-year breeding cycle of rainbow trout (Oncorhynchus mykiss) fed a plant-based diet, totally free of marine resources: consequences for reproduction, fatty acid composition and progeny survival.

Author: Viviana Lazzarotto, Geneviève Corraze, Amandine Leprevost, Edwige Quillet, Mathilde Dupont-Nivet, and Françoise Médale
Subjects: Medicine, Science
Abstract: 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.
Published: 2015
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18. The positive impact of the early-feeding of a plant-based diet on its future acceptance and utilisation in rainbow trout.

Author: Inge Geurden, Peter Borchert, Mukundh N Balasubramanian, Johan W Schrama, Mathilde Dupont-Nivet, Edwige Quillet, Sadasivam J Kaushik, Stéphane Panserat, and Françoise Médale
Subjects: Medicine, Science
Abstract: 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 (P0.05). 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.
Published: 2013
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19. Selection for adaptation to dietary shifts: towards sustainable breeding of carnivorous fish.

Author: Richard Le Boucher, Mathilde Dupont-Nivet, Marc Vandeputte, Thierry Kerneïs, Lionel Goardon, Laurent Labbé, Béatrice Chatain, Marie Josée Bothaire, Laurence Larroquet, Françoise Médale, and Edwige Quillet
Subjects: Medicine, Science
Abstract: Genetic adaptation to dietary environments is a key process in the evolution of natural populations and is of great interest in animal breeding. In fish farming, the use of fish meal and fish oil has been widely challenged, leading to the rapidly increasing use of plant-based products in feed. However, high substitution rates impair fish health and growth in carnivorous species. We demonstrated that survival rate, mean body weight and biomass can be improved in rainbow trout (Oncorhynchus mykiss) after a single generation of selection for the ability to adapt to a totally plant-based diet (15.1%, 35.3% and 54.4%, respectively). Individual variability in the ability to adapt to major diet changes can be effectively used to promote fish welfare and a more sustainable aquaculture.
Published: 2012
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20. Prediction of fatty acids composition in the rainbow trout Oncorhynchus mykiss by using Raman micro-spectroscopy

Author: Mathilde Dupont-Nivet, Enora Prado, Carole Blay, V. Petit, P. Haffray, Geneviève Corraze, David Causeur, G. Taupier, Virginie Nazabal, L. Labbé, C. Eklouh-Molinier, F. Enez, A. Moreac, J. Bugeon, Synthèse Caractérisation Analyse de la Matière (ScanMAT), Université de Rennes (UR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Institut de Recherche Mathématique de Rennes (IRMAR), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pisciculture Expérimentale INRAE des Monts d'Arrée (PEIMA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Les Sources de l’Avance, Institut de Physique de Rennes (IPR), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Maritime and Fisheries Fund, FranceAgrimer, European Project: PFEA470017FA1000008,Omega-Truite, Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes)
Subjects: Docosahexaenoic Acids, Fish farming, adipocytes, Adipose tissue, Spectrum Analysis, Raman, 01 natural sciences, Biochemistry, Gas Chromatography-Mass Spectrometry, Analytical Chemistry, 03 medical and health sciences, symbols.namesake, Adipocytes, Environmental Chemistry, Animals, Humans, Food science, calibration model, Fatty acids, Spectroscopy, 030304 developmental biology, chemistry.chemical_classification, [PHYS]Physics [physics], 0303 health sciences, Chemistry, Ridge regression method, [SDV.BA]Life Sciences [q-bio]/Animal biology, 010401 analytical chemistry, Fatty Acids, ridge, Eicosapentaenoic acid, rainbow trout, 0104 chemical sciences, Rainbow trout, Oncorhynchus mykiss, regression method, Raman spectroscopy, symbols, Composition (visual arts), lipids (amino acids, peptides, and proteins), Gas chromatography, ridge regression method, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Polyunsaturated fatty acid, Calibration model
Abstract: International audience; The importance of poly-unsaturated fatty acids (PUFAs) in food is crucial for the animal and human development and health. As a complementary strategy to nutrition approaches, genetic selection has been suggested to improve fatty acids (FAs) composition in farmed fish. Gas chromatography (GC) is used as a reference method for the quantification of FAs; nevertheless, the high cost prevents large scale phenotyping as needed in breeding programs. Therefore, a calibration by means of Raman scattering spectrometry has been established in order to predict FA composition in rainbow trout Onchorhynchus mykiss adipose tissue. FA composition of visceral adipose tissue was analysed by both GC and Raman micro-spectrometry techniques on 268 individuals fed with three different feeds, which have different FA compositions. Among the possible regression methods, the ridge regression method, was found to be efficient to establish calibration models from the GC and spectral data. The best cross-validated R2 values were obtained for total PUFAs, omega-6 (Ω-6) and omega-3 (Ω-3) PUFA (0.79, 0.83 and 0.66, respectively). For individual Ω-3 PUFAs, α-linolenic acid (ALA, C18:3), eicosapentaenoic acid (EPA, C20:5) and docosahexenoic acid (DHA, C22:6) were found to have the best R2 values (0.82, 0.76 and 0.81, respectively). This study demonstrates that Raman spectroscopy could be used to obtain good correlation coefficients on adipocytes allowing to predict PUFAs, and calibration models can be used to predict PUFAs contents for large scale and high throughput phenotyping in rainbow trout
Published: 2022
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21. Genetic architecture and genomic selection of fatty acid composition predicted by Raman spectroscopy in rainbow trout

Author: Jonathan D’Ambrosio, Geneviève Corraze, Enora Prado, Pierrick Haffray, David Causeur, Florence Phocas, Jérôme Bugeon, Virginie Nazabal, Florian Enez, Christophe Eklouh-Molinier, Mathilde Dupont-Nivet, Carole Blay, Vincent Petit, Nicolas Dechamp, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Synthèse Caractérisation Analyse de la Matière (ScanMAT), Université de Rennes (UR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche Mathématique de Rennes (IRMAR), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Les Sources de l’Avance, Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), European Maritime and Fisheries Fund, FranceAgrimer (OmegaTruite project)P FEA470017FA1000008, Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), and Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Chimie du CNRS (INC)
Subjects: Genetic correlations, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Docosahexaenoic Acids, QTL, Linoleic acid, QH426-470, Spectrum Analysis, Raman, 03 medical and health sciences, chemistry.chemical_compound, Fish meal, Fish Oils, [MATH.MATH-ST]Mathematics [math]/Statistics [math.ST], Genetics, Animals, Humans, GWAS, 14. Life underwater, Genetic variability, Food science, Raman, Accuracy, 030304 developmental biology, chemistry.chemical_classification, 0303 health sciences, biology, Genomic selection, Research, Fatty Acids, 04 agricultural and veterinary sciences, Genomics, Heritability, Fish oil, Fish products, biology.organism_classification, Fatty acid, Trout, Fish, chemistry, Oncorhynchus mykiss, 040102 fisheries, 0401 agriculture, forestry, and fisheries, TP248.13-248.65, Polyunsaturated fatty acid, Biotechnology
Abstract: 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.
Published: 2021
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22. Evaluation of genetic gain in rainbow trout fed standard of 'future' diet after 10 generations of multi-trait selection in the Aqualande selective breeding program

Author: Marc Vandeputte, Geneviève Corraze, Jérôme Doerflinger, Florian Enez, Frédéric Clota, Frédéric Terrier, Mathilde Horat, Laurence Larroquet, Nicolas Dechamp, Vincent Petit, Pierrick Haffray, Sandrine Skiba-Cassy, Mathilde Dupont-Nivet, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Aqualande, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), and 3AS Station Expérimentale d'Aquaculture Ifremer, Chemin de Maguelone, 34250, Palavas-les-Flots, France
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2021

23. Prediction of fatty acids in the rainbow trout Oncorhynchus mykiss: a Raman scattering spectroscopy approach

Author: Enora Prado, Mathilde Dupont-Nivet, Pierrick Haffray, Virginie Nazabal, F. Enez, D. Guemene, G. Taupier, V. Petit, C. Eklouh-Molinier, D. Causeur, A. Moreac, Laurent Labbé, Geneviève Corraze, C. Blay, Synthèse Caractérisation Analyse de la Matière (ScanMAT), Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Pisciculture Expérimentale INRAE des Monts d'Arrée (PEIMA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Sources de l'Avance, Institut de Physique de Rennes (IPR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Centre National de la Recherche Scientifique (CNRS), Nutrition, Métabolisme, Aquaculture (NuMéA), Université de Pau et des Pays de l'Adour (UPPA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut de Recherche Mathématique de Rennes (IRMAR), AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Université de Rennes 2 (UR2), Université de Rennes (UNIV-RENNES)-École normale supérieure - Rennes (ENS Rennes)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA), Institut des Sciences Chimiques de Rennes (ISCR), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Université de Rennes (UNIV-RENNES)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), European Project: PFEA470017FA1000008,Omega-Truite, Centre National de la Recherche Scientifique (CNRS)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Institut de Chimie du CNRS (INC), Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Université de Rennes (UR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université de Rennes (UR)-Centre National de la Recherche Scientifique (CNRS), Université de Rennes (UR)-Institut National des Sciences Appliquées - Rennes (INSA Rennes), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-École normale supérieure - Rennes (ENS Rennes)-Université de Rennes 2 (UR2)-Centre National de la Recherche Scientifique (CNRS)-INSTITUT AGRO Agrocampus Ouest, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), and Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Ecole Nationale Supérieure de Chimie de Rennes (ENSCR)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)
Subjects: Linolenic acid, Linoleic acid, 01 natural sciences, chemistry.chemical_compound, [CHIM.ANAL]Chemical Sciences/Analytical chemistry, 14. Life underwater, Food science, Fatty acids, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biochemistry [q-bio.BM], chemistry.chemical_classification, [PHYS]Physics [physics], biology, 010401 analytical chemistry, 0402 animal and dairy science, food and beverages, 04 agricultural and veterinary sciences, biology.organism_classification, 040201 dairy & animal science, Eicosapentaenoic acid, 0104 chemical sciences, Trout, chemistry, Docosahexaenoic acid, Raman spectroscopy, Rainbow trout, Gas chromatography, Polyunsaturated fatty acid, Calibration model
Abstract: International audience; Poly-unsaturated fatty acids (PUFAs) are important to improve animal and Human development and health. A potential to improve relative PUFAs composition by genetic selection was previously reported in fishes. However, analytical methods, such as gas chromatography (GC), have some disadvantages such as the use of consumables and solvent and their too high cost preventing large scale phenotyping as needed in breeding programs. Thus, it is crucial to develop alternative technologies to overcome these drawbacks. In this study, Raman spectroscopy has been used in order to determine the chemical composition of rainbow trout adipocytes in a non-destructive manner, and to correlate with the results obtained by gas chromatography. Two groups of trout have been created based to their diets: marine-based and plant-based. Then, visceral adipose tissues were collected and analysed by GC and Raman micro-spectroscopy. Two regression methods were used to establish calibration models from the GC and spectral data: ridge and partial least square (PLS). GC results confirmed that α-linolenic acid (ALA) is more present in the plant-based diet group, whereas eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and linoleic acid (LA) are more present in the marine-based diet group. By using both ridge and PLS regression methods on GC and spectral data, R2 showed high values for ALA, EPA, DHA and LA. Thus, this methodology shows that good correlation coefficients can be obtained to predict PUFAs, and calibration models can be used to predict PUFAs contents for large scale and high throughput phenotyping in rainbow trout.
Published: 2020
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24. How to genetically increase fillet yield in fish: Relevant genetic parameters and methods to predict genetic gain

Author: Anastasia Bestin, Clémence Fraslin, Martin Kocour, Pierrick Haffray, Martin Prchal, Marc Vandeputte, François Allal, Mathilde Dupont-Nivet, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), University of South Bohemia, Ministry of Education, Youth and Sports of the Czech Republic - project 'CENAKVA' LM2018099, Ministry of Education, Youth and Sports of the Czech Republic - project Biodiverzita CZ.02.1.01/0.0/0.0/16_025/0007370, Ministry of Agriculture - project of the Czech NAAR (NAZV) QK1910430, European Project: 613611,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,FISHBOOST(2014), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: Residual fillet weight, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Aquaculture, Aquatic Science, Biology, Residual, Body weight, Heritability, 03 medical and health sciences, Aquaculture Genetics, Prediction methods, Statistics, Genetics, Linear index, Selection response, Fillet (mechanics), Selection, 030304 developmental biology, Processing yields, 0303 health sciences, 04 agricultural and veterinary sciences, Regression, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Genetic gain, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, 040102 fisheries, Trait, 0401 agriculture, forestry, and fisheries, Simulation
Abstract: International audience; 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.
Published: 2020
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25. Genetic architecture and genomic selection of female reproduction traits in rainbow trout

Author: D. Guémené, Mathilde Dupont-Nivet, Sophie Brard-Fudulea, Romain Morvezen, Jonathan D’Ambrosio, Pierrick Haffray, Florence Phocas, A. Acin Perez, Charles Poncet, Anastasia Bestin, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Biologie des Oiseaux et Aviculture (BOA), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Viviers de Sarrance, Génétique Diversité et Ecophysiologie des Céréales (GDEC), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), ANRT [2017/0239], FranceAgrimer [2017–0239], European Project: 2017–0239,EMFF, AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF ), Génétique Diversité et Ecophysiologie des Céréales - Clermont Auvergne (GDEC), Université Clermont Auvergne (UCA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: 0106 biological sciences, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, lcsh:QH426-470, QTL, lcsh:Biotechnology, [SDV]Life Sciences [q-bio], Population, Zoology, Quantitative trait locus, 01 natural sciences, Genetic correlation, Polymorphism, Single Nucleotide, Spawn weight, Heritability, 03 medical and health sciences, lcsh:TP248.13-248.65, Genetic variation, Genetics, Animals, GWAS, 14. Life underwater, Selection, Genetic, education, Egg weight, 030304 developmental biology, 0303 health sciences, education.field_of_study, biology, urogenital system, Reproduction, Egg size, Genomics, Marker-assisted selection, Body weight, biology.organism_classification, Genetic architecture, Trout, lcsh:Genetics, Phenotype, Fish, Fecundity, Oncorhynchus mykiss, Female, Spawning date, 010606 plant biology & botany, Biotechnology, Research Article, Genome-Wide Association Study
Abstract: BackgroundRainbow trout is a significant fish farming species under temperate climates. Female reproduction traits play an important role in the economy of breeding companies with the sale of fertilized eggs. The objectives of this study are threefold: to estimate the genetic parameters of female reproduction traits, to determine the genetic architecture of these traits by the identification of quantitative trait loci (QTL), and to assess the expected efficiency of a pedigree-based selection (BLUP) or genomic selection for these traits.ResultsA pedigreed population of 1343 trout were genotyped for 57,000 SNP markers and phenotyped for seven traits at 2 years of age: spawning date, female body weight before and after spawning, the spawn weight and the egg number of the spawn, the egg average weight and average diameter. Genetic parameters were estimated in multi-trait linear animal models. Heritability estimates were moderate, varying from 0.27 to 0.44. The female body weight was not genetically correlated to any of the reproduction traits. Spawn weight showed strong and favourable genetic correlation with the number of eggs in the spawn and individual egg size traits, but the egg number was uncorrelated to the egg size traits. The genome-wide association studies showed that all traits were very polygenic since less than 10% of the genetic variance was explained by the cumulative effects of the QTLs: for any trait, only 2 to 4 QTLs were detected that explained in-between 1 and 3% of the genetic variance. Genomic selection based on a reference population of only one thousand individuals related to candidates would improve the efficiency of BLUP selection from 16 to 37% depending on traits.ConclusionsOur genetic parameter estimates made unlikely the hypothesis that selection for growth could induce any indirect improvement for female reproduction traits. It is thus important to consider direct selection for spawn weight for improving egg production traits in rainbow trout breeding programs. Due to the low proportion of genetic variance explained by the few QTLs detected for each reproduction traits, marker assisted selection cannot be effective. However genomic selection would allow significant gains of accuracy compared to pedigree-based selection.
Published: 2020
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26. Analysis of genomewide patterns of DNA methylation in response to an early temperature stress in rainbow trout

Author: Delphine Lallias, Edwige Quillet, Maria Bernard, Céline Ciobotaru, Nicolas Dechamp, Jean-Michel Le Calvez, Marjorie Bideau, Lionel Goardon, Laurent Labbé, Mathilde Dupont-Nivet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), and Institut National de la Recherche Agronomique (INRA)
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

27. How to genetically increase fillet yield in fish: relevant genetic parameters and methods for the estimation of genetic gain

Author: Marc Vandeputte, Clémence Fraslin, Pierrick Haffray, Anastasia Bestin, François Allal, Martin Prchal, Martin Kocour, Mathilde Dupont-Nivet, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Faculty of Fisheries and Protection of Waters [University of South Bohemia], and University of South Bohemia
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.SA.SPA]Life Sciences [q-bio]/Agricultural sciences/Animal production studies, [SDV.SA.STP]Life Sciences [q-bio]/Agricultural sciences/Sciences and technics of fishery, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

28. Successful realized selection response for fillet yield in rainbow trout Oncorhynchus mykiss

Author: Marc Vandeputte, Jérôme Bugeon, Anastasia Bestin, Alexandre Desgranges, Sébastien Courant, Jean Michel Allamellou, Anne Sophie Tyran, François Allal, Mathilde Dupont-Nivet, Pierrick Haffray, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Syndicat des Sélectionneurs Avicoles et Aquacoles Français, Les Aquaculteurs Bretons, Independent, Institut National de la Recherche Agronomique (INRA), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), and European Aquaculture Society (EAS).
Subjects: Truite arc-en-ciel, Salmonide, Oncorhynchus mykiss, [SDV]Life Sciences [q-bio], Sélection, Croissance, Poisson, Filet de poisson, ComputingMilieux_MISCELLANEOUS
Abstract: Successful realized selection response for fillet yield in rainbow trout Oncorhynchus mykiss. World Aquaculture 2018
Published: 2019

29. Factors of variation of genomic selection accuracy for female reproduction traits with a constant reference population size of rainbow trouts

Author: Ambrosio, Jonathan D., Romain Morvezen, Brard-Fudulea, S., Anastasia Bestin, Pierrick Haffray, Mathilde Dupont-Nivet, Florence Phocas, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF)
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2019

30. Genetic parameters of resistance to gastroenteritis (rtge) and rainbow trout fry syndrome (rtfs) in rainbow trout oncorhynchus mykiss and their genetic correlations with production traits

Author: Pierrick Haffray, Anastasia Bestin, Florian Enez, Sébastien Courant, Daniel Guemene, Alexandre Desgranges, François Allal, Mathilde Dupont-Nivet, Marc Vandeputte, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Independent, Biologie des Oiseaux et Aviculture (BOA), Institut National de la Recherche Agronomique (INRA)-Université de Tours, Les Aquaculteurs Bretons, Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Université de Tours (UT), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], [INFO]Computer Science [cs], ComputingMilieux_MISCELLANEOUS
Abstract: National audience
Published: 2018

31. Analysis of genetic variability of DNA methylation in response to an early temperature stress in rainbow trout

Author: Delphine Lallias, Edwige Quillet, Maria Bernard, Nicolas Dechamp, Jean-Michel Le Calvez, Marjorie Bideau, Lionel Goardon, Laurent Labbé, Mathilde Dupont-Nivet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris Saclay (COmUE), Institut National de la Recherche Agronomique (INRA), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), and European Project: 652831,H2020,H2020-INFRAIA-2014-2015,AQUAEXCEL2020(2015)
Subjects: DNA methylation, epigenetics, early stress, [SDV.BA]Life Sciences [q-bio]/Animal biology, temperature, rainbow trout, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2018

32. How to genetically increase fillet yield in fish: New insights from simulations based on field data

Author: Marc Vandeputte, Mathilde Dupont-Nivet, Anastasia Bestin, Pierrick Haffray, Clémence Fraslin, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Section Aquacole, Syndicat des sélectionneurs avicoles et aquacoles français (SYSAAF), and Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF)
Subjects: 0301 basic medicine, Field data, [SDV]Life Sciences [q-bio], selection, Aquaculture, Aquatic Science, Biology, heritability, Body weight, Genetic correlation, Heritability, 03 medical and health sciences, Animal science, Genetics, genetics, 14. Life underwater, Fillet (mechanics), Selection, Processing yields, Flesh, 04 agricultural and veterinary sciences, 030104 developmental biology, aquaculture, 040102 fisheries, 0401 agriculture, forestry, and fisheries, processing yields
Abstract: International audience; Fillet yield (i.e. the proportion of edible flesh from a given amount of fish) is a trait of high economic interest for species sold as fillets. Improving it by selective breeding is not an easy task, as it is a ratio trait, which causes mathematical difficulties. It is moreover a specific ratio where numerator ( fillet weight) and denominator (body weight) are very strongly correlated (genetic and phenotypic correlations in the range 0.89 – 0.99). This led some authors to conclude that they have the same genetic and phenotypic basis, precluding selection for improved fillet yield. In this study, we propose to study fillet yield as a component of two traits, fillet weight and waste weight (waste weight = body weight- fillet weight, so the sum of head, bones, fins and viscera weight), which we expect to be less correlated. Using data from 5 batches of fish from 3 species (sea bass, sea bream, rainbow trout), we show that as expected, fillet weight and waste weight are less correlated than fillet weight and body weight (on average, r A = 0.91 and r P = 0.88 vs. r A = 0.987, r P = 0.981). We used stochastic simulation to generate genotypes and phenotypes of fish using those genetic parameters for fillet weight and waste weight. We simulated 10 generations of selection for increased fillet yield using nine selection indices. Five indices had rather similar performances, residual fillet weight (the residual of the regression of fillet weight to body weight), fillet yield, fillet to waste ratio, restricted selection index (a linear index aimed at improving fillet weight while keeping waste weight constant) and linear index (optimized to improve fillet/waste ratio). With these indices, the average selection gain was +0.66% of fillet yield per generation (range 0.30 to 0.95% using real genetic parameters from 5 fish batches). Selection for the difference between fillet weight and waste weight was 30% less efficient, while selection for increased fillet weight or increased body weight was 55 – 65% less efficient. Selection against waste weight had a null or even negative impact on fillet yield. Factors favorable to higher selection gains are low initial fillet yield, different heritabilities and CVs of fillet weight and waste weight, low genetic correlation and high phenotypic correlation of fillet weight and waste weight. These results suggest that although fillet weight and body weight are strongly correlated and proportional to each other, moderate selection gains on fillet yield are possible. We consider it would be useful to add waste weight in the parameters recorded in future genetic studies on fillet yield.
Published: 2018
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33. Regulation of genes related to cholesterol metabolism in rainbow trout (Oncorhynchus mykiss) fed a plant-based diet

Author: Tengfei Zhu, Edwige Quillet, Elisabeth Plagnes-Juan, Geneviève Corraze, Sandrine Skiba-Cassy, Mathilde Dupont-Nivet, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, Physiology, chemistry.chemical_compound, Homeostasis, métabolisme du cholestérol, 2. Zero hunger, chemistry.chemical_classification, oncorhynchus mykiss, biology, microRNA, Diet, Vegetarian, [SDV.BA]Life Sciences [q-bio]/Animal biology, cholestérol, 04 agricultural and veterinary sciences, Fish oil, Adaptation, Physiological, rainbow trout, Trout, Cholesterol, Animal Nutritional Physiological Phenomena, lipids (amino acids, peptides, and proteins), animal feeding, expression des gènes, Fish Proteins, medicine.medical_specialty, alimentation animale, Nutritional Status, Cholesterol 7 alpha-hydroxylase, digestive system, Gene Expression Regulation, Enzymologic, Bile Acids and Salts, 03 medical and health sciences, Fish meal, Physiology (medical), Internal medicine, medicine, Animals, lxr, nutrition animale, fish, aliment à base de plante, Fatty acid, Lipid metabolism, biology.organism_classification, Lipid Metabolism, Animal Feed, MicroRNAs, 030104 developmental biology, Endocrinology, chemistry, plant-based diet, srebp-2, animal nutrition, 040102 fisheries, cholesterol metabolism, 0401 agriculture, forestry, and fisheries, Rainbow trout
Abstract: 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 growth.
Published: 2018
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34. Hepatic Glucose Metabolic Responses to Digestible Dietary Carbohydrates in Two Isogenic Lines of Rainbow Trout

Author: Stéphane Panserat, Edwige Quillet, Mathilde Dupont-Nivet, Lucie Marandel, Inge Geurden, Xuerong Song, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, X. Song gratefully acknowledges the financial assistance provided by University of Chinese Academy of Sciences (UCAS) for the fellowship., European Project: 652831,H2020,H2020-INFRAIA-2014-2015,AQUAEXCEL2020(2015), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, animal diseases, No keyword, poisson, glucose, Biology (General), ComputingMilieux_MISCELLANEOUS, Animal biology, trout, oncorhynchus mykiss, Carnivorous, biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, 04 agricultural and veterinary sciences, rainbow trout, Trout, nutrition, Biochemistry, animal feeding, General Agricultural and Biological Sciences, Phosphofructokinase, expression des gènes, Research Article, endocrine system, animal structures, alimentation animale, QH301-705.5, Science, education, Carbohydrate metabolism, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, rainbow, Biologie animale, Genetics, 14. Life underwater, nutrition animale, métabolisme du glucose, Glucokinase, urogenital system, Metabolism, biology.organism_classification, glucide, Metabolism pathway, 030104 developmental biology, Gluconeogenesis, animal nutrition, 040102 fisheries, 0401 agriculture, forestry, and fisheries, fish nutrition, carnivorous, genetics, metabolism pathway, gene expression, Rainbow trout, Fish nutrition, Gene expression, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Pyruvate kinase, truite arc en ciel
Abstract: Rainbow trout (Oncorhynchus mykiss) was recognized as a typical ‘glucose-intolerant’ fish and poor dietary carbohydrate user. Our first objective was to test the effect of dietary carbohydrates themselves (without modification of dietary protein intake) on hepatic glucose gene expression (taking into account the paralogs). The second aim was to research if two isogenic trout lines had different responses to carbohydrate intake, showing one with a better use dietary carbohydrates. Thus, we used two isogenic lines of rainbow trout (named A32h and AB1h) fed with either a high carbohydrate diet or a low carbohydrate diet for 12 weeks. We analysed the zootechnical parameters, the plasma metabolites, the hepatic glucose metabolism at the molecular level and the hormonal-nutrient sensing pathway. Globally, dietary carbohydrate intake was associated with hyperglycaemia and down regulation of the energy sensor Ampk, but also with atypical regulation of glycolysis and gluconeogenesis in the liver. Indeed, the first steps of glycolysis and gluconeogenesis catalysed by the glucokinase and the phospenolpyruvate carboxykinase are regulated at the molecular level by dietary carbohydrates as expected (i.e. induction of the glycolytic gck and repression of the gluconeogenic pck); by contrast, and surprisingly, for two other key glycolytic enzymes (phosphofructokinase enzyme – pfkl and pyruvate kinase – pk) some of the paralogs (pfklb and pklr) are inhibited by carbohydrates whereas some of the genes coding gluconeogenic enzymes (the glucose-6-phosphatase enzyme g6pcb1b and g6pcb2a gene and the fructose1-6 biphosphatase paralog fbp1a) are induced. On the other hand, some differences for the zootechnical parameters and metabolic genes were also found between the two isogenic lines, confirming the existence of genetic polymorphisms for nutritional regulation of intermediary metabolism in rainbow trout. In conclusion, our study determines some new and unexpected molecular regulations of the glucose metabolism in rainbow trout which may partly lead to the poor utilization of dietary carbohydrates and it underlines the existence of differences in molecular regulation of glucose metabolism between two isogenic lines which provides arguments for future selection of rainbow trout., Summary: Using isogenic lines, this study determines some new, unexpected molecular regulation of the glucose metabolism in rainbow trout, which may partly lead to the poor utilization of dietary carbohydrates.
Published: 2018
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35. Accuracy of BLUP breeding values in a factorial mating design with mixed families and marker-based parentage assignment in rainbow trout Oncorhynchus mykiss

Author: Mathilde Dupont-Nivet, Pierrick Haffray, Béatrice Chatain, Marc Vandeputte, Jérôme Bugeon, Florian Enez, Hervé Chapuis, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Syndicat des Sélectionneurs Avicoles et Aquacoles Français, Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris-Saclay, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), 083/08/C, French National Interprofessional Office for Marine and Aquaculture Products, 30900/2009, European Fisheries Fund, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, French National Interprofessional Office for Marine and Aquaculture Products, and European Fisheries Fund
Subjects: 0301 basic medicine, Animal breeding, [SDV]Life Sciences [q-bio], Sélection, Aquaculture, Aquatic Science, Biology, Best linear unbiased prediction, Filiation, Crossbreed, 03 medical and health sciences, Animal science, Salmonide, salmonids, 14. Life underwater, Croissance, DNA parentage assignment, Marqueur microsatellite, Truite arc-en-ciel, Sib selection, Salmonids, Factorial experiment, Mating design, Heritability, Poisson, Espèce aquacole, 030104 developmental biology, aquaculture, Oncorhynchus mykiss, Microsatellite, Rainbow trout, Commercialisation, Qualité, EBV accuracy
Abstract: International audience; 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 ﬁ llet 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
Published: 2018
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36. Impact of selection for better utilization of 100 % plant-based diet on disease resistance in rainbow trout

Author: Mathilde Dupont-Nivet, Margaux Crusot, Nicolas Dechamp, Dimitri Rigaudeau, Françoise Médale, Pierre Boudinot, Calvez, S., Jean Francois Bernardet, Edwige Quillet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Infectiologie Expérimentale des Rongeurs et Poissons (IERP), Institut National de la Recherche Agronomique (INRA), Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Unité de recherche Virologie et Immunologie Moléculaires (VIM), ANR Agreenfish, and Unité de recherche Virologie et Immunologie Moléculaires (VIM (UR 0892))
Subjects: endocrine system, animal structures, urogenital system, animal diseases, [SDV]Life Sciences [q-bio], digestive system
Abstract: Impact of selection for better utilization of 100 % plant-based diet on disease resistance in rainbow trout. Aquaculture Europe 2017
Published: 2017

37. Ability to grow and survive with 100 % plant-based diet in rainbow trout : contrasted genotypes help to understand underlying mechanisms

Author: Mathilde Dupont-Nivet, Thérèse Callet, Inge Geurden, Laurent Labbé, Denis Laloë, Florence Jaffrezic, Sandrine Skiba, Edwige Quillet, Françoise Médale, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), and ANR
Subjects: [SDV]Life Sciences [q-bio]
Abstract: Ability to grow and survive with 100 % plant-based diet in rainbow trout : contrasted genotypes help to understand underlying mechanisms. XVI congreso nacional de acuicultura - Journée Franco Espagnole
Published: 2017

38. Metapopulation patterns of additive and nonadditive genetic variance in the sea bass (Dicentrarchus labrax)

Author: Mathilde Dupont-Nivet, Béatrice Chatain, Pierrick Haffray, Hervé Chavanne, Marc Vandeputte, Bruno Guinand, Alain Vergnet, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD [France-Ouest]), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Istituto Sperimentale Italiano Lazzaro Spallanzani, Guinand, Bruno, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF), Istituto Spallanzani, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), and École Pratique des Hautes Études (EPHE)
Subjects: 0106 biological sciences, 0301 basic medicine, additive and nonadditive variance, mito-nuclear epistasis, mito‐nuclear epistasis, Darwin's corollary, [SDV]Life Sciences [q-bio], Population, Introgression, Metapopulation, Biology, 010603 evolutionary biology, 01 natural sciences, Diallel cross, 03 medical and health sciences, Hybrid zone, Genetic variation, pleiotropy, heterosis, 14. Life underwater, Sea bass, education, Ecology, Evolution, Behavior and Systematics, Original Research, Nature and Landscape Conservation, education.field_of_study, Ecology, Reproductive isolation, 030104 developmental biology, Evolutionary biology
Abstract: Ajouter clé UT WOS; Describing and explaining the geographic within-species variation in phenotypes ("phenogeography") in the sea over a species distribution range is central to our understanding of a variety of eco-evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full-sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria-Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.
Published: 2017
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39. How can we select for fillet yield in fish ? A simulation study

Author: Clémence Fraslin, Mathilde Dupont-Nivet, Anastasia Bestin, Pierrick Haffray, Marc Vandeputte, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Université Paris Saclay (COmUE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), European Project: 613611,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,FISHBOOST(2014), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: [SDV.GEN]Life Sciences [q-bio]/Genetics, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

40. Mechanisms Related to a Plant Based Diet Utilization in Three Isogenic Lines of Rainbow Trout (Oncorhynchus Mykiss) Assessed by Transcriptomic Analysis

Author: Thérèse Callet, Mathilde Dupont-Nivet, Inge Geurden, Florence Jaffrezic, Denis Laloë, Sandrine Skiba, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Nutrition, Métabolisme, Aquaculture (NuMéA), and Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA)
Subjects: No keyword, [SDV.BA]Life Sciences [q-bio]/Animal biology, ComputingMilieux_MISCELLANEOUS
Abstract: International audience
Published: 2016

41. Quantitative genetic variation for post-stress cortisol and swimming performance in growth-selected and control populations of European sea bass ([i]Dicentrarchus labrax[/i])

Author: B. Chatain, Marc Vandeputte, Patrick Prunet, Jean-Denis Porte, B. Auperin, Alain Vergnet, Claudiane Valotaire, Mathilde Dupont-Nivet, Guy Claireaux, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, L-3AS, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), MARine Biodiversity Exploitation and Conservation (UMR MARBEC), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS), Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), Institut de Recherche pour le Développement (IRD)-Institut Universitaire Européen de la Mer (IUEM), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), INRA-Ifremer Research group 'Amélioration génétique pour une pisciculture durable' & COMPETUS project funded by the European Union (project COOP-CT-2005-017633), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Institut de Recherche pour le Développement (IRD)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Institut de Recherche pour le Développement (IRD), Institut de Recherche pour le Développement (IRD)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université de Brest (UBO)-Institut Universitaire Européen de la Mer (IUEM), and Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)
Subjects: 0301 basic medicine, medicine.medical_specialty, Animal breeding, [SDV]Life Sciences [q-bio], Aquaculture, Aquatic Science, Selective breeding, Crossbreed, Genetic correlation, Heritability, 03 medical and health sciences, Animal science, Internal medicine, Genetic variation, medicine, 14. Life underwater, Sea bass, Correlated response, biology, ACL, Stress response, biology.organism_classification, Maximum sustained swimming speed, 030104 developmental biology, Endocrinology, Dicentrarchus, [SDE.BE]Environmental Sciences/Biodiversity and Ecology
Abstract: Sea bass is a major species in Mediterranean aquaculture, and is now being subject to selective breeding programmes for faster growth. In terrestrial species, it was demonstrated that fast growth may be linked to a correlated degradation of fitness traits. In this experiment, we evaluated 600 young sea bass from a factorial mating of 76 sires and 13 dams. The sires were from four genetic groups, wild (W), domesticated (D), and selected for growth (2 groups, M and P). The 600 offspring were submitted to two acute confinement stress challenges at 6 weeks intervals, and plasma cortisol at one hour post stress was measured. The same fish were also submitted to two swimming challenges at a 5 days interval, where the maximum sustained swimming speed ( U max ) of each fish was evaluated. Parentage was assessed by genotyping of 12 microsatellites. 554 fish had both valid parentage and phenotypes. Cortisol had a low repeatability (r = 0.30 between the two successive measurements) while repeatability was moderate for U max (r = 0.62). However, genetic correlations between successive measurements were very high (> 0.96) for both traits, indicating that successive measurements were related to the same trait. Heritability was moderate for mean post-stress cortisol (h 2 = 0.34 ± 0.09) and U max (h 2 = 0.48 ± 0.08). When U max was expressed in m.s − 1 , it was negatively correlated to cortisol (r A = − 0.48 ± 0.08) and weakly correlated to body weight (r A = 0.12 ± 0.16), but figures changed when it was expressed in Body Lengths.s − 1 (h 2 = 0.55 ± 0.08, r A = − 0.10 ± 0.19 with cortisol and r A = − 0.64 ± 0.07 with body weight, respectively). Cortisol was moderately negatively correlated with body weight (r A = − 0.36 ± 0.18). The four lines did not differ for cortisol or U max , but when U max was expressed in BL.s − 1 it tended to be lower in the two selected lines — which were also significantly larger. However, this is likely due to a phenotypic decrease of relative U max with increasing body size. We conclude that selection for growth and/or domestication should not impact maximum sustained swimming speed in the European sea bass, but may tend to favour animals with low cortisol responsiveness. These traits could be used to orientate functional capabilities other than productivity in sea bass. Statement of relevance We estimate heritability of cortisol stress response and (for the first time) in European sea bass, as well as their correlations with growth. We show moderate correlations, and no correlated response to selection for growth. We also provide methods to evaluate these traits on large number of fishes. This can be useful to monitor and design breeding programmes.
Published: 2016
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42. Molecular pathways associated with the nutritional programming of plant-based diet acceptance in rainbow trout following an early feeding exposure

Author: Mukundh Balasubramanian, Mathilde Dupont-Nivet, Françoise Médale, Sadasivam Kaushik, Jérôme Montfort, Inge Geurden, Edwige Quillet, Stéphane Panserat, Aurélie Le Cam, Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), This work was part of a Postdoctoral fellowship programme to MNB funded by INRA, under the INRA-WUR Aquaculture platform. The study was partly funded by INRA (Department Phase, Crédit Incitatif), by the VEGEAQUA project (FUI funding, French government) and by the EU-funded ARRAINA project No. 288925: Advanced Research Initiatives for Nutrition & Aquaculture (EU Seventh Framework Programme), European Project: 288925,EC:FP7:KBBE,FP7-KBBE-2011-5,ARRAINA(2012), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA), European Project: 288925, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, alimentation animale, Animal feed, animal diseases, mécanisme moléculaire, Transcriptome, 03 medical and health sciences, Animal science, poisson, Aquaculture, Biologie animale, Genetics, Animals, Food and Nutrition, Juvenile, Gene Regulatory Networks, 14. Life underwater, Genetic Association Studies, Animal biology, oncorhynchus mykiss, biology, business.industry, Gene Expression Profiling, transcriptomique, [SDV.BA]Life Sciences [q-bio]/Animal biology, Computational Biology, Reproducibility of Results, programmation nutritionnelle, biology.organism_classification, Animal Feed, Biotechnology, Trout, Gene Ontology, juvénile, 030104 developmental biology, Gene Expression Regulation, Organ Specificity, alimentation végétale, Alimentation et Nutrition, Animal Nutritional Physiological Phenomena, Rainbow trout, business, Oviparity, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, Research Article
Abstract: 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. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2804-1) contains supplementary material, which is available to authorized users.
Published: 2016
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43. Adaptive capacities from survival to stress responses of two isogenic lines of rainbow trout fed a plant-based diet

Author: Françoise Médale, Bastien Sadoul, Lionel Goardon, A. Foucard, Inge Geurden, Patrick Prunet, Mathilde Dupont-Nivet, Laurent Labbé, Edwige Quillet, Claudiane Valotaire, Violaine Colson, Jean Michel Lecalvez, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Institut National de la Recherche Agronomique (INRA)-Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique ), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), Nutrition, Métabolisme, Aquaculture (NuMéA), Institut National de la Recherche Agronomique (INRA)-Université de Pau et des Pays de l'Adour (UPPA), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, European Project: 262336,EC:FP7:INFRA,FP7-INFRASTRUCTURES-2010-1,AQUAEXCEL(2011), AgroParisTech-Institut National de la Recherche Agronomique (INRA), European Project: 262336, and Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de la Recherche Agronomique (INRA)
Subjects: 0301 basic medicine, food intake, [SDV]Life Sciences [q-bio], comportement, bien-être animal, Aquaculture, adaptation, stress, poisson, salmonids, Adaptation, Psychological, ComputingMilieux_MISCELLANEOUS, salmonidae, trout, alimentation, oncorhynchus mykiss, Multidisciplinary, Ecology, 04 agricultural and veterinary sciences, Plants, Fish oil, rainbow trout, survie, régime alimentaire, nutrition, Composition (visual arts), Animal Nutritional Physiological Phenomena, Period (gene), growth, Fisheries, Biology, survival, Article, animal welfare, 03 medical and health sciences, Fish meal, Animal science, Fish Oils, isogenic line, Stress, Physiological, rainbow, capacité d'adaptation, réponse au stress, Animals, 14. Life underwater, fish, behavior, Plant based, Animal Feed, croissance, Diet, 030104 developmental biology, alimentation végétale, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Rainbow trout, Apathetic behaviour, Decreased growth, lignée isogénique, truite arc en ciel
Abstract: The composition of feed for farmed salmonids has strongly evolved during the last decades due to the substitution of fishery-derived fish oil and fishmeal by ingredients of plant origin. Little information is available regarding the effects of this transition on adaptive capacities in fish. Two rainbow trout isogenic lines, known for their divergent ability to grow on a plant-based diet (PBD), were fed for seven months from first feeding either a fully PBD or a control marine-resources diet and were compared for their growing and survival capacities over time and their behavioral and stress responses at similar sizes but different ages. Although fish displayed similar appetitive behaviour, the two lines were highly affected by the PBD translated in decreased growth and apathetic behaviour, but also stronger stress responses displayed by stronger cortisol increases and more stress-related behaviour when isolated. The two lines were found to be similarly sensitive to a PBD for the assessed stress-related parameters, but one line displayed a lower survival during the early rearing period. Overall, these results suggest that a PBD supplied to fish from the alevin stage has strong effects on physiological and behavioural parameters, with possible impairment of fish welfare, but also genome-dependent survival.
Published: 2016
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44. Three-year breding cycle of rainbow trout (Oncorhynchus mykiss) fed a plant-based diet, totally free of marine resources : consequences for reproduction, fatty acid composition and progeny survival

Author: Geneviève Corraze, Mathilde Dupont-Nivet, Amandine Leprevost, Françoise Médale, Viviana Lazzarotto, Edwige Quillet, Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, This work was supported by the FP7 European project ARRAINA (n° 288925) and by the FUI progect VegeAqua, European Project: 288925,EC:FP7:KBBE,FP7-KBBE-2011-5,ARRAINA(2012), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA), AgroParisTech-Institut National de la Recherche Agronomique (INRA), European Project: 288925, and Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1 (UB)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)
Subjects: composition en acide gras, lcsh:Medicine, Aquaculture, lcsh:Science, chemistry.chemical_classification, Animal biology, 0303 health sciences, Multidisciplinary, [SDV.BA]Life Sciences [q-bio]/Animal biology, Fatty Acids, progéniture, food and beverages, 04 agricultural and veterinary sciences, Fish oil, Trout, survie, Liver, Oncorhynchus mykiss, Alimentation et Nutrition, Female, Research Article, Polyunsaturated fatty acid, descendance, Linolenic acid, Biology, Commercial fish feed, reproduction, 03 medical and health sciences, Fish meal, Animal science, Biologie animale, Animals, Food and Nutrition, 14. Life underwater, 030304 developmental biology, business.industry, lcsh:R, biology.organism_classification, Animal Feed, Diet, Fishery, chemistry, alimentation végétale, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Rainbow trout, lcsh:Q, business, [SDV.AEN]Life Sciences [q-bio]/Food and Nutrition, truite arc en ciel
Abstract: 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.
Published: 2015
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45. Genotype by diet interactions on growth and processing traits in rainbow trout ([i]Oncorhynchus mykiss[/i]), European sea bass ([i]Dicentrarchus labrax[/i]), gilthead sea bream ([i]Sparus aurata[/i]) and meagre [i](Argyrosomus regius)[/i] fed diets with almost complete substitution of both fish meal and fish oil by vegetal ingredients

Author: Anastasia Bestin, Mathilde Dupont-Nivet, Pierrick Haffray, Françoise Médale, Edwige Quillet, Marc Vandeputte, Cariou, S., Desgranges, A., Laureau, S., Ricoux, R., Beutin, C., Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Ferme Marine du Douhet, Bretagne Truite, Ecloserie Marine de Gravelines, Les Poissons du Soleil, Pôle Aquimer, and Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF)
Subjects: aquaculture, [SDV]Life Sciences [q-bio], plant based diet
Abstract: absent
Published: 2014

46. Multi-site evaluation of the rearing performances of 5 wild populations of European sea bass (Dicentrarchus labrax)

Author: Mathilde Dupont-Nivet, R. Ricoux, Carlos Mazorra, Pierrick Haffray, Pedro Marques, Stanislas Laureau, Glen Pagelson, Marc Vandeputte, Romain Garouste, Béatrice Chatain, Tetsuzan Benny Ron, Marta Gameiro, Hervé Chavanne, Alain Vergnet, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Intensification raisonnée et écologique pour une pisciculture durable (UMR INTREPID), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Istituto Sperimentale Italiano Lazzaro Spallanzani, Ecloserie Marine de Gravelines, National Center for Mariculture, Israel Oceanographic and Limnological Research, Department of Human Nutrition, Food & Animal Sciences, CTAHR, University of Hawaii, Ardag Red Sea Mariculture (ARDAG), Tinamenor S.A, Les Poissons du Soleil, Foros de Galeado, Viveiro Vilanova S.A., This work is part of the COMPETUS project, funded by Ardag Red Sea Mariculture (Eilat, Israel), Ecloserie Marine de Gravelines (Gravelines, France), Les Poissons du Soleil (Balaruc, France), Tinamenor SA (Pesues, Cantabria, Spain), Viveiro Vila Nova (Vila Nova de Milfontes, Portugal) and the European Union (project COOP-CT-2005-017633). It is also part of the program of the Research Group 'Fish Genetic Improvement' between INRA and Ifremer., Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA)-IFR140, and Istituto Spallanzani
Subjects: Mediterranean climate, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Genotype by environment interaction, Artificial fertilization, growth, Population, european sea bass, Population genetics, Zoology, Growth, Aquatic Science, genotype by environment interaction, Diallel cross, Aquaculture, Dicentrarchus labrax, 14. Life underwater, European sea bass, Sea bass, education, selective breeding, Processing yields, education.field_of_study, biology, business.industry, Ecology, processing yield, biology.organism_classification, Selective breeding, Dicentrarchus, business, dicentrarchus labrax
Abstract: Chantier qualité GA; International audience; Sea bass is a major species in Mediterranean aquaculture, but has a distribution area ranging from North Atlantic to South Mediterranean, with a population structure previously revealed by population genetics. To test the farming performances of wild sea bass populations, we produced a partial diallel cross mating scheme, using sires originating from North Atlantic (NAT), South Atlantic (SAT), West Mediterranean (WEM), North-East Mediterranean (NEM) and South-East Mediterranean (SEM). Fifteen sires per origin were mated in a full-factorial design using artificial fertilization with 9 NAT dams and 17 WEM dams, producing 10 population crosses and 1950 potential full-sib families. All fish were reared together, then tagged at an average weight of 20 g and distributed to four different sites (1800 fish per site). They were grown to an objective of 200 g mean weight, where 737 to 775 fish were slaughtered in each site, and their parentage was recovered using 6 to 7 microsatellite loci, resulting in 98.9% unique assignments. All populations had similar growth rates until tagging size (20 g), but differences appeared later on. No heterosis appeared for growth rate, and genotype by environment interaction (G × E) at the population level was limited, with a significant re-ranking only in one rearing site, while strong G × E for growth rate was observed within populations. Populations were different in shape, muscular fat content, and carcass yield, but not in fillet yield. In general, heterosis was absent and G × E was very limited between populations. No "ideal" population combining all favorable traits was identified. Differences between extreme populations ranged between 3 and 49% of the mean, depending on the traits. Interestingly, in almost all cases, these differences were within the reach of one generation of intense (5%) phenotypic selection.
Published: 2014
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47. Assessment of genetic variability of fish personality traits using rainbow trout isogenic lines

Author: Mathilde Dupont-Nivet, Samuel Péan, Sandie Millot, Thierry Kerneis, Marie-Laure Bégout, Laurent Labbé, Edwige Quillet, Laboratoire Ressources halieutiques, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Pisciculture Expérimentale INRA des Monts d'Arrée (PEIMA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), ANR ADD COSADD [06-PADD-05], and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: media_common.quotation_subject, [SDV]Life Sciences [q-bio], Biology, Genotype, Spatial exploration, Genetics, Personality, Animals, Risk taking, 14. Life underwater, Genetic variability, Big Five personality traits, Domestication, Genetics (clinical), Ecology, Evolution, Behavior and Systematics, media_common, Behavior, Animal, Stressor, Genetic Variation, Oncorhynchus mykiss, Isogenic lines, Trait, Rainbow trout
Abstract: 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.
Published: 2014
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48. Early-feeding exposure to a plant-based diet improves its future acceptance and utilization in rainbow trout

Author: Geurden I, Borchert P, Balasubramanian M, Schrama J, Mathilde Dupont-Nivet, Quillet E, Kaushik S, Panserat P, Médale F, Nutrition, Aquaculture et Génomique (NUAGE), Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1-Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Aquaculture and Fisheries Group, Wageningen Institute of Animal Science, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER)-Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA), and AgroParisTech-Institut National de la Recherche Agronomique (INRA)
Subjects: Animal biology, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, oncorhynchus mykiss, alimentation animale, [SDV.BA]Life Sciences [q-bio]/Animal biology, education, Fisheries, Animal Feed, croissance, Diet, protéine végétale, alimentation végétale, Larva, Biologie animale, Animals, Animal Nutritional Physiological Phenomena, Digestion, métabolisme, human activities, huile végétale, health care economics and organizations
Abstract: Résumé poster; absent
Published: 2013

49. Genetics of behavioural adaptation of livestock to farming conditions

Author: Florence Phocas, Sandrine Mignon-Grasteau, Mathilde Dupont-Nivet, Laurianne Canario, Laboratoire de Génétique Cellulaire (LGC), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Institut National de la Recherche Agronomique (INRA)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Unité de Recherches Avicoles (URA), and Institut National de la Recherche Agronomique (INRA)-AgroParisTech
Subjects: pig, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Livestock, Range (biology), Sus scrofa, Biology, Breeding, Environment, behavioural genetics, fish, cattle, pig, poultry, SF1-1100, 03 medical and health sciences, Species Specificity, Stress, Physiological, Genetic variation, Animals, Animal Husbandry, Behavioural genetics, 030304 developmental biology, 2. Zero hunger, Genetics, Social stress, fish, 0303 health sciences, Behavior, Animal, business.industry, Ecology, poultry, Stressor, 0402 animal and dairy science, Fishes, Genetic Variation, 04 agricultural and veterinary sciences, 040201 dairy & animal science, Adaptation, Physiological, Animal culture, Agricultural sciences, cattle, behaviour, genetic, Agriculture, Animal Science and Zoology, Adaptation, business, Sciences agricoles
Abstract: Chantier qualité GA; Behavioural adaptation of farm animals to environmental changes contributes to high levels of production under a wide range of farming conditions, from highly controlled indoor systems to harsh outdoor systems. The genetic variation in livestock behaviour is considerable. Animals and genotypes with a larger behavioural capacity for adaptation may cope more readily with varying farming conditions than those with a lower capacity for adaptation. This capacity should be exploited when the aim is to use a limited number of species extensively across the world. The genetics of behavioural traits is understood to some extent, but it is seldom accounted for in breeding programmes. This review summarizes the estimates of genetic parameters for behavioural traits in cattle, pigs, poultry and fish. On the basis of the major studies performed in the last two decades, we focus the review on traits of common interest in the four species. These concern the behavioural responses to both acute and chronic stressors in the physical environment (feed, temperature, etc.) and those in the social environment (other group members, progeny, humans). The genetic strategies used to improve the behavioural capacity for adaptation of animals differ between species. There is a greater emphasis on responses to acute environmental stress in fish and birds, and on responses to chronic social stress in mammals.
Published: 2013
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50. Minimizing maternal effect in salmonid families mixed since eyed stages and a posteriori DNA-pedigreed

Author: Mathilde Dupont-Nivet, Edwige Quillet, Hervé Chapuis, Marc Vandeputte, Cédric Pincent, Vincent Petit, Bernard Coudurier, Pierrick Haffray, Béatrice Chatain, J-Claude Meriaux, Station commune de Recherches en Ichtyophysiologie, Biodiversité et Environnement (SCRIBE), Institut National de la Recherche Agronomique (INRA)-IFR140, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Institut National de la Recherche Agronomique (INRA), Recherches Avicoles (SRA), Institut National de la Recherche Agronomique (INRA), Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Collège de Direction, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Aqualande, Station IFREMER de Palavas-les-Flots, Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), Unité de Recherches Avicoles (URA), and Collège de Direction (CODIR)
Subjects: maternal effect, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, growth, triploid, Fingerprint, fingerprint, Triploid, Growth, Biology, heritability, Body weight, Condition factor, Heritability, 03 medical and health sciences, Human fertilization, Animal science, Maternal effect, 14. Life underwater, Selection (genetic algorithm), 030304 developmental biology, Genetics, 0303 health sciences, General Veterinary, 04 agricultural and veterinary sciences, rainbow trout, Rainbow trout, 040102 fisheries, 0401 agriculture, forestry, and fisheries, %22">Fish , Animal Science and Zoology
Abstract: Application of DNA parentage assignment for commercial selection in aquaculture is still rare. An experiment was performed to quantify and to minimize maternal effects on growth in rainbow trout. Six hundred families were reared until 198 day post fertilization (dpf) according to two different procedures. In the first procedure (NORM), all families were pooled at eyed stage. In the second procedure (MIN), where maternal effects due to differences in egg size were expected to be minimal, the spawns were divided into sub-groups with similar mean egg weight at eyed stage. These sub-groups were then pooled when they achieved the same mean body length (147 dpf). Genetic parameters were estimated for body weight, body length and condition factor at 198 dpf, with 2964 fish assigned to their parents using microsatellites. Significant maternal effects were observed in the NORM group for body weight and body length (m(2) = 0.08 +/- 0.03). The heritability of body weight was 0.16 +/- 0.07 in the NORM group and 0.36 +/- 0.06 in the MIN group, in which maternal effects were not significant It is concluded that, when eggs of different females are mixed at eyed stage, maternal effects persist at least until 198 dpf. The proposed procedure efficiently limits maternal effects, substantially increasing the heritability for growth, and therefore the expected selection response. (C) 2012 Elsevier B.V. All rights reserved.
Published: 2012
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