Author: "Pierrick Haffray" - Searchworks@Jio Institute Digital Library Search Results

Your search keyword '"Pierrick Haffray"' showing total 157 results

Start Over Author "Pierrick Haffray"

157 results on '"Pierrick Haffray"'

1. Multi-genome comparisons reveal gain-and-loss evolution of anti-Mullerian hormone receptor type 2 as a candidate master sex-determining gene in Percidae

Author: Heiner Kuhl, Peter T. Euclide, Christophe Klopp, Cédric Cabau, Margot Zahm, Céline Lopez-Roques, Carole Iampietro, Claire Kuchly, Cécile Donnadieu, Romain Feron, Hugues Parrinello, Charles Poncet, Lydia Jaffrelo, Carole Confolent, Ming Wen, Amaury Herpin, Elodie Jouanno, Anastasia Bestin, Pierrick Haffray, Romain Morvezen, Taina Rocha de Almeida, Thomas Lecocq, Bérénice Schaerlinger, Dominique Chardard, Daniel Żarski, Wesley A. Larson, John H. Postlethwait, Serik Timirkhanov, Werner Kloas, Sven Wuertz, Matthias Stöck, and Yann Guiguen
Subjects: Sex-determination, Genome, Perches, Pikeperches, Sex chromosomes, Biology (General), QH301-705.5
Abstract: Abstract Background The Percidae family comprises many fish species of major importance for aquaculture and fisheries. Based on three new chromosome-scale assemblies in Perca fluviatilis, Perca schrenkii, and Sander vitreus along with additional percid fish reference genomes, we provide an evolutionary and comparative genomic analysis of their sex-determination systems. Results We explored the fate of a duplicated anti-Mullerian hormone receptor type-2 gene (amhr2bY), previously suggested to be the master sex-determining (MSD) gene in P. flavescens. Phylogenetically related and structurally similar amhr2 duplicates (amhr2b) were found in P. schrenkii and Sander lucioperca, potentially dating this duplication event to their last common ancestor around 19–27 Mya. In P. fluviatilis and S. vitreus, this amhr2b duplicate has been likely lost while it was subject to amplification in S. lucioperca. Analyses of the amhr2b locus in P. schrenkii suggest that this duplication could be also male-specific as it is in P. flavescens. In P. fluviatilis, a relatively small (100 kb) non-recombinant sex-determining region (SDR) was characterized on chromosome 18 using population-genomics approaches. This SDR is characterized by many male-specific single-nucleotide variations (SNVs) and no large duplication/insertion event, suggesting that P. fluviatilis has a male heterogametic sex-determination system (XX/XY), generated by allelic diversification. This SDR contains six annotated genes, including three (c18h1orf198, hsdl1, tbc1d32) with higher expression in the testis than in the ovary. Conclusions Together, our results provide a new example of the highly dynamic sex chromosome turnover in teleosts and provide new genomic resources for Percidae, including sex-genotyping tools for all three known Perca species.
Published: 2024
Full Text: View/download PDF

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
Full Text: View/download PDF

3. Genetically superior European sea bass (Dicentrarchus labrax) and nutritional innovations: Effects of functional feeds on fish immune response, disease resistance, and gut microbiota

Author: Simona Rimoldi, Daniel Montero, Silvia Torrecillas, Antonio Serradell, Felix Acosta, Pierrick Haffray, Barbara Hostins, Ramon Fontanillas, François Allal, Aline Bajek, and Genciana Terova
Subjects: Bacilli, DNA barcoding, Firmicutes, Metagenomics, Proteobacteria, Aquaculture. Fisheries. Angling, SH1-691
Abstract: The objective of this study was to determine if selected fish genotypes could benefit from the use of functional additives in novel aqua feed formulations to improve growth performance, gut microbiota, immune response, and disease resistance in fish. Two batches of juvenile European sea bass selected for high growth (HG; selected sires x selected dams), and wild types (WT; wild sires x selected females) were fed a “future diet” coated with three different functional additives for 12 weeks as follows: (i) 2 weeks with a high dose, followed by (ii) 10 weeks with a low dose. The functional additives tested were a mixture of probiotics (PROB), organic acids (ORG), and phytogens (PHYTO). A pathogen challenge test (Vibrio anguillarum) and a stress condition (overcrowding) were performed after each dose. At the end of the feeding experiment, fish from the HG group performed better than fish from the WT group in terms of body weight, relative growth, SGR, and DGI. The results of the two challenge tests performed after two weeks of high dose and ten weeks of low dose showed a significant effect of diet on fish survival. GALT-associated gene expression analysis revealed an interaction between the genotype and diet for il-1β in the distal gut. Finally, regarding the gut microbiota, discriminant analysis showed no clear separation between fish fed the future diet and those fed the same diet with experimental additives. Nevertheless, the relative abundance of certain taxa varied between experimental groups. For example, fish fed the ORG diet had higher relative abundance of Streptococcus in both genotypes, whereas fish fed the PHYTO diet had higher abundance of Lactobacillales. In contrast, fish fed PROB had lower abundance of Pseudomonas and Acinetobacter.
Published: 2023
Full Text: View/download PDF

4. Whole‐genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass

Author: Emilie Delpuech, Marc Vandeputte, Romain Morvezen, Anastasia Bestin, Mathieu Besson, Joseph Brunier, Aline Bajek, Boudjema Imarazene, Yoannah François, Olivier Bouchez, Xavier Cousin, Charles Poncet, Thierry Morin, Jean-Sébastien Bruant, Béatrice Chatain, Pierrick Haffray, Florence Phocas, and François Allal
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background Viral nervous necrosis (VNN) is a major disease that affects European sea bass, and understanding the biological mechanisms that underlie VNN resistance is important for the welfare of farmed fish and sustainability of production systems. The aim of this study was to identify genomic regions and genes that are associated with VNN resistance in sea bass. Results We generated a dataset of 838,451 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation of two commercial populations (A: 2371 individuals and B: 3428 individuals) of European sea bass with phenotypic records for binary survival in a VNN challenge. For each population, three cohorts were submitted to a red-spotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, quantitative trait loci (QTL) were mapped using a Bayesian sparse linear mixed model (BSLMM). We found several QTL regions that were specific to one of the populations on different linkage groups (LG), and one 127-kb QTL region on LG12 that was shared by both populations and included the genes ZDHHC14, which encodes a palmitoyltransferase, and IFI6/IFI27-like, which encodes an interferon-alpha induced protein. The most significant SNP in this QTL region was only 1.9 kb downstream of the coding sequence of the IFI6/IFI27-like gene. An unrelated population of four large families was used to validate the effect of the QTL. Survival rates of susceptible genotypes were 40.6% and 45.4% in populations A and B, respectively, while that of the resistant genotype was 66.2% in population B and 78% in population A. Conclusions We have identified a genomic region that carries a major QTL for resistance to VNN and includes the ZDHHC14 and IFI6/IFI27-like genes. The potential involvement of the interferon pathway, a well-known anti-viral defense mechanism in several organisms (chicken, human, or fish), in survival to VNN infection is of particular interest. Our results can lead to major improvements for sea bass breeding programs through marker-assisted genomic selection to obtain more resistant fish.
Published: 2023
Full Text: View/download PDF

5. 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
Full Text: View/download PDF

6. 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
Full Text: View/download PDF

7. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes

Author: María Saura, Armando Caballero, Enrique Santiago, Almudena Fernández, Elisabeth Morales-González, Jesús Fernández, Santiago Cabaleiro, Adrián Millán, Paulino Martínez, Christos Palaiokostas, Martin Kocour, Muhammad L. Aslam, Ross D. Houston, Martin Prchal, Luca Bargelloni, Kostas Tzokas, Pierrick Haffray, Jean-Sebastien Bruant, and Beatriz Villanueva
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot (Scophthalmus maximus), gilthead seabream (Sparus aurata), European seabass (Dicentrarchus labrax) and common carp (Cyprinus carpio) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes.
Published: 2021
Full Text: View/download PDF

8. Functional Additives in a Selected European Sea Bass (Dicentrarchus labrax) Genotype: Effects on the Stress Response and Gill Antioxidant Response to Hydrogen Peroxide (H2O2) Treatment

Author: Antonio Serradell, Daniel Montero, Genciana Terova, Simona Rimoldi, Alex Makol, Félix Acosta, Aline Bajek, Pierrick Haffray, François Allal, and Silvia Torrecillas
Subjects: phytogenics, galactomannan-oligosaccharides, selective breeding, European sea bass (Dicentrarchus labrax), oxidative stress, stress response, Veterinary medicine, SF600-1100, Zoology, QL1-991
Abstract: Functional ingredients have profiled as suitable candidates for reinforcing the fish antioxidant response and stress tolerance. In addition, selective breeding strategies have also demonstrated a correlation between fish growth performance and susceptibility to stressful culture conditions as a key component in species domestication processes. The aim of the present study is to evaluate the ability of a selected high-growth genotype of 300 days post-hatch European sea bass (Dicentrarchus labrax) juveniles to use different functional additives as endogenous antioxidant capacity and stress resistance boosters when supplemented in low fish meal (FM) and fish oil (FO) diets. Three isoenergetic and isonitrogenous diets (10% FM/6% FO) were supplemented with 200 ppm of a blend of garlic and Labiatae plant oils (PHYTO0.02), 1000 ppm of a mixture of citrus flavonoids and Asteraceae and Labiatae plant essential oils (PHYTO0.1) or 5000 ppm of galactomannan-oligosaccharides (GMOS0.5). A reference diet was void of supplementation. The fish were fed the experimental diets for 72 days and subjected to a H2O2 exposure oxidative stress challenge. The fish stress response was evaluated through measuring the circulating plasma cortisol levels and the fish gill antioxidant response by the relative gene expression analysis of nfΚβ2, il-1b, hif-1a, nd5, cyb, cox, sod, cat, gpx, tnf-1α and caspase 9. After the oxidative stress challenge, the genotype origin determined the capacity of the recovery of basal cortisol levels after an acute stress response, presenting GS fish with a better pattern of recovery. All functional diets induced a significant upregulation of cat gill gene expression levels compared to fish fed the control diet, regardless of the fish genotype. Altogether, suggesting an increased capacity of the growth selected European sea bass genotype to cope with the potential negative side-effects associated to an H2O2 bath exposure.
Published: 2023
Full Text: View/download PDF

9. 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
Full Text: View/download PDF

10. Potential for genomic selection on feed efficiency in gilthead sea bream (Sparus aurata), based on individual feed conversion ratio, carcass and lipid traits

Author: Mathieu Besson, Nicky Rombout, Germain Salou, Alain Vergnet, Sophie Cariou, Jean-Sébastien Bruant, Marisol Izquierdo, Anastasia Bestin, Frédéric Clota, Pierrick Haffray, François Allal, and Marc Vandeputte
Subjects: Fine phenotyping, Selective breeding, Aquaculture, Genomic, Restricted feeding, Individual feed efficiency, Aquaculture. Fisheries. Angling, SH1-691
Abstract: Genetic improvement of feed efficiency is key to improve the economic and environmental sustainability of fish farming. However, it requires individual phenotypes of feed efficiency, which are difficult if not impossible to obtain when fish are reared in tanks or cages. Here, we applied and validated on gilthead sea bream a method to evaluate individual feed efficiency based on individual rearing of fish in aquariums under restricted feeding. We collected individual phenotypes of feed efficiency in aquariums on 538 sea bream (average weight = 54.50 g). Based on these individual phenotypes, fish (average weight = 174.6 g) were reared in groups of divergent phenotypes (high or low feed efficiency), validating that individual feed efficiency had an impact on group feed efficiency at a later stage. All 538 fish, their parents as well as 794 sibs reared in cages in a production environment, were genotyped on a 57k SNP array to estimate genomic heritability and correlations between traits. We showed that feed efficiency was heritable but did not find significant associated QTLs. We also showed that feed efficiency was negatively genetically correlated to viscera yield, indicating that the most efficient fish had less viscera than the least efficient ones. Altogether, these results support that measuring individual feed efficiency in aquariums under restricted feeding may be used as a reliable phenotyping method to genetically improve feed efficiency, despite the bias intrinsically linked to individual rearing.
Published: 2022
Full Text: View/download PDF

11. Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

Author: Clémence Fraslin, Florence Phocas, Anastasia Bestin, Mathieu Charles, Maria Bernard, Francine Krieg, Nicolas Dechamp, Céline Ciobotaru, Chris Hozé, Florent Petitprez, Marine Milhes, Jérôme Lluch, Olivier Bouchez, Charles Poncet, Philippe Hocdé, Pierrick Haffray, Yann Guiguen, and Edwige Quillet
Subjects: Medicine, Science
Abstract: Abstract Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout.
Published: 2020
Full Text: View/download PDF

12. Corrigendum: Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, The European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata)

Author: Ronan Griot, François Allal, Florence Phocas, Sophie Brard-Fudulea, Romain Morvezen, Pierrick Haffray, Yoannah François, Thierry Morin, Anastasia Bestin, Jean-Sébastien Bruant, Sophie Cariou, Bruno Peyrou, Joseph Brunier, and Marc Vandeputte
Subjects: genomic selection, dicentrarchus labrax, sparus aurata, disease resistance, aquacultrure, Genetics, QH426-470
Published: 2021
Full Text: View/download PDF

13. Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

Author: Pierre Boudry, François Allal, Muhammad L. Aslam, Luca Bargelloni, Tim P. Bean, Sophie Brard-Fudulea, Marine S.O. Brieuc, Federico C.F. Calboli, John Gilbey, Pierrick Haffray, Jean-Baptiste Lamy, Romain Morvezen, Catherine Purcell, Paulo A. Prodöhl, Marc Vandeputte, Geoffrey C. Waldbieser, Anna K. Sonesson, and Ross D. Houston
Subjects: Aquaculture, Selective breeding, Genomic selection, SNP array, Genotyping by sequencing, Aquaculture. Fisheries. Angling, SH1-691
Abstract: Selective breeding has been successfully applied to improve profitability and sustainability in numerous aquatic species. Recent developments of high throughput genotyping technology now enable the implementation of genomic selection, a method aiming to predict the breeding value of candidates based on their genotype at genome-wide markers. In this review article, we review the state of the arts, challenges and prospects for the application of genomic selection in aquaculture species. The particular focus is on the status of genomic selection in several major aquaculture species of International Council for the Exploration of the Sea (ICES) member countries: Atlantic salmon, rainbow trout, Atlantic cod, American catfish, Pacific oyster, European sea bass and gilthead sea bream. While the potential of genomic selection is clear, tailored species-specific applications will be needed to maximise its benefit for the aquaculture sector.
Published: 2021
Full Text: View/download PDF

14. Optimization of Genomic Selection to Improve Disease Resistance in Two Marine Fishes, the European Sea Bass (Dicentrarchus labrax) and the Gilthead Sea Bream (Sparus aurata)

Author: Ronan Griot, François Allal, Florence Phocas, Sophie Brard-Fudulea, Romain Morvezen, Pierrick Haffray, Yoannah François, Thierry Morin, Anastasia Bestin, Jean-Sébastien Bruant, Sophie Cariou, Bruno Peyrou, Joseph Brunier, and Marc Vandeputte
Subjects: genomic selection, dicentrarchus labrax, Sparus aurata, disease resistance, aquaculture, Genetics, QH426-470
Abstract: Disease outbreaks are a major threat to the aquaculture industry, and can be controlled by selective breeding. With the development of high-throughput genotyping technologies, genomic selection may become accessible even in minor species. Training population size and marker density are among the main drivers of the prediction accuracy, which both have a high impact on the cost of genomic selection. In this study, we assessed the impact of training population size as well as marker density on the prediction accuracy of disease resistance traits in European sea bass (Dicentrarchus labrax) and gilthead sea bream (Sparus aurata). We performed a challenge to nervous necrosis virus (NNV) in two sea bass cohorts, a challenge to Vibrio harveyi in one sea bass cohort and a challenge to Photobacterium damselae subsp. piscicida in one sea bream cohort. Challenged individuals were genotyped on 57K–60K SNP chips. Markers were sampled to design virtual SNP chips of 1K, 3K, 6K, and 10K markers. Similarly, challenged individuals were randomly sampled to vary training population size from 50 to 800 individuals. The accuracy of genomic-based (GBLUP model) and pedigree-based estimated breeding values (EBV) (PBLUP model) was computed for each training population size using Monte-Carlo cross-validation. Genomic-based breeding values were also computed using the virtual chips to study the effect of marker density. For resistance to Viral Nervous Necrosis (VNN), as one major QTL was detected, the opportunity of marker-assisted selection was investigated by adding a QTL effect in both genomic and pedigree prediction models. As training population size increased, accuracy increased to reach values in range of 0.51–0.65 for full density chips. The accuracy could still increase with more individuals in the training population as the accuracy plateau was not reached. When using only the 6K density chip, accuracy reached at least 90% of that obtained with the full density chip. Adding the QTL effect increased the accuracy of the PBLUP model to values higher than the GBLUP model without the QTL effect. This work sets a framework for the practical implementation of genomic selection to improve the resistance to major diseases in European sea bass and gilthead sea bream.
Published: 2021
Full Text: View/download PDF

15. 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
Full Text: View/download PDF

16. 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
Full Text: View/download PDF

17. Potential for Genetic Improvement of Resistance to Perkinsus olseni in the Manila Clam, Ruditapes philippinarum, Using DNA Parentage Assignment and Mass Spawning

Author: Morgan Smits, Florian Enez, Serena Ferraresso, Giulia Dalla Rovere, Emilie Vetois, Jean-François Auvray, Lucie Genestout, Rachid Mahla, Giuseppe Arcangeli, Christine Paillard, Pierrick Haffray, and Luca Bargelloni
Subjects: Manila clam (Ruditapes philippinarum), Perkinsus olseni infection, disease resistance, genetic selection, genetic parameter estimation, Veterinary medicine, SF600-1100
Abstract: The Manila clam Ruditapes philippinarum, a major cultured shellfish species, is threatened by infection with the microparasite Perkinsus olseni, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against P. olseni, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR. A mixed-family cohort of potentially 1,479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of P. olseni had previously been reported. Growth and parasite load were monitored every month and, after 1 year, more than 1,000 individuals were collected for DNA samples and phenotype recording. A pooled sequencing approach was carried out using DNA samples from the hatchery broodstock and from a Venice lagoon clam population, providing candidate markers used to develop a 245-SNP panel. Parentage assignment for 246 F1 individuals showed sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.23 ± 0.11–0.35 ± 0.13) was estimated for growth traits (shell length, shell weight, total weight), while parasite load showed high heritability, estimated at 0.51 ± 0.20. No significant genetic correlations were found between growth-associated traits and parasite load. Overall, the preliminary results provided by this study show high potential for selecting clams resistant to parasite load. Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions.
Published: 2020
Full Text: View/download PDF

18. 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
Full Text: View/download PDF

19. Genetics of resistance to photobacteriosis in gilthead sea bream (Sparus aurata) using 2b-RAD sequencing

Author: Muhammad L Aslam, Roberta Carraro, Anastasia Bestin, Sophie Cariou, Anna K. Sonesson, Jean-Sébastien Bruant, Pierrick Haffray, Luca Bargelloni, and Theo H. E. Meuwissen
Subjects: Photobacteriosis, 2b-RAD, Single nucleotide polymorphisms, Linkage mapping, Genome-wide association study, Quantitative trait loci, Genetics, QH426-470
Abstract: Abstract Background Photobacteriosis is an infectious disease developed by a Gram-negative bacterium Photobacterium damselae subsp. piscicida (Phdp), which may cause high mortalities (90–100%) in sea bream. Selection and breeding for resistance against infectious diseases is a highly valuable tool to help prevent or diminish disease outbreaks, and currently available advanced selection methods with the application of genomic information could improve the response to selection. An experimental group of sea bream juveniles was derived from a Ferme Marine de Douhet (FMD, Oléron Island, France) selected line using ~ 109 parents (~ 25 females and 84 males). This group of 1187 individuals represented 177 full-sib families with 1–49 sibs per family, which were challenged with virulent Phdp for a duration of 18 days, and mortalities were recorded within this duration. Tissue samples were collected from the parents and the recorded offspring for DNA extraction, library preparation using 2b-RAD and genotyping by sequencing. Genotypic data was used to develop a linkage map, genome wide association analysis and for the estimation of breeding values. Results The analysis of genetic variation for resistance against Phdp revealed moderate genomic heritability with estimates of ~ 0.32. A genome-wide association analysis revealed a quantitative trait locus (QTL) including 11 SNPs at linkage group 17 presenting significant association to the trait with p-value crossing genome-wide Bonferroni corrected threshold P ≤ 2.22e-06. The proportion total genetic variance explained by the single top most significant SNP was ranging from 13.28–16.14% depending on the method used to compute the variance. The accuracies of predicting breeding values obtained using genomic vs. pedigree information displayed 19–24% increase when using genomic information. Conclusion The current study demonstrates that SNPs-based genotyping of a sea bream population with 2b-RAD approach is effective at capturing the genetic variation for resistance against Phdp. Prediction accuracies obtained using genomic information were significantly higher than the accuracies obtained using pedigree information which highlights the importance and potential of genomic selection in commercial breeding programs.
Published: 2018
Full Text: View/download PDF

20. Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing

Author: Christos Palaiokostas, Sophie Cariou, Anastasia Bestin, Jean-Sebastien Bruant, Pierrick Haffray, Thierry Morin, Joëlle Cabon, François Allal, Marc Vandeputte, and Ross D. Houston
Subjects: Animal culture, SF1-1100, Genetics, QH426-470
Abstract: Abstract Background European sea bass (Dicentrarchus labrax) is one of the most important species for European aquaculture. Viral nervous necrosis (VNN), commonly caused by the redspotted grouper nervous necrosis virus (RGNNV), can result in high levels of morbidity and mortality, mainly during the larval and juvenile stages of cultured sea bass. In the absence of efficient therapeutic treatments, selective breeding for host resistance offers a promising strategy to control this disease. Our study aimed at investigating genetic resistance to VNN and genomic-based approaches to improve disease resistance by selective breeding. A population of 1538 sea bass juveniles from a factorial cross between 48 sires and 17 dams was challenged with RGNNV with mortalities and survivors being recorded and sampled for genotyping by the RAD sequencing approach. Results We used genome-wide genotype data from 9195 single nucleotide polymorphisms (SNPs) for downstream analysis. Estimates of heritability of survival on the underlying scale for the pedigree and genomic relationship matrices were 0.27 (HPD interval 95%: 0.14-0.40) and 0.43 (0.29–0.57), respectively. Classical genome-wide association analysis detected genome-wide significant quantitative trait loci (QTL) for resistance to VNN on chromosomes (unassigned scaffolds in the case of ‘chromosome’ 25) 3, 20 and 25 (P
Published: 2018
Full Text: View/download PDF

21. Potential for Genetic Improvement of the Main Slaughter Yields in Common Carp With in vivo Morphological Predictors

Author: Martin Prchal, Jérôme Bugeon, Marc Vandeputte, Antti Kause, Alain Vergnet, Jinfeng Zhao, David Gela, Lucie Genestout, Anastasia Bestin, Pierrick Haffray, and Martin Kocour
Subjects: heritability estimates, genetic correlations, indirect selection, morphological landmarks, slaughter yields, ultrasound imagery, Genetics, QH426-470
Abstract: Common carp is a major aquaculture species worldwide, commonly sold alive but also as processed headless carcass or filets. However, recording of processing yields is impossible on live breeding candidates, and alternatives for genetic improvement are either sib selection based on slaughtered fish, or indirect selection on correlated traits recorded in vivo. Morphological predictors that can be measured on live fish and that correlate with real slaughter yields hence remain a possible alternative. To quantify the power of morphological predictors for genetic improvement of yields, we estimated genetic parameters of slaughter yields and various predictors in 3-year-old common carp reared communally under semi-intensive pond conditions. The experimental stock was established by a partial factorial design of 20 dams and 40 sires, and 1553 progenies were assigned to their parents using 12 microsatellites. Slaughter yields were highly heritable (h2 = 0.46 for headless carcass yield, 0.50 for filet yield) and strongly genetically correlated with each other (rg = 0.96). To create morphological predictors, external (phenotypes, 2D digitization) and internal measurements (ultrasound imagery) were recorded and combined by multiple linear regression to predict slaughter yields. The accuracy of the phenotypic prediction was high for headless carcass yield (R2 = 0.63) and intermediate for filet yield (R2 = 0.49). Interestingly, heritability of predicted slaughter yields (0.48–0.63) was higher than that of the real yields to predict, and had high genetic correlations with the real yields (rg = 0.84–0.88). In addition, both predicted yields were highly phenotypically and genetically correlated with each other (0.95 for both), suggesting that using predicted headless carcass yield in a breeding program would be a good way to also improve filet yield. Besides, two individual predictors (P1 and P2) included in the prediction models and two simple internal measurements (E4 and E23) exhibited intermediate to high heritability estimates (h2 = 0.34 – 0.72) and significant genetic correlations to the slaughter yields (rg = |0.39 – 0.83|). The results show that there is a solid potential for genetic improvement of slaughter yields by selecting for predictor traits recorded on live breeding candidates of common carp.
Published: 2018
Full Text: View/download PDF

22. Survival, growth and reproduction of cryopreserved larvae from a marine invertebrate, the Pacific oyster (Crassostrea gigas).

Author: Marc Suquet, Catherine Labbé, Sophie Puyo, Christian Mingant, Benjamin Quittet, Myrina Boulais, Isabelle Queau, Dominique Ratiskol, Blandine Diss, and Pierrick Haffray
Subjects: Medicine, Science
Abstract: This study is the first demonstration of successful post-thawing development to reproduction stage of diploid cryopreserved larvae in an aquatic invertebrate. Survival, growth and reproductive performances were studied in juvenile and adult Pacific oysters grown from cryopreserved embryos. Cryopreservation was performed at three early stages: trochophore (13±2 hours post fertilization: hpf), early D-larvae (24±2 hpf) and late D-larvae (43±2 hpf). From the beginning (88 days) at the end of the ongrowing phase (195 days), no mortality was recorded and mean body weights did not differ between the thawed oysters and the control. At the end of the growing-out phase (982 days), survival of the oysters cryopreserved at 13±2 hpf and at 43±2 hpf was significantly higher (P
Published: 2014
Full Text: View/download PDF

23. Functional Additives in a Selected European Sea Bass (Dicentrarchus labrax) Genotype: Effects on the Stress Response and Gill Antioxidant Response to Hydrogen Peroxide (H2O2) Treatment

Author: Torrecillas, Antonio Serradell, Daniel Montero, Genciana Terova, Simona Rimoldi, Alex Makol, Félix Acosta, Aline Bajek, Pierrick Haffray, François Allal, and Silvia
Subjects: phytogenics, galactomannan-oligosaccharides, selective breeding, European sea bass (Dicentrarchus labrax), oxidative stress, stress response
Abstract: Functional ingredients have profiled as suitable candidates for reinforcing the fish antioxidant response and stress tolerance. In addition, selective breeding strategies have also demonstrated a correlation between fish growth performance and susceptibility to stressful culture conditions as a key component in species domestication processes. The aim of the present study is to evaluate the ability of a selected high-growth genotype of 300 days post-hatch European sea bass (Dicentrarchus labrax) juveniles to use different functional additives as endogenous antioxidant capacity and stress resistance boosters when supplemented in low fish meal (FM) and fish oil (FO) diets. Three isoenergetic and isonitrogenous diets (10% FM/6% FO) were supplemented with 200 ppm of a blend of garlic and Labiatae plant oils (PHYTO0.02), 1000 ppm of a mixture of citrus flavonoids and Asteraceae and Labiatae plant essential oils (PHYTO0.1) or 5000 ppm of galactomannan-oligosaccharides (GMOS0.5). A reference diet was void of supplementation. The fish were fed the experimental diets for 72 days and subjected to a H2O2 exposure oxidative stress challenge. The fish stress response was evaluated through measuring the circulating plasma cortisol levels and the fish gill antioxidant response by the relative gene expression analysis of nfΚβ2, il-1b, hif-1a, nd5, cyb, cox, sod, cat, gpx, tnf-1α and caspase 9. After the oxidative stress challenge, the genotype origin determined the capacity of the recovery of basal cortisol levels after an acute stress response, presenting GS fish with a better pattern of recovery. All functional diets induced a significant upregulation of cat gill gene expression levels compared to fish fed the control diet, regardless of the fish genotype. Altogether, suggesting an increased capacity of the growth selected European sea bass genotype to cope with the potential negative side-effects associated to an H2O2 bath exposure.
Published: 2023
Full Text: View/download PDF

24. 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, Martin Prchal, Yoannah François, Jonathan D’Ambrosio, Emilien Segret, Ana Acin-Perez, Frederic Cachelou, Pierrick Haffray, Audrey Dehaullon, Mathilde Dupont-Nivet, and Florence Phocas
Abstract: BackgroundSelective breeding is a promising solution to reduce fish farms vulnerability to heat peaks which intensity and frequency are predicted to increase due to climate change. 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 batch (N=1,382) was phenotyped for acute hyperthermia resistance at nine months, and the second batch (N=1,506) was phenotyped for main production traits (growth, body length, muscle fat content and carcass yield) at twenty months. Fish were genotyped on a 57K SNP array, and their genotypes were imputed at high-density thanks to their parents being genotyped on a 665K SNP array.ResultsThe heritability estimate of resistance to acute hyperthermia in juveniles was 0.29 ± 0.05, confirming the potential of selective breeding for this trait. Genetic correlations between acute hyperthermia resistance and main production traits at near harvest age were all close to zero. Hence, selecting for acute hyperthermia resistance should not impact the main production traits, and reversely.The genome-wide association study revealed that resistance to acute hyperthermia is highly polygenic; altogether, the six detected QTL explained less than 5% of the genetic variance. Two of these QTL, including the most significant one, might explain acute hyperthermia resistance differences across INRAE isogenic lines of rainbow trout. The phenotypic mean differences between homozygotes at peak SNP were up to 69% of the phenotypic standard deviation, showing promising potential for marker-assisted selection. We identified 89 candidate genes within the six QTL regions, among which the most convincing functional candidate genes werednajc7,hsp70b,nkiras2,cdk12,phb,fkbp10,ddx5,cygb1,enpp7,pdhxandacly.ConclusionsThis study provides valuable insight on the genetic architecture of acute hyperthermia resistance in juvenile rainbow trout. The potential for the selective breeding of this trait was shown to be substantial and should not interfere with selection for main production traits. Identified functional candidate genes give a new insight on physiological mechanisms involved in acute hyperthermia resistance, such as protein chaperoning, oxidative stress response, homeostasis maintenance and cell survival.
Published: 2022
Full Text: View/download PDF

25. Whole-genome sequencing identifies interferon induced protein IFI6 as a strong candidate gene for VNN resistance in European sea bass

Author: Emilie Delpuech, Marc Vandeputte, Romain Morvezen, Anastasia Bestin, Mathieu Besson, Joseph Brunier, Aline Bajek, Boudjema Imarazene, Yoannah François, Olivier Bouchez, Xavier Cousin, Charles Poncet, Thierry Morin, Jean-Sébastien Bruant, Béatrice Chatain, Pierrick Haffray, Florence Phocas, and François Allal
Abstract: BackgroundViral Nervous Necrosis (VNN) is major disease affecting of European sea bass. Understanding the biological mechanisms that underlie VNN resistance is thus important for the welfare of farmed fish and the sustainability of production systems. This study aimed at identifying key genomic regions and genes that determine VNN resistance in sea bass.ResultsWe generated a dataset of around 900,000 single nucleotide polymorphisms (SNPs) identified from whole-genome sequencing (WGS) in the parental generation in two different commercial populations (pop A and pop B) comprising 2371 and 3428 European sea bass with phenotypic records for binary survival in a VNN challenge. In each commercial population, three cohorts were submitted to the redspotted grouper nervous necrosis virus (RGNNV) challenge by immersion and genotyped on a 57K SNP chip. After imputation of WGS SNPs from their parents, QTL mapping was performed using a Bayesian Sparse Linear Mixed Model (BSLMM). We found several QTL regions on different linkage groups (LG), most of which are specific to a single population, but a QTL region on LG12 was shared by both commercial populations. This QTL region is only 127 kB wide, and we identified IFI6, an interferon induced protein at only 1.9 kB of the most significant SNP. An unrelated validation population with 4 large families was used to validate the effect of the QTL, for which the survival of the susceptible genotype ranges from 39.8 to 45.4%, while that of the resistant genotype ranges from 63.8 to 70.8%.ConclusionsWe could precisely locate the genomic region implied in the main resistance QTL at less than 1.9 kb of the interferon alpha inducible protein 6 (IFI6), which has already been identified as a key player for other viral infections such as hepatitis B and C. This will lead to major improvements for sea bass breeding programs, allowing for greater genetic gain by using marker-assisted genomic selection to obtain more resistant fish. Further functional analyses are needed to evaluate the impact of the variant on the expression of this gene.
Published: 2022
Full Text: View/download PDF

26. Impact of a divergent selective breeding programme on individual feed conversion ratio in Nile tilapia Oreochromis niloticus measured in groups by video-recording

Author: Vincent Douchet, Hugues de Verdal, Pierrick Haffray, Marc Vandeputte, 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), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), 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)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), 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), European Marine and fisheries Fund (EMFF), and French government
Subjects: food.ingredient, Efficacité conversion alimentaire, Fish farming, Feed efficiency, [SDV]Life Sciences [q-bio], Sélection, chemical and pharmacologic phenomena, Aquaculture, Aquatic Science, Biology, Selective breeding, Genetic correlation, Feed conversion ratio, 03 medical and health sciences, Nile tilapia, Animal science, food, Selection response, Pisciculture, 030304 developmental biology, 2. Zero hunger, L02 - Alimentation animale, 0303 health sciences, Oreochromis niloticus, Tilapia, 04 agricultural and veterinary sciences, Heritability, Genetic parameters, biology.organism_classification, L10 - Génétique et amélioration des animaux, génétique animale, Oreochromis, 040102 fisheries, 0401 agriculture, forestry, and fisheries, M12 - Production de l'aquaculture, Amélioration des animaux, Alimentation des poissons, sustainable aquaculture [EN]
Abstract: International audience; Feed conversion ratio (FCR) is an important trait to target in breeding programs in order to improve fish farming sustainability and increase environmental efficiency. Due to the complexity of accurately measuring the individual feed consumption of fish, developing a selective breeding programme to improve FCR is a challenge. Using video-recordings of several consecutive meals in tilapia groups, we selected two divergent lines of Nile tilapia for high (FCR+) and low (FCR-) FCR at juvenile stage (12.2 g) combining BLUP and within family selection. After two generations, we observed a 12% realized difference in FCR between both divergent lines, indicating that the inclusion of FCR in a selective breeding programme can be efficient in practice. This divergence was in line with a realized heritability of 0.19 for FCR. The divergence in estimated breeding values of FCR between the two lines was reduced (3%) but still present. Another important result was that the realized genetic correlation between FCR and Daily Weight Gain (DWG) was highly negative (rg = -0.69 + 0.16), meaning that improving growth by selective breeding would also indirectly improve FCR in juvenile Nile tilapia, although direct selection for FCR would be more efficient than indirect selection through growth to improve FCR.
Published: 2022
Full Text: View/download PDF

27. 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
Full Text: View/download PDF

28. Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes

Author: Paulino Martínez, Enrique Santiago, Muhammad Luqman Aslam, Jesús Fernández, Beatriz Villanueva, Kostas Tzokas, Christos Palaiokostas, Almudena Fernández, Maria Saura, Jean-Sébastien Bruant, Pierrick Haffray, Adrián Millán, Ross D. Houston, Luca Bargelloni, Martin Prchal, Martin Kocour, Armando Caballero, Elisabeth Morales-González, Santiago Cabaleiro, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universidade de Vigo, Universidad de Oviedo [Oviedo], Cluster Acuicultura Galicia (CETGA), Geneaqua, Universidade de Santiago de Compostela [Spain] (USC ), University of Edinburgh, University of South Bohemia, Norwegian Institute of Food,Fisheries and Aquaculture Research (NOFIMA), Università degli Studi di Padova = University of Padua (Unipd), Andromeda Group SA, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Ferme Marine de Douhet, This work was supported by the European Union’s Seventh Framework Programme (KBBE.2013.1.2‑659 10 under Grant Agreement No. 613611 FISHBOOST project), the European Commission Horizon 2020 (H2020) Framework Programme through grant agreement no 727315 MedAID project (Mediterranean Aquaculture Integrated Development), by Ministerio de Ciencia e Innovación (CGL2016‑75904‑C2), MCIN/AEI/https:// doi. org/ 10.13039/ 50110 00110 33 (PID2020‑114426GB‑C22 and PID2020‑114426GB‑C2), Xunta de Galicia (GRC, ED431C 2020‑05) and Centro singular de investigación de Galicia accreditation 2019–2022, and the European Union (European Regional Development Fund—ERDF), Fondos Feder 'Unha maneira de facer Europa'. MK and MP were also supported by Ministry of Education, Youth and Sports of the Czech Republic—project Biodiverzity (CZ.02.1.01/0.0/0.0/16_025/0007370). The Roslin Institute was partly funded by Biotechnology and Biological Sciences Research Council Institute Strategic Programme grants (BBS/E/D/20241866, BBS/E/D/20002172 and BBS/E/D/20002174)., European Project: 613611,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,FISHBOOST(2014), European Project: 727315,MedAID, European Commission, Ministerio de Ciencia e Innovación (España), Xunta de Galicia, Saura, María [0000-0002-2744-2840], Caballero, Armando [0000-0001-7391-6974], Santiago, Enrique [0000-0002-5524-5641], Morales-González, Elisabeth [0000-0002-5614-5044], Fernández, Jesús [0000-0001-8269-1893], Cabaleiro, Santiago [0000-0002-3866-8810], Millán, Adrián [0000-0003-2914-3067], Martínez, Paulino [0000-0001-8438-9305], Kocour, Martin [0000-0003-2984-1412], Houston, Ross D [0000-0003-1805-0762], Prchal, Martin [0000-0002-5059-2812], Bargelloni, Luca [0000-0003-4351-2826], Tzokas, Kostas [0000-0002-2037-9594], Haffray, Pierrick [0000-0001-8604-4562], Bruant, Jean-Sebastien [0000-0001-7078-9332], Saura, María, Caballero, Armando, Santiago, Enrique, Morales-González, Elisabeth, Fernández, Jesús, Cabaleiro, Santiago, Millán, Adrián, Martínez, Paulino, Kocour, Martin, Houston, Ross D, Prchal, Martin, Bargelloni, Luca, Tzokas, Kostas, Haffray, Pierrick, and Bruant, Jean-Sebastien
Subjects: Carps, [SDV]Life Sciences [q-bio], Short Communication, Zoology, Biology, QH426-470, Selective breeding, SF1-1100, Common carp, Cyprinus carpio, Scophthalmus maximus, Effective population size, Genetics, Animals, Humans, Dicentrarchus labrax, Scophthalmidae, Genetic variability, Domestication, Ecology, Evolution, Behavior and Systematics, Selection (genetic algorithm), Population Density, Cyprinus carpi, Population size, General Medicine, Fecundity, Sea Bream, Animal culture, Flatfishes, Selective Breeding, Bass, Animal Science and Zoology
Abstract: 8 Pág. Departamento de Mejora Genética Animal (INIA), This work was supported by the European Union’s Seventh Framework Programme (KBBE.2013.1.2-659 10 under Grant Agreement No. 613611 FISHBOOST project), the European Commission Horizon 2020 (H2020) Framework Programme through grant agreement no 727315 MedAID project (Mediterranean Aquaculture Integrated Development), by Ministerio de Ciencia e Innovación (CGL2016-75904-C2), MCIN/AEI/https://doi.org/10.13039/501100011033 (PID2020-114426GB-C22 and PID2020-114426GB-C2), Xunta de Galicia (GRC, ED431C 2020-05) and Centro singular de investigación de Galicia accreditation 2019–2022, and the European Union (European Regional Development Fund—ERDF), Fondos Feder “Unha maneira de facer Europa”. MK and MP were also supported by Ministry of Education, Youth and Sports of the Czech Republic—project Biodiverzity (CZ.02.1.01/0.0/0.0/16_025/0007370). The Roslin Institute was partly funded by Biotechnology and Biological Sciences Research Council Institute Strategic Programme grants (BBS/E/D/20241866, BBS/E/D/20002172 and BBS/E/D/20002174).
Published: 2021
Full Text: View/download PDF

29. Genetic correlations between processing traits and individual feed efficiency in a gilthead sea bream (Sparus aurata) commercial line

Author: Anastasia Bestin, Mathieu Besson, Alain Vergnet, François Allal, Frédéric Clota, Cariou Sophie, Jean-Sebastien Bruant, Pierrick Haffray, Marc Vandeputte, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), 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), and Ferme Marine de Douhet
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

30. Sex identification in immature Eurasian perch ( Perca fluviatilis ) using ultrasonography

Author: Anastasia Bestin, Dominique Chardard, Pascal Fontaine, Romain Morvezen, Maud Alix, Bérénice Schaerlinger, Pierrick Haffray, Yannick Ledoré, Unité de Recherches Animal et Fonctionnalités des Produits Animaux (URAFPA), Université de Lorraine (UL)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), and This study was partly supported by the PERCIHATCH program (funding by the European Maritime and Fisheries Fund and FranceAgrimer project) and Sex’NPerch program (funding by the European Maritime and Fisheries Fund and FranceAgrimer project).
Subjects: 0106 biological sciences, Perch, biology, sex identification, business.industry, ultrasound, 010604 marine biology & hydrobiology, [SDV]Life Sciences [q-bio], Zoology, food and beverages, 04 agricultural and veterinary sciences, Aquatic Science, biology.organism_classification, 01 natural sciences, Perca fluviatilis, eurasian perch, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Identification (biology), 14. Life underwater, Ultrasonography, business
Abstract: International audience; One of the keys for an optimal Eurasian perch aquaculture broodstock management is being able to determine the sex of individuals. For Eurasian perch, compared with other methods of sex identification of fish and according to the 3R principle (replacement, reduction and refinement), ultrasonography is a rapid, non-lethal, non-invasive and accurate method. During two successive experiments, we used ultrasound to identify the gender of two immature Eurasian perch broodstock. In the last experiment, females were identified with 98.9% accuracy (n = 180) and males with 98.8% accuracy (n = 92). This method can be very beneficial for perch fish farmers or aquaculture research.
Published: 2021
Full Text: View/download PDF

31. Rainbow trout resistance to bacterial cold water disease: two new quantitative trait loci identified after a natural disease outbreak on a French farm

Author: Pierrick Haffray, Sophie Brard-Fudulea, Anastasia Bestin, Mathieu Charles, Jonathan D’Ambrosio, Florence Phocas, Edwige Quillet, Clémence Fraslin, Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Université Paris-Saclay, Section Aquacole, Syndicat des Sélectionneurs Avicoles et Aquacoles Français, FEAMP - FranceAgriMer (no. 2015-0638), and Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF)
Subjects: 0301 basic medicine, [SDV]Life Sciences [q-bio], Quantitative Trait Loci, Flavobacterium psychrophilum, Genome-wide association study, heritability, Biology, Quantitative trait locus, Flavobacterium, Bacterial cold water disease, Disease Outbreaks, 03 medical and health sciences, Flavobacteriaceae Infections, Genetics, Animals, Selection, Poultry Diseases, Disease Resistance, genome-wide association study, 0402 animal and dairy science, Outbreak, 04 agricultural and veterinary sciences, General Medicine, Heritability, biology.organism_classification, 040201 dairy & animal science, Genetic architecture, Trout, 030104 developmental biology, aquaculture, Oncorhynchus mykiss, Animal Science and Zoology, France
Abstract: International audience; In rainbow trout farming, Flavobacterium psychrophilum, the causative agent of bacterial cold water disease, is responsible for important economic losses. Resistance to F. psychrophilum is heritable, and several quantitative trait loci (QTL) with moderate effects have been detected, opening up promising perspectives for the genetic improvement of resistance. In most studies however, resistance to F. psychrophilum was assessed in experimental infectious challenges using injection as the infection route, which is not representative of natural infection. Indeed, injection bypasses external barriers, such as mucus and skin, that likely play a protective role against the infection. In this study, we aimed at describing the genetic architecture of the resistance to F. psychrophilum after a natural disease outbreak. In a 2000-fish cohort, reared on a French farm, 720 fish were sampled and genotyped using the medium-throughput Axiom (TM) Trout Genotyping Array. Overall mortality at the end of the outbreak was 25%. Genome-wide association studies were performed under two different models for time to death measured on 706 fish with validated genotypes for 30 060 SNPs. This study confirms the polygenic inheritance of resistance to F. psychrophilum with a few QTL with moderate effects and a large polygenic background, the heritability of the trait being estimated at 0.34. Two new chromosome-wide significant QTL and three suggestive QTL were detected, each of them explaining between 1% and 4% of genetic variance.
Published: 2019
Full Text: View/download PDF

32. 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

33. Current status and potential of genomic selection to improve selective breeding in the main aquaculture species of International Council for the Exploration of the Sea (ICES) member countries

Author: Marine S. O. Brieuc, Pierre Boudry, Marc Vandeputte, Sophie Brard-Fudulea, Jean-Baptiste Lamy, Luca Bargelloni, Catherine Purcell, Paulo A. Prodöhl, Tim P. Bean, Muhammad Luqman Aslam, Romain Morvezen, Ross D. Houston, Anna K. Sonesson, François Allal, Federico C. F. Calboli, Pierrick Haffray, John Gilbey, Geoffrey C. Waldbieser, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), 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), 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), Norwegian Institute of Food,Fisheries and Aquaculture Research (NOFIMA), University of Padova [Padova, Italy], The Roslin Institute, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), University of Oslo (UiO), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Marine Scotland Science (MSS), Institut Français de Recherche pour l'Exploitation de la Mer (IFREMER), National Oceanic and Atmospheric Administration (NOAA), Queen's University [Belfast] (QUB), Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), United States Department of Agriculture (USDA), 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 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)-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), Università degli Studi di Padova = University of Padua (Unipd), Biotechnology and Biological Sciences Research Council (BBSRC), and AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: [SDE.MCG]Environmental Sciences/Global Changes, SH1-691, Aquaculture, Aquatic Science, Selective breeding, 03 medical and health sciences, Aquaculture. Fisheries. Angling, 14. Life underwater, Sea bass, 030304 developmental biology, 0303 health sciences, biology, Genomic selection, business.industry, 04 agricultural and veterinary sciences, Pacific oyster, biology.organism_classification, Fishery, Geography, SNP array, Genotyping by sequencing, Sustainability, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Animal Science and Zoology, Rainbow trout, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, business, Atlantic cod
Abstract: WOS:000672569700006; International audience; Selective breeding has been successfully applied to improve profitability and sustainability in numerous aquatic species. Recent developments of high throughput genotyping technology now enable the implementation of genomic selection, a method aiming to predict the breeding value of candidates based on their genotype at genome-wide markers. In this review article, we review the state of the arts, challenges and prospects for the application of genomic selection in aquaculture species. The particular focus is on the status of genomic selection in several major aquaculture species of International Council for the Exploration of the Sea (ICES) member countries: Atlantic salmon, rainbow trout, Atlantic cod, American catfish, Pacific oyster, European sea bass and gilthead sea bream. While the potential of genomic selection is clear, tailored species-specific applications will be needed to maximise its benefit for the aquaculture sector.
Published: 2021
Full Text: View/download PDF

34. Toward a selection to improve turbot (Scophthalmus maximus) resistance to Edwardsiellosis

Author: Yoannah, Marie Villa, Bruno Peyrou, Pierrick Haffray, Thierry Morin, Anastasia Bestin, Bestin, Anastasia, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Ecloserie Marine de Gravelines, Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), and Aquanord
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Fish, Scophthalmus maximus, [SDV.BA] Life Sciences [q-bio]/Animal biology, [SDV.BA]Life Sciences [q-bio]/Animal biology, [SDV]Life Sciences [q-bio], [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, Turbot, Selection, ComputingMilieux_MISCELLANEOUS, Edwardsiellosis
Abstract: International audience
Published: 2021

35. Genome-wide association studies for resistance to viral nervous necrosis in three populations of European sea bass (Dicentrarchus labrax) using a novel 57k SNP array DlabChip

Author: Alain Vergnet, Yoannah François, Sophie Brard-Fudulea, Pierre-Alexandre Gagnaire, Charles Poncet, Joseph Brunier, Romain Morvezen, Anastasia Bestin, Jean-Sébastien Bruant, Florence Phocas, Pierrick Haffray, Marc Vandeputte, Sophie Cariou, Thierry Morin, Bruno Peyrou, Ronan Griot, François Allal, Génétique Animale et Biologie Intégrative (GABI), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Biologie des Oiseaux et Aviculture (BOA), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire de Ploufragan-Plouzané-Niort [ANSES], Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Ferme Marine de Douhet, Ecloserie Marine de Gravelines, Aquanord, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, GeneSea project - French Government R FEA 4700 16 FA 100 0005, European Union (EMFF, European Maritime and Fisheries Fund) at the 'Appels a projets Innovants', ANRT (doctoralscholarshipn°2017/0731), EMG breeding company through SYSAAF organisation, FMD breeding company through SYSAAF organisation, 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), 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), Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Laboratoire Service d' Experimentations Aquacoles [Palavas les Flots] (LSEA 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)-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 Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: QTL, [SDV]Life Sciences [q-bio], VNN, Genome-wide association study, Single-nucleotide polymorphism, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Aquatic Science, Biology, Quantitative trait locus, 03 medical and health sciences, Genetic variation, GWAS, 14. Life underwater, Genotyping, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, Genetic association, Genetics, Whole genome sequencing, Disease resistance, [SDV.GEN]Life Sciences [q-bio]/Genetics, 0303 health sciences, Linkage map, 04 agricultural and veterinary sciences, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, Fish, [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, 0401 agriculture, forestry, and fisheries, SNP array
Abstract: International audience; Viral Nervous Necrosis (VNN) is a major threat for the European sea bass (Dicentrarchus labrax) aquaculture industry. The improvement of disease resistance through selective breeding is a promising option to reduce outbreaks. With the development of high-throughput genotyping technologies, identification of genomic regions involved in the resistance could improve the efficiency of selective breeding. The aim of this study was to identify quantitative trait loci (QTL) involved in VNN resistance and to quantify their effect.Four experimental backcross families comprising 378, 454, 291 and 211 individuals and two commercial populations A and B comprising 1027 and 1042 individuals obtained from partial factorial crosses (59 male x 20 female for pop A; 39 male x 14 female for pop B) were submitted to a redspotted grouper nervous necrosis virus (RGNNV) challenge by bath. A high-density single nucleotide polymorphism (SNP) chip panel was designed to develop the ThermoFisher Axiom (TM) 57k SNP DlabChip, which was used for genotyping all individuals and building a high quality linkage map. In the backcross families, composite interval mapping was performed on 30,917, 23,592, 30,656 and 31,490 markers, respectively. In the commercial populations, 40,263 markers in pop A and 41,166 markers in pop B were used to perform genome-wide association studies (GWAS) using a GBLUP and a BayesC pi approach.One QTL was identified on chromosome LG12 in three of the four experimental backcross families, and one additional QTL on LG8 was detected in only one family. In commercial populations, QTL mapping revealed a total of seven QTLs, among which the previously mentioned QTL on LG12 was detected in both. This QTL, which was mapped to an interval of 3.45 cM, explained 9.21% of the total genetic variance in pop A, while other identified QTLs individually explained less than 1% of the total genetic variance.The identification of QTL regions involved in VNN resistance in European sea bass, with one having a strong effect, should have a great impact on the aquaculture industry. Future work could focus on the fine mapping of the causal mutation present on LG12 using whole genome sequencing.
Published: 2021
Full Text: View/download PDF

36. Genome wide association studies revealed one strong effect QTLfor viral nervous necrosis resistance in European sea bass (Dicentrarchus labrax)

Author: Ronan Griot, François Allal, Phocas, F., Sophie Brard-Fudulea, Romain Morvezen, Pierrick Haffray, Anastasia Bestin, Yoannah, Thierry Morin, Charles Poncet, Alain Vergnet, Sophie Cariou, Joseph Brunier, Jean-Sebastien Bruant, Bruno Peyrou, Pierre-Alexandre Gagnaire, Marc Vandeputte, Bestin, Anastasia, 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), 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), Agence nationale de sécurité sanitaire de l'alimentation, de l'environnement et du travail (ANSES), Génétique Diversité et Ecophysiologie des Céréales (GDEC), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Clermont Auvergne (UCA), Ferme Marine du Douhet, Ecloserie Marine de Gravelines, Aquanord, Ferme Marine de Douhet, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, 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), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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 Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE)
Subjects: [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, [SDV.GEN.GA] Life Sciences [q-bio]/Genetics/Animal genetics, ComputingMilieux_MISCELLANEOUS
Abstract: Visioconference - Online Meeting; International audience
Published: 2021

37. Can we identify wild-born salmon from parentage assignment data? A case study in the Garonne-Dordogne rivers salmon restoration programme in France

Author: Stéphane Bosc, Pierrick Haffray, Olivier Menchi, Jean-Michel Allamellou, Marc Vandeputte, Anastasia Bestin, Louarn Fauchet, 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), Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Association pour la restauration et la gestion des poissons MIgrateurs du bassin de la GAronne et de la DOrdogne - MIGADO (FRANCE), 'Programme general de restauration du saumon en Nouvelle Aquitaine' (European Union FEDER programme)2019-8015210'Programme general de restauration du saumon en Nouvelle Aquitaine' (Agence de l'Eau Adour Garonne)240.24.2120'Programme general de restauration du saumon en Nouvelle Aquitaine' (Region Nouvelle Aquitaine)EL8949220Office Francais de la Biodiversite'Programme de restauration des migrateurs du bassin de la Garonne en Occitanie' (European Union FEDER programme)MP0025359'Programme de restauration des migrateurs du bassin de la Garonne en Occitanie' (Agence de l'Eau Adour Garonne)240.31.2335, 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: 0106 biological sciences, 0303 health sciences, education.field_of_study, [SDV]Life Sciences [q-bio], Population, Broodstock, Parentage assignment, Aquatic Science, Biology, 010603 evolutionary biology, 01 natural sciences, Hatchery, Fishery, restocking, 03 medical and health sciences, fisheries, [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, %22">Fish , 14. Life underwater, Mating, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, education, 030304 developmental biology
Abstract: International audience; Parentage assignment with genomic markers provides an opportunity to monitor salmon restocking programs. Most of the time, it is used to study the fate of hatchery-born fish in those programs, as well as the genetic impacts of restocking. In such analyses, only fish that are assigned to their parents are considered. In the Garonne-Dordogne river basin in France, native salmon have disappeared, and supportive breeding is being used to try to reinstate a self-sustained population. It is therefore of primary importance to assess the numbers of wild-born returning salmon, which could appear as wrongly assigned or not assigned, depending on the power of the marker set and on the size of the mating plan. We used the genotypes at nine microsatellites of the 5800 hatchery broodstock which were used from 2008 to 2014, and of 884 upstream migrating fish collected from 2008 to 2016, to assess our ability to identify wild-born salmon. We simulated genotypes of hatchery fish and wild-born fish and assessed how they were identified by the parentage assignment software Accurassign. We showed that 98.7% of the fish assigned within the recorded mating plan could be considered hatchery fish, while 93.3% of the fish in other assignment categories (assigned out of the mating plan, assigned to several parent pairs, not assigned) could be considered wild-born. Using a Bayesian approach, we showed that 31.3% of the 457 upstream migrating fish sampled from 2014 to 2016 were wild-born. This approach is thus efficient to identify wild-born fish in a restoration program. It remains dependent on the quality of the recording of the mating plan, which we showed was rather good (
Published: 2021
Full Text: View/download PDF

38. Genetic Parameters and Genome-Wide Association Studies of Quality Traits Characterised Using Imaging Technologies in Rainbow Trout

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: fat content, aquaculture, QTL, Genetics, food and beverages, magnetic resonance imaging, Fatmeter, flesh colour, computer vision, Original Research, genetic correlations
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: 2020

39. Genetic determinism of spontaneous masculinisation in XX female rainbow trout: new insights using medium throughput genotyping and whole-genome sequencing

Author: Charles Poncet, Florent Petitprez, Maria Bernard, Edwige Quillet, Chris Hoze, Nicolas Dechamp, Philippe Hocdé, Anastasia Bestin, Céline Ciobotaru, Yann Guiguen, Pierrick Haffray, Marine Milhes, Florence Phocas, Olivier Bouchez, Jérôme Lluch, Clémence Fraslin, Mathieu Charles, Francine Krieg, Génétique Animale et Biologie Intégrative (GABI), AgroParisTech-Université Paris-Saclay-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Edinburgh, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Allice, Ligue Nationale Contre le Cancer - Paris, Ligue Nationale Contre le Cancer (LNCC), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université de Toulouse (UT)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), Pisciculture Charles Murgat, 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), European Maritime and Fisheries Fund and France Agrimer co-funded this work (NeoBio project, n° RFEA470016FA1000008), Ligue Nationnale Contre le Cancer, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Université Paris-Saclay-AgroParisTech-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Ecole Nationale Vétérinaire de Toulouse (ENVT), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse)
Subjects: 0106 biological sciences, 0301 basic medicine, Male, Candidate gene, QTL, animal diseases, [SDV]Life Sciences [q-bio], Masculinisation des poissons, Genome-wide association study, heritability, 01 natural sciences, Genome-wide association studies, Genetics, 0303 health sciences, education.field_of_study, Multidisciplinary, biology, Reproduction, 04 agricultural and veterinary sciences, Genomics, Poisson, Trout, Phenotype, Oncorhynchus mykiss, maleness, Medicine, Female, Sex, Maleness, Heterogametic sex, endocrine system, animal structures, Genotype, Science, Population, Quantitative trait locus, Déterminisme génétique du sexe, 010603 evolutionary biology, Article, Heritability, 03 medical and health sciences, Salmonide, Genetic variation, sex, Animals, 14. Life underwater, education, 030304 developmental biology, Genetic association, Animal breeding, fish, Whole Genome Sequencing, urogenital system, Truite arc-en-ciel, 0402 animal and dairy science, Sex Determination Processes, biology.organism_classification, 040201 dairy & animal science, 030104 developmental biology, Fish, Rainbow trout, Sequençage
Abstract: Rainbow trout has a male heterogametic (XY) sex determination system controlled by a major sex-determining gene, sdY. Unexpectedly, a few phenotypically masculinised fish are regularly observed in all-female farmed trout stocks. To better understand the genetic determinism underlying spontaneous maleness in XX-rainbow trout, we recorded the phenotypic sex of 20,210 XX-rainbow trout from a French farm population at 10 and 15 months post-hatching. The overall masculinisation rate was 1.45%. We performed two genome-wide association studies (GWAS) on a subsample of 1139 individuals classified as females, intersex or males using either medium-throughput genotyping (31,811 SNPs) or whole-genome sequencing (WGS, 8.7 million SNPs). The genomic heritability of maleness ranged between 0.48 and 0.62 depending on the method and the number of SNPs used for the estimation. At the 31K SNPs level, we detected four QTL on three chromosomes (Omy1, Omy12 and Omy20). Using WGS information, we narrowed down the positions of the two QTL detected on Omy1 to 96 kb and 347 kb respectively, with the second QTL explaining up to 14% of the total genetic variance of maleness. Within this QTL, we detected three putative candidate genes, fgfa8, cyp17a1 and an uncharacterised protein (LOC110527930), which might be involved in spontaneous maleness of XX-female rainbow trout.
Published: 2020
Full Text: View/download PDF

40. Potential for Genetic Improvement of Resistance to Perkinsus olseni in the Manila Clam, Ruditapes philippinarum, Using DNA Parentage Assignment and Mass Spawning

Author: Luca Bargelloni, Jean-François Auvray, Lucie Genestout, Serena Ferraresso, Emilie Vetois, Giulia Dalla Rovere, Pierrick Haffray, Florian Enez, Morgan Smits, Rachid Mahla, Giuseppe Arcangeli, Christine Paillard, Laboratoire des Sciences de l'Environnement Marin (LEMAR) (LEMAR), 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), 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 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)-Centre National de la Recherche Scientifique (CNRS), Interdisciplinary Graduate School for the Blue planet, ANR-17-EURE-0015,ISBlue,Interdisciplinary Graduate School for the Blue planet(2017), 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: disease resistance, genetic parameter estimation, genetic selection, Manila clam (Ruditapes philippinarum), Perkinsus olseni infection, 040301 veterinary sciences, Population, Zoology, Ruditapes, Broodstock, Biology, Selective breeding, Genetic correlation, Parasite load, 0403 veterinary science, 03 medical and health sciences, 14. Life underwater, education, 030304 developmental biology, 0303 health sciences, education.field_of_study, lcsh:Veterinary medicine, General Veterinary, 04 agricultural and veterinary sciences, Heritability, biology.organism_classification, [SDE]Environmental Sciences, lcsh:SF600-1100, Microparasite
Abstract: International audience; The Manila clam Ruditapes philippinarum, a major cultured shellfish species, is threatened by infection with the microparasite Perkinsus olseni, whose prevalence increases with high water temperatures. Under the current trend of climate change, the already severe effects of this parasitic infection might rapidly increase the frequency of mass mortality events. Treating infectious diseases in bivalves is notoriously problematic, therefore selective breeding for resistance represents a key strategy for mitigating the negative impact of pathogens. A crucial step in initiating selective breeding is the estimation of genetic parameters for traits of interest, which relies on the ability to record parentage and accurate phenotypes in a large number of individuals. Here, to estimate the heritability of resistance against P. olseni, a field experiment mirroring conditions in industrial clam production was set up, a genomic tool was developed for parentage assignment, and parasite load was determined through quantitative PCR. A mixed-family cohort of potentially 1,479 clam families was produced in a hatchery by mass spawning of 53 dams and 57 sires. The progenies were seeded in a commercial clam production area in the Venice lagoon, Italy, where high prevalence of P. olseni had previously been reported. Growth and parasite load were monitored every month and, after 1 year, more than 1,000 individuals were collected for DNA samples and phenotype recording. A pooled sequencing approach was carried out using DNA samples from the hatchery broodstock and from a Venice lagoon clam population, providing candidate markers used to develop a 245-SNP panel. Parentage assignment for 246 F1 individuals showed sire and dam representation were high (75 and 85%, respectively), indicating a very limited risk of inbreeding. Moderate heritability (0.23 ± 0.11–0.35 ± 0.13) was estimated for growth traits (shell length, shell weight, total weight), while parasite load showed high heritability, estimated at 0.51 ± 0.20. No significant genetic correlations were found between growth-associated traits and parasite load. Overall, the preliminary results provided by this study show high potential for selecting clams resistant to parasite load. Breeding for resistance may help limit the negative effects of climate change on clam production, as the prevalence of the parasite is predicted to increase under a future scenario of higher temperatures. Finally, the limited genetic correlation between resistance and growth suggests that breeding programs could incorporate dual selection without negative interactions
Published: 2020
Full Text: View/download PDF

41. 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
Full Text: View/download PDF

42. Genetic architecture and genomic selection of female reproduction traits in rainbow trout

Author: Jonathan D’Ambrosio, Romain Morvezen, Sophie Brard-Fudulea, Anastasia Bestin, Charles Poncet, Pierrick Haffray, Mathilde Dupont-Nivet, and Florence Phocas
Abstract: Background Rainbow trout is a significant fish farming industry 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. Results A pedigreed population of 1,343 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. Conclusions Our 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
Full Text: View/download PDF

43. 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
Full Text: View/download PDF

44. 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
Full Text: View/download PDF

45. A 180 My-old female-specific genome region in sturgeon reveals the oldest known vertebrate sex determining system with undifferentiated sex chromosomes

Author: Emmanuel Bonpunt, Romain Morvezen, Christophe Klopp, Kang Du, Christin Höhne, Pierre Patrice, Elena Santidrian Yebra-Pimentel, Mitica Ciorpac, Radu Suciu, Jörn Gessner, Matthias Stöck, Dunja K. Lamatsch, Dmitry Yu Prokopov, Wibke Kleiner, Pierrick Haffray, Anastasia Bestin, Bastien Debeuf, Heiner Kuhl, Manfred Schartl, Yann Guiguen, Eva Kreuz, Klaus Kohlmann, Sven Wuertz, Daniela Holostenco, Ron P. Dirks, Céline Lopez-Roques, Werner Kloas, Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), 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), University of Würzburg = Universität Würzburg, The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Plateforme Bio-Informatique - Génotoul, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Future Genomics Technologies, « Danube Delta » National Institute for Research and Development [Tulcea], Academy of Agricultural and Forestry Sciences 'Gheorghe Ionescu-Sisesti' (A.A.F.S.), University of Innsbruck, Siberian Branch of the Russian Academy of Sciences (SB RAS), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), L’Esturgeonnière, SCEA Sturgeon, This work was funded through COFASP/ERANET (STURGEoNOMICS) by the German Federal Ministry of Food andAgriculture through the Federal Office for Agriculture and Food (grant nos. 2816ERA04G, 2816ERA05G) to M. Stöck,S.W., J.G. and M. Schartl, by the French National Research Agency (grant nos. ANR-16-COFA-0002) to YG, CK and CR,and by the Romanian Executive Agency for Higher Education, Research Development and Innovation Funding(UEFISCDI, contract 3/2017) to RS, MC and DH. This research was also in part supported by the Russian ScienceFoundation (RSF) to DP (grant number 18-44-04-007), by the Deutsche Forschungsgemeinschaft to MSch (DFG SCHA408/14-1), and by a European Maritime and Fisheries Fund to YG (EMFF/FEAMP project SIBERSEX). Research onA.gueldenstaedtii was supported by a European Maritime and Fisheries Fund to YG (EMFF/FEAMP project S’STURGEON)., ANR-16-COFA-0002,STURGEoNOMICS,Genome-based approaches for improvement of aquaculture in two marine sturgeon species: Atlantic sturgeon (Acipenser oxyrinchus) and Beluga (Huso huso)(2016), University of Würzburg, Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Génome et Transcriptome - Plateforme Génomique ( GeT-PlaGe), Plateforme Génome & Transcriptome (GET), Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-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-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), This work was funded through COFASP/ERANET (STURGEoNOMICS) by the German Federal Ministry of Food and Agriculture through the Federal Office for Agriculture and Food (grant nos. 2816ERA04G and 2816ERA05G) to M.Stöck, S.W., J.G. and M.Schartl, by the French National Research Agency (grant nos. ANR-16-COFA-0002) to Y.G., C.K. and C.L.R., and by the Romanian Executive Agency for Higher Education, Research Development and Innovation Funding (UEFISCDI, contract 3/2017) to RS, MC and DH. H.K. was funded by the German Research Foundation (DFG) (Eigene Stelle grant no. KU 3596/1-1, Project No. 324050651). This research was also in part supported by the Russian Science Foundation (RSF) to D.P. (grant no. 18-44-04-007), by the Deutsche Forschungsgemeinschaft to MSch (DFG SCHA 408/14-1), and by a European Maritime and Fisheries Fund to Y.G. (EMFF/FEAMP project SIBERSEX). Research on A. gueldenstaedtii was supported by a European Maritime and Fisheries Fund to Y.G. (EMFF/FEAMP project S'STURGEON)., Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3)
Subjects: 0301 basic medicine, 0106 biological sciences, Evolution, [SDV]Life Sciences [q-bio], Acipenseridae, Sturgeon, Huso, Biology, 010603 evolutionary biology, 01 natural sciences, Genome, General Biochemistry, Genetics and Molecular Biology, [SDV.BDLR.RS]Life Sciences [q-bio]/Reproductive Biology/Sexual reproduction, Evolution, Molecular, Polyploidy, 03 medical and health sciences, Phylogenetics, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], biology.animal, Sex-determination system, Animals, 14. Life underwater, Acipenser ruthenus, Evolution - stars, Clade, Phylogeny, Research Articles, 030304 developmental biology, 0303 health sciences, Fishes, Chromosome, Vertebrate, Sex chromosomes, Articles, Sex Determination Processes, biology.organism_classification, Female-specific, 030104 developmental biology, Evolutionary biology, Female, General Agricultural and Biological Sciences
Abstract: Several hypotheses explain the prevalence of undifferentiated sex chromosomes in poikilothermic vertebrates. Turnovers change the master sex determination gene, the sex chromosome or the sex determination system (e.g. XY to WZ). Jumping master genes stay main triggers but translocate to other chromosomes. Occasional recombination (e.g. in sex-reversed females) prevents sex chromosome degeneration. Recent research has uncovered conserved heteromorphic or even homomorphic sex chromosomes in several clades of non-avian and non-mammalian vertebrates. Sex determination in sturgeons (Acipenseridae) has been a long-standing basic biological question, linked to economical demands by the caviar-producing aquaculture. Here, we report the discovery of a sex-specific sequence from sterlet ( Acipenser ruthenus ). Using chromosome-scale assemblies and pool-sequencing, we first identified an approximately 16 kb female-specific region. We developed a PCR-genotyping test, yielding female-specific products in six species, spanning the entire phylogeny with the most divergent extant lineages ( A. sturio, A. oxyrinchus versus A. ruthenus, Huso huso ), stemming from an ancient tetraploidization. Similar results were obtained in two octoploid species ( A. gueldenstaedtii, A. baerii ). Conservation of a female-specific sequence for a long period, representing 180 Myr of sturgeon evolution, and across at least one polyploidization event, raises many interesting biological questions. We discuss a conserved undifferentiated sex chromosome system with a ZZ/ZW-mode of sex determination and potential alternatives. This article is part of the theme issue ‘Challenging the paradigm in sex chromosome evolution: empirical and theoretical insights with a focus on vertebrates (Part I)’.
Published: 2020
Full Text: View/download PDF

46. Cryopreservation of Pacific oyster ( Crassostrea gigas ) larvae: Revisiting the practical limitations and scaling up the procedure for application to hatchery

Author: Flore Rimond, Marc Suquet, Pierrick Haffray, Christian Mingant, Serean L. Adams, Catherine Labbé, H. Robin Tervit, Benjamin Quittet, Blandine Diss, 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 (SYSAAF), SATMAR, AgResearch, Cawthron Institute, CRECHE (Ofimer-FEP 136/08/C,30906-2009), CRYOAQUA (French CCRB/IBiSA 2009-2011), SCORE(FEP 2012-2014), and by the French PAI CRB Anim project«Investissements d'avenir», ANR-11-INBS-0003 (2012-2019)., and ANR-11-INBS-0003,CRB-Anim,Réseau de Centres de Ressources Biologiques pour les animaux domestiques(2011)
Subjects: 0301 basic medicine, Oyster, animal structures, Cryoprotectant, [SDV]Life Sciences [q-bio], Aquatic Science, Hatchery, Cryopreservation, Cryobanking, 03 medical and health sciences, Human fertilization, Aquaculture, biology.animal, High throughput, 14. Life underwater, Ethylene glycol, biology, business.industry, D stage, fungi, 04 agricultural and veterinary sciences, Pacific oyster, biology.organism_classification, Horticulture, 030104 developmental biology, 040102 fisheries, 0401 agriculture, forestry, and fisheries, Crassostrea, business
Abstract: International audience; Pacific oyster Crassostrea gigas is one major species for aquaculture, and the development of breeding programs and the need for preservation of wild stock genetic resources prompted the need for larvae cryopreservation. The objective of the present study was to choose the most reliable protocol from several existing publications, to test its biological and practical limitations, and to adapt it to hatchery conditions. The selected protocol was characterized by a very slow freezing rate without seeding, and by the use of ethylene glycol and sucrose as cryoprotectant. The best survivals after thawing and rearing up to 48 h post fertilization (hpf) were obtained with larvae that were frozen at late trochophore (20 hpf) and early-D (24 hpf) stages. Increasing the larvae concentration in the straws and using high throughput straw filling and freezing devices did not alter the cryopreservation outcome. The whole procedure was applied to cryopreservation in a commercial hatchery (Satmar, France), and the thawed larvae yielded 9.4 ± 4.5% survivals at 12 days post fertilization. The overall success was dampened by some variability in the larvae survival that is likely due to the physiological status of the larvae. In all, the proposed procedure is robust and reliable and can be used for cryobanking of oyster genetic resources.
Published: 2018
Full Text: View/download PDF

47. Quantitative genetic parameters of growth and fatty acid content in the hemolymph of the Whiteleg shrimp Litopenaeus vannamei

Author: Pierrick Haffray, Elena Palacios-Mechetnov, Ricardo Perez-Enriquez, Anastasia Bestin, Florian Enez, and Héctor Rodrigo Nolasco-Alzaga
Subjects: 0301 basic medicine, Muscle tissue, chemistry.chemical_classification, biology, Litopenaeus, Fatty acid, Single-nucleotide polymorphism, 04 agricultural and veterinary sciences, Aquatic Science, Heritability, biology.organism_classification, Genetic correlation, 03 medical and health sciences, 030104 developmental biology, medicine.anatomical_structure, Biochemistry, chemistry, Hemolymph, Whiteleg shrimp, 040102 fisheries, medicine, 0401 agriculture, forestry, and fisheries, Food science
Abstract: The heritability of fatty acid composition of the Whiteleg shrimp Litopenaeus vannamei has not yet been evaluated. Highly unsaturated fatty acids (HUFA), particularly EPA, DHA, and ARA, provide structural and physiological stability to cells and tissues, playing a substantial role in stress response and immune system. Thus, genetic improvement for these characteristics would be possible if the heritability for HUFA is relevant. The purpose of the present study was to estimate genetic parameters for growth and the proportion of several fatty acids relative to their content in hemolymph of this species. Progeny from 79 full-sib families were reared under a common environment until they reached an average size of 22 g. Individuals were sampled (n = 674) for muscle tissue and hemolymph for DNA and fatty acid analyses, respectively. Parentage assignment of juveniles was done by genetic exclusion tests, using a 76-loci SNPs panel. Heritability was estimated for growth and for fatty acid percentage of 20 fatty acids and related measurements (n = 532). Intermediate heritability for growth (h2 = 0.42 ± 0.09) was estimated for the first time in this species in a mixed family reared design assisted with DNA parentage assignment. Limited heritabilities for fatty acids were estimated; nevertheless, some important fatty acids, such as EPA and DHA, proved to have significant variance among families with heritability values of 0.07 ± 0.05 and 0.12 ± 0.06, respectively. In contrast, ARA, which is tightly linked to the immune response, showed a value not significantly different from zero (
Published: 2018
Full Text: View/download PDF

48. Genetic parameters of caviar yield, color, size and firmness using parentage assignment in an octoploid fish species, the Siberian sturgeon Acipenser baerii

Author: D. Guémené, R. Mahla, H. Chapuis, Marc Vandeputte, Pierrick Haffray, P. Benoit, B. Debeuf, O. Brunel, A. Malledant, Anastasia Bestin, Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), SCEA Sturgeon, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Institut National de la Recherche Agronomique (INRA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), 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-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Biologie des Oiseaux et Aviculture (BOA), Université de Tours (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), 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), FranceAgriMer (National Institute for agri-cultural and sea products) Project KViar (contract n◦2014-0827) and to Bureau des Ressources Génétiques (project APACHE contract n◦2009-1549, and Université de Tours-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Subjects: heritability, Aquatic Science, Selective breeding, 03 medical and health sciences, Sturgeon, Animal science, Aquaculture, Polyploid, 14. Life underwater, Domestication, selective breeding, polyploidy, 030304 developmental biology, 0303 health sciences, biology, business.industry, Hatching, egg production, 04 agricultural and veterinary sciences, Acipenser baerii, Heritability, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 040102 fisheries, 0401 agriculture, forestry, and fisheries, business
Abstract: International audience; Aquaculture is presently the only sustainable way of enhancing sturgeon caviar production as the use of wild stocks is banned throughout the world. Hence sustainable management and efficient genetic improvement of domesticated populations are major challenges for the development of farmed caviar. We estimated genetic parameters of caviar yields and quality traits (size, color and firmness) in the polyploid Siberian sturgeon A. baerii, one of the major sturgeon species farmed for meat and caviar worldwide. This study was performed in commercial breeding conditions, where two factorial mating plans were created to produce 77 families. Larvae were pooled at hatching and reared in common environment until the age of caviar production. We phenotyped 494 females, which were successfully assigned to their parents with microsatellite markers using a newly developed software, designed to manage genotypes with varying ploidy levels, up to 8 N. The genetic parameters were estimated using heteroscedastic multi-trait BLUP animal models. Heritability of body weight, ovary weight, caviar weight, caviar (egg) size, caviar yield, caviar firmness and caviar color were moderate to high (0.13 to 0.66) depending on the trait. Moderate negative genetic correlations were estimated between growth and caviar yields (−0.28 to −0.37) while genetic correlations between caviar (egg) size and caviar yield were more negative (−0.70 to −0.76). These results provide favorable grounds to improve the efficiency of farmed caviar production by selective breeding.
Published: 2021
Full Text: View/download PDF

49. Genetic variation of resistance to Viral Nervous Necrosis and genetic correlations with production traits in wild populations of the European sea bass ( Dicentrarchus labrax )

Author: Pierrick Haffray, Alain Vergnet, Béatrice Chatain, François Allal, Gilles Breuil, Q Khanh Doan, Marc Vandeputte, 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), Laboratoire Service d' Experimentations Aquacoles [Palavas les Flots] (LSEA 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)-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), TNU, Thai Nguyen University of Agriculture and Forestry, Institut National de la Recherche Agronomique (INRA)-AgroParisTech, INRA Bat.16 Campus de Beaulieu, and Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF)
Subjects: 0301 basic medicine, Genetic correlation, VNN resistance, VNN disease, [SDV]Life Sciences [q-bio], Betanodavirus, Zoology, [SDV.SA.ZOO]Life Sciences [q-bio]/Agricultural sciences/Zootechny, Aquatic Science, Biology, Heritability, 03 medical and health sciences, Mediterranean sea, Genetic variation, 14. Life underwater, Sea bass, ComputingMilieux_MISCELLANEOUS, Ecology, Sire, 04 agricultural and veterinary sciences, biology.organism_classification, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, [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, 0401 agriculture, forestry, and fisheries, Dicentrarchus
Abstract: International audience; Viral Nervous Necrosis (VNN) disease is considered as one of the most serious threats for European sea bass cultured in Mediterranean Sea, with no simple and effective procedures to treat this disease. In this study, 1472 offspring resulting from artificial full factorial mating of western Mediterranean dams with sires from four different wild populations of European sea bass (Northern Atlantic, NAT; Western Mediterranean, WEM; Northern-East Mediterranean, NEM; and Southern-East Mediterranean, SEM) were challenged by experimental infection to W80 betanodavirus strain in order to evaluate genetic variations for VNN resistance among populations and genetic correlations between VNN resistance and production traits. The results showed a large variation of VNN resistance between the four populations tested as well as between sire families within strain. The survivals between pure wild populations SEM, NEM, WEM and NAT were estimated at 99%, 94%, 62%, and 44%, respectively. A moderate intra-population heritability of VNN resistance, calculated based on liability scale with sire model, was recorded for the first time in European sea bass (h2 u =0.26 ± 0.11). Finally, moderate negative genetic correlations between VNN resistance and daily growth coefficient (DGC) and body weight (BW) were also demonstrated (−0.28 ± 0.20, −0.35 ± 0.14, respectively) while the genetic correlation between resistance to VNN and fillet adiposity (FA) was weakly negative and not significant (−0.13 ± 0.19). These results give good prospects of selective breeding of European sea bass for improved resistance to VNN disease.
Published: 2017
Full Text: View/download PDF

50. Morphological predictors of slaughter yields using 3D digitizer and their utilization in common carp breeding program

Author: Martin Prchal, Jérôme Bugeon, Marc Vandeputte, Kause, A., Alain Vergnet, Zhao, J., Gela, D., Genestout, L., Anastasia Bestin, Pierrick Haffray, Kocour, M., Faculty of Fisheries and Protection of Waters [University of South Bohemia], University of South Bohemia, 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 ), 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), Biometrical Genetics, Myllytie 1, Institute for Natural Resources, Laboratoire d'Analyse Génétique pour les Espèces Animales (LABOGENA), Institut National de la Recherche Agronomique (INRA), Syndicat des Sélectionneurs Avicoles et Aquacoles Français (SYSAAF), European Aquaculture Society (EAS). BEL., European Project: 613611,EC:FP7:KBBE,FP7-KBBE-2013-7-single-stage,FISHBOOST(2014), Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, AgroParisTech-Institut National de la Recherche Agronomique (INRA), INRA Laboratoire de Physiologie et Génomique des Poissons, and Syndicats des sélectionneurs avicoles et aquacoles français (SYSAAF)
Subjects: fish, cyprinus carpio, rendement à l'abattage, analyse morphologique, carp, [SDV]Life Sciences [q-bio], paramètre génétique, carpe, poisson, cyprinidae, morphological analysis, sélection, genetic variance, analyse d'image 3d
Abstract: Morphological predictors of slaughter yields using 3D digitizer and their utilization in common carp breeding program. Aquaculture Europe 2019
Published: 2019

Catalog

Books, media, physical & digital resources

See catalog results

Searchworks

Select search scope, currently: Articles Catalog books, media & more in Jio Institute collections Articles journal articles & other e-resources

Search

Search Constraints

Refine your results

Search Limiters

Topic

Publication Year Range

Language

Publication Type

Journal

Database

Publisher

157 results on '"Pierrick Haffray"'

Search Results

Catalog

Select search scope, currently: Articles

Catalog

books, media & more in Jio Institute collections

Articles

journal articles & other e-resources