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Serradell A, Montero D, Terova G, Rimoldi S, Makol A, Acosta F, Bajek A, Haffray P, Allal F, Torrecillas S. Functional Additives in a Selected European Sea Bass ( Dicentrarchus labrax) Genotype: Effects on the Stress Response and Gill Antioxidant Response to Hydrogen Peroxide (H 2O 2) Treatment. Animals (Basel) 2023; 13:2265. [PMID: 37508043 PMCID: PMC10376812 DOI: 10.3390/ani13142265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/06/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
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.
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Affiliation(s)
- Antonio Serradell
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Spain
| | - Daniel Montero
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Spain
| | - Genciana Terova
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Simona Rimoldi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J.H. Dunant, 3, 21100 Varese, Italy
| | - Alex Makol
- Global Solution Aquaculture Unit, Delacon Biotechnik Gmbh, 4209 Engerwitzdorf, Austria
| | - Félix Acosta
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Spain
| | - Aline Bajek
- Ecloserie Marine de Graveline Ichtus, Route des Enrochements, 59820 Gravelines, France
| | - Pierrick Haffray
- SYSAAF, French Association of Poultry and Aquaculture Breeders, Campus de Beaulieu, 35042 Rennes, France
| | - François Allal
- MARBEC, University of Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Silvia Torrecillas
- Grupo de Investigación en Acuicultura (GIA), IU-ECOAQUA, Universidad de las Palmas de Gran Canaria, Crta. Taliarte s/n, 35214 Telde, Las Palmas, Spain
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Nati JJH, Blasco FR, Rodde C, Vergnet A, Allal F, Vandeputte M, McKenzie DJ. In a marine teleost, the significance of oxygen supply for acute thermal tolerance depends upon the context and the endpoint used. J Exp Biol 2023:310181. [PMID: 37183759 DOI: 10.1242/jeb.245210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 05/05/2023] [Indexed: 05/16/2023]
Abstract
Eight juvenile European seabass were exposed to two thermal ramping protocols with different levels of aerobic activity and tolerance endpoint: the critical thermal maximum for swimming (CTSmax) while exercising aerobically until fatigue, and the critical thermal maximum (CTmax) under static conditions until loss of equilibrium (LOE). In the CTSmax, warming caused a profound increase in oxygen uptake rate (M˙O2) culminating in a gait transition, from steady aerobic towards unsteady anaerobic swimming, then fatigue at 30.3±0.4°C (mean±SE). Gait transition and fatigue presumably indicate an oxygen limitation, an inability to meet the combined demands of swimming plus warming. The CTmax also elicited an increase in M˙O2, culminating in LOE at 34.0±0.4°C, significantly warmer than fatigue at CTSmax. The maximum M˙O2 achieved in the CTmax was, however, less than 30% of that achieved in the CTSmax. Therefore, the static CTmax did not exploit full cardiorespiratory capacity for oxygen supply, indicating that LOE was not caused by systemic oxygen limitation. Consequently, systemic oxygen supply can be significant for tolerance of acute warming in seabass but this depends upon the physiological context and the endpoint used.
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Affiliation(s)
- Julie J H Nati
- MARBEC, Univ Montpellier, CNRS, Ifremer, INRAE, IRD, 34250 Palavas-les-Flots, France
| | - Felipe R Blasco
- Department of Physiological Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Charles Rodde
- MARBEC, Univ Montpellier, CNRS, Ifremer, INRAE, IRD, 34250 Palavas-les-Flots, France
- UMR ISEM, Univ Montpellier, CIRAD, CNRS, Ifremer, IRD, 34398 Montpellier, France
| | - Alain Vergnet
- MARBEC, Univ Montpellier, CNRS, Ifremer, INRAE, IRD, 34250 Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ Montpellier, CNRS, Ifremer, INRAE, IRD, 34250 Palavas-les-Flots, France
| | - Marc Vandeputte
- MARBEC, Univ Montpellier, CNRS, Ifremer, INRAE, IRD, 34250 Palavas-les-Flots, France
| | - David J McKenzie
- MARBEC, Univ Montpellier, CNRS, Ifremer, INRAE, IRD, 34250 Palavas-les-Flots, France
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Delpuech E, Vandeputte M, Morvezen R, Bestin A, Besson M, Brunier J, Bajek A, Imarazene B, François Y, Bouchez O, Cousin X, Poncet C, Morin T, Bruant JS, Chatain B, Haffray P, Phocas F, Allal F. Whole-genome sequencing identifies interferon-induced protein IFI6/IFI27-like as a strong candidate gene for VNN resistance in European sea bass. Genet Sel Evol 2023; 55:30. [PMID: 37143017 PMCID: PMC10161657 DOI: 10.1186/s12711-023-00805-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 04/18/2023] [Indexed: 05/06/2023] Open
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.
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Affiliation(s)
- Emilie Delpuech
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France.
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.
| | - Marc Vandeputte
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Romain Morvezen
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | - Anastasia Bestin
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | - Mathieu Besson
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | - Joseph Brunier
- Ecloserie Marine de Gravelines-Ichtus, Gloria Maris Group, 59273, Gravelines, France
| | - Aline Bajek
- Ecloserie Marine de Gravelines-Ichtus, Gloria Maris Group, 59273, Gravelines, France
| | | | - Yoannah François
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
- ANSES, Unit Virology, Immunology and Ecotoxicology of Fish, Technopôle Brest-Iroise, 29280, Plouzané, France
| | - Olivier Bouchez
- US 1426, GeT-PlaGe, INRAE, Genotoul, Castanet-Tolosan, France
| | - Xavier Cousin
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Charles Poncet
- INRAE-UCA, UMR 1095 GDEC, 63000, Clermont-Ferrand, France
| | - Thierry Morin
- ANSES, Unit Virology, Immunology and Ecotoxicology of Fish, Technopôle Brest-Iroise, 29280, Plouzané, France
| | | | - Béatrice Chatain
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
| | - Pierrick Haffray
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, 35042, Rennes, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - François Allal
- MARBEC, Univ. Montpellier, CNRS, Ifremer, IRD, INRAE, 34250, Palavas-Les-Flots, France
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Goikoetxea A, Servili A, Houdelet C, Mouchel O, Hermet S, Clota F, Aerts J, Fernandino JI, Allal F, Vandeputte M, Blondeau-Bidet E, Geffroy B. Natural cortisol production is not linked to the sexual fate of European sea bass. Fish Physiol Biochem 2022; 48:1117-1135. [PMID: 35917042 DOI: 10.1007/s10695-022-01104-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 07/14/2022] [Indexed: 06/15/2023]
Abstract
In this study, we aimed to investigate the relationship between cortisol and the determination of sexual fate in the commercially important European sea bass (Dicentrarchus labrax). To test our hypothesis, we designed two temperature-based experiments (19 ℃, 21 ℃ and 23 ℃, experiment 1; 16 ℃ and 21 ℃, experiment 2) to assess the effects of these thermal treatments on European sea bass sex determination and differentiation. In the fish from the first experiment, we evaluated whether blood cortisol levels and expression of stress key regulatory genes were different between differentiating (149 to 183 dph) males and females. In the second experiment, we assessed whether cortisol accumulated in scales over time during the labile period for sex determination as well as the neuroanatomical localisation of brain cells expressing brain aromatase (cyp19a1b) and corticotropin-releasing factor (crf) differed between males and females undergoing molecular sex differentiation (117 to 124 dph). None of the gathered results allowed to detect differences between males and females regarding cortisol production and regulatory mechanisms. Altogether, our data provide strong physiological, molecular and histochemical evidence, indicating that in vivo cortisol regulation has no major effects on the sex of European sea bass.
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Affiliation(s)
| | - Arianna Servili
- Ifremer, IFREMER, Univ Brest, CNRS, IRD, LEMAR, 29280, Plouzané, France
| | - Camille Houdelet
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Olivier Mouchel
- Ifremer, IFREMER, Univ Brest, CNRS, IRD, LEMAR, 29280, Plouzané, France
| | - Sophie Hermet
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Fréderic Clota
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | - Johan Aerts
- Stress Physiology Research Group, Faculty of Sciences, Ghent University, Ostend, Belgium
| | | | - François Allal
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Marc Vandeputte
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Benjamin Geffroy
- MARBEC Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
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Abstract
To date, genomic prediction has been conducted in about 20 aquaculture species, with a preference for intra-family genomic selection (GS). For every trait under GS, the increase in accuracy obtained by genomic estimated breeding values instead of classical pedigree-based estimation of breeding values is very important in aquaculture species ranging from 15% to 89% for growth traits, and from 0% to 567% for disease resistance. Although the implementation of GS in aquaculture is of little additional investment in breeding programs already implementing sib testing on pedigree, the deployment of GS remains sparse, but could be boosted by adaptation of cost-effective imputation from low-density panels. Moreover, GS could help to anticipate the effect of climate change by improving sustainability-related traits such as production yield (e.g., carcass or fillet yields), feed efficiency or disease resistance, and by improving resistance to environmental variation (tolerance to temperature or salinity variation). This chapter synthesized the literature in applications of GS in finfish, crustaceans and molluscs aquaculture in the present and future breeding programs.
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Affiliation(s)
- François Allal
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France.
| | - Nguyen Hong Nguyen
- School of Science, Technology and Engineering, University of the Sunshine Coast, Sippy Downs, QLD, Australia
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Geffroy B, Besson M, Sánchez-Baizán N, Clota F, Goikoetxea A, Sadoul B, Ruelle F, Blanc MO, Parrinello H, Hermet S, Blondeau-Bidet E, Pratlong M, Piferrer F, Vandeputte M, Allal F. Unraveling the genotype by environment interaction in a thermosensitive fish with a polygenic sex determination system. Proc Natl Acad Sci U S A 2021; 118:e2112660118. [PMID: 34880131 PMCID: PMC8685686 DOI: 10.1073/pnas.2112660118] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/28/2021] [Indexed: 01/03/2023] Open
Abstract
In most animals, sex determination occurs at conception, when sex chromosomes are segregated following Mendelian laws. However, in multiple reptiles and fishes, this genetic sex can be overridden by external factors after fertilization or birth. In some species, the genetic sex may also be governed by multiple genes, further limiting our understanding of sex determination in such species. We used the European sea bass (Dicentrarchus labrax) as a model and combined genomic (using a single nucleotide polymorphism chip) and transcriptomic (RNA-Sequencing) approaches to thoroughly depict this polygenic sex determination system and its interaction with temperature. We estimated genetic sex tendency (eGST), defined as the estimated genetic liability to become a given sex under a liability threshold model for sex determination, which accurately predicts the future phenotypic sex. We found evidence that energetic pathways, concerning the regulation of lipids and glucose, are involved in sex determination and could explain why females tend to exhibit higher energy levels and improved growth compared to males. Besides, early exposure to high-temperature up-regulated sox3, followed by sox9a in individuals with intermediate eGST, but not in individuals showing highly female-biased eGST, providing the most parsimonious explanation for temperature-induced masculinization. This gonadal state was maintained likely by DNA methylation and the up-regulation of several genes involved in histone modifications, including jmjd1c Overall, we describe a sex determination system resulting from continuous genetic and environmental influences in an animal. Our results provide significant progress in our understanding of the mechanisms underlying temperature-induced masculinization in fish.
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Affiliation(s)
- Benjamin Geffroy
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France;
| | - Mathieu Besson
- SYSAAF, Station LPGP/INRAE, 35042 Rennes, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - Núria Sánchez-Baizán
- Institut de Ciències del Mar, Spanish National Research Council, Barcelona, Spain
| | - Frederic Clota
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | | | - Bastien Sadoul
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
- ESE, Ecology and Ecosystem Health, Institut Agro, INRAE, Rennes, France
| | - François Ruelle
- Laboratoire Service d'Expérimentations Aquacoles, Ifremer, Palavas-les-Flots, France
| | - Marie-Odile Blanc
- Laboratoire Service d'Expérimentations Aquacoles, Ifremer, Palavas-les-Flots, France
| | - Hugues Parrinello
- MGX, BCM, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Sophie Hermet
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Eva Blondeau-Bidet
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Montpellier, France
| | - Marine Pratlong
- MGX, BCM, Université de Montpellier, CNRS, INSERM, Montpellier, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Spanish National Research Council, Barcelona, Spain
| | - Marc Vandeputte
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - François Allal
- MARBEC Université de Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
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Griot R, Allal F, Phocas F, Brard-Fudulea S, Morvezen R, Haffray P, François Y, Morin T, Bestin A, Bruant JS, Cariou S, Peyrou B, Brunier J, Vandeputte M. 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). Front Genet 2021; 12:754416. [PMID: 34707643 PMCID: PMC8543739 DOI: 10.3389/fgene.2021.754416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 09/13/2021] [Indexed: 11/29/2022] Open
Affiliation(s)
- Ronan Griot
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Romain Morvezen
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France
| | | | | | - Thierry Morin
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Viral Fish Diseases Unit, National Reference Laboratory for Regulated Fish Diseases, Technopôle Brest-Iroise, Plouzané, France
| | | | | | | | - Bruno Peyrou
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Joseph Brunier
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Marc Vandeputte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
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8
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Griot R, Allal F, Phocas F, Brard-Fudulea S, Morvezen R, Haffray P, François Y, Morin T, Bestin A, Bruant JS, Cariou S, Peyrou B, Brunier J, Vandeputte M. 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). Front Genet 2021; 12:665920. [PMID: 34335683 PMCID: PMC8317601 DOI: 10.3389/fgene.2021.665920] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 06/25/2021] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Ronan Griot
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - Florence Phocas
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France
| | | | - Romain Morvezen
- SYSAAF, Station LPGP/INRAE, Campus de Beaulieu, Rennes, France
| | | | | | - Thierry Morin
- ANSES, Ploufragan-Plouzané-Niort Laboratory, Viral Fish Diseases Unit, National Reference Laboratory for Regulated Fish Diseases, Technopôle Brest-Iroise, Plouzané, France
| | | | | | | | - Bruno Peyrou
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Joseph Brunier
- Ecloserie Marine de Gravelines-Ichtus, Gravelines, France
| | - Marc Vandeputte
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, Jouy-en-Josas, France.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
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9
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Geffroy B, Gesto M, Clota F, Aerts J, Darias MJ, Blanc MO, Ruelle F, Allal F, Vandeputte M. Parental selection for growth and early-life low stocking density increase the female-to-male ratio in European sea bass. Sci Rep 2021; 11:13620. [PMID: 34193934 PMCID: PMC8245542 DOI: 10.1038/s41598-021-93116-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 06/21/2021] [Indexed: 11/09/2022] Open
Abstract
In European sea bass (Dicentrarchus labrax), as in many other fish species, temperature is known to influence the sex of individuals, with more males produced at relatively high temperatures. It is however unclear to what extent growth or stress are involved in such a process, since temperature is known to influence both growth rate and cortisol production. Here, we designed an experiment aiming at reducing stress and affecting early growth rate. We exposed larvae and juveniles originating from both captive and wild parents to three different treatments: low stocking density, food supplemented with tryptophan and a control. Low stocking density and tryptophan treatment respectively increased and decreased early growth rate. Each treatment influenced the stress response depending on the developmental stage, although no clear pattern regarding the whole-body cortisol concentration was found. During sex differentiation, fish in the low-density treatment exhibited lower expression of gr1, gr2, mr, and crf in the hypothalamus when compared to the control group. Fish fed tryptophan displayed lower crf in the hypothalamus and higher level of serotonin in the telencephalon compared to controls. Overall, fish kept at low density produced significantly more females than both control and fish fed tryptophan. Parents that have been selected for growth for three generations also produced significantly more females than parents of wild origin. Our findings did not allow to detect a clear effect of stress at the group level and rather point out a key role of early sexually dimorphic growth rate in sex determination.
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Affiliation(s)
- Benjamin Geffroy
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France.
| | - Manuel Gesto
- Techn Section for Aquaculture, DTU Aqua, Technical University of Denmark, Willemoesvej 2, 9850, Hirtshals, Denmark
| | - Fréderic Clota
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Johan Aerts
- Stress Physiology Research Group, Faculty of Sciences, Ghent University, Ostend, Belgium
| | - Maria J Darias
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Marie-Odile Blanc
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - François Ruelle
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - François Allal
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France
| | - Marc Vandeputte
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-Les-Flots, France.,Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
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10
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Rodde C, de Verdal H, Vandeputte M, Allal F, Nati J, Besson M, Blasco FR, Benzie JAH, McKenzie DJ. An investigation of links between metabolic rate and feed efficiency in European sea bass Dicentrarchus labrax. J Anim Sci 2021; 99:skab152. [PMID: 33966070 PMCID: PMC8219042 DOI: 10.1093/jas/skab152] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 05/05/2021] [Indexed: 11/15/2022] Open
Abstract
Feed efficiency (FE) is the amount of body weight gain for a given feed intake. Improving FE through selective breeding is key for sustainable finfish aquaculture but its evaluation at individual level is technically challenging. We therefore investigated whether individual routine metabolic rate (RMR) was a predictor of individual FE in the European sea bass Dicentrarchus labrax, a major species in European mariculture. The European sea bass has three genetically distinct populations across its geographical range, namely Atlantic (AT), West Mediterranean (WM), and East Mediterranean (EM). We compared FE and RMR of fish from these three populations at 18 or 24 °C. We held 200 fish (62 AT, 66 WM, and 72 EM) in individual aquaria and fed them from ad libitum down to fasting. FI was assessed for an ad libitum feeding rate and for a fixed restricted ration (1% of metabolic body weight·day-1, with metabolic body weight = body weight0.8). After being refed 12 wk in a common tank, individual RMR was measured over 36 h by intermittent flow respirometry. There was a significant effect of temperature whereby fish at 18 °C had greater mean FE (P < 0.05) and lower RMR (P < 0.001). There was also a significant effect of population, where AT fish had lower FE (P < 0.05) and greater RMR (P < 0.001) than WM and EM, at both temperatures. Despite these differences in temperature and population means, individual FE and RMR were not significantly correlated (P > 0.05). Therefore, although the results provide evidence of an association between metabolic rate and FE, RMR was not a predictor of individual FE, for reasons that require further investigation.
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Affiliation(s)
- Charles Rodde
- CIRAD, UMR ISEM, 34398 Montpellier, France
- ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
- Worldfish, Jalan Batu Maung, Bayan Lepas, 11960 Penang, Malaysia
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Hugues de Verdal
- CIRAD, UMR ISEM, 34398 Montpellier, France
- ISEM, Université de Montpellier, CNRS, EPHE, IRD, 34095 Montpellier, France
| | - Marc Vandeputte
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350 Jouy-en-Josas, France
| | - François Allal
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Julie Nati
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
| | - Mathieu Besson
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
- SYSAAF Section Aquacole, Campus de Beaulieu, 35000 Rennes, France
| | - Felipe R Blasco
- Laboratório de Zoofisiologia e Bioquímica Comparativa, Departamento de Ciências Fisiológicas, Universidade Federal de São Carlos, São Paulo 13565-905, Brasil
| | - John A H Benzie
- Worldfish, Jalan Batu Maung, Bayan Lepas, 11960 Penang, Malaysia
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork T12 K8AF, Ireland
| | - David J McKenzie
- MARBEC, Université de Montpellier, CNRS, Ifremer, IRD, 34250 Palavas-les-Flots, France
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11
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Peñaloza C, Manousaki T, Franch R, Tsakogiannis A, Sonesson AK, Aslam ML, Allal F, Bargelloni L, Houston RD, Tsigenopoulos CS. Development and testing of a combined species SNP array for the European seabass (Dicentrarchus labrax) and gilthead seabream (Sparus aurata). Genomics 2021; 113:2096-2107. [PMID: 33933591 PMCID: PMC8276775 DOI: 10.1016/j.ygeno.2021.04.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/30/2021] [Accepted: 04/27/2021] [Indexed: 12/23/2022]
Abstract
SNP arrays are powerful tools for high-resolution studies of the genetic basis of complex traits, facilitating both selective breeding and population genomic research. The European seabass (Dicentrarchus labrax) and the gilthead seabream (Sparus aurata) are the two most important fish species for Mediterranean aquaculture. While selective breeding programmes increasingly underpin stock supply for this industry, genomic selection is not yet widespread. Genomic selection has major potential to expedite genetic gain, particularly for traits practically impossible to measure on selection candidates, such as disease resistance and fillet characteristics. The aim of our study was to design a combined-species 60 K SNP array for European seabass and gilthead seabream, and to test its performance on farmed and wild populations from numerous locations throughout the species range. To achieve this, high coverage Illumina whole-genome sequencing of pooled samples was performed for 24 populations of European seabass and 27 populations of gilthead seabream. This resulted in a database of ~20 million SNPs per species, which were then filtered to identify high-quality variants and create the final set for the development of the ‘MedFish’ SNP array. The array was then tested by genotyping a subset of the discovery populations, highlighting a high conversion rate to functioning polymorphic assays on the array (92% in seabass; 89% in seabream) and repeatability (99.4–99.7%). The platform interrogates ~30 K markers in each species, includes features such as SNPs previously shown to be associated with performance traits, and is enriched for SNPs predicted to have high functional effects on proteins. The array was demonstrated to be effective at detecting population structure across a wide range of fish populations from diverse geographical origins, and to examine the extent of haplotype sharing among Mediterranean farmed fish populations. In conclusion, the new MedFish array enables efficient and accurate high-throughput genotyping for genome-wide distributed SNPs for each fish species, and will facilitate stock management, population genomics approaches, and acceleration of selective breeding through genomic selection. Α 60 K SNP array (MedFish) was designed for European seabass and gilthead seabream from wild and domesticated populations. The array exhibited a high conversion rate (92% in seabass; 89% in seabream) and repeatability (99.4 and 99.7%). The MedFish array is expected to facilitate stock management and acceleration of selective breeding via genomic selection.
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Affiliation(s)
- C Peñaloza
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK
| | - T Manousaki
- Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
| | - R Franch
- Padova University, Via Ugo Bassi, 58yB, I-35131 Padova, Italy
| | - A Tsakogiannis
- Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece
| | - A K Sonesson
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box 210, N-1432 Ås, Norway
| | - M L Aslam
- Nofima, Norwegian Institute of Food, Fisheries and Aquaculture Research, PO Box 210, N-1432 Ås, Norway
| | - F Allal
- MARBEC, University of Montpellier, Ifremer, CNRS, IRD, 34250 Palavas-les-Flots, France
| | - L Bargelloni
- Padova University, Via Ugo Bassi, 58yB, I-35131 Padova, Italy
| | - R D Houston
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian EH25 9RG, UK.
| | - C S Tsigenopoulos
- Hellenic Centre for Marine Research, Thalassocosmos Gournes Pediados, 71500 Irakleio, Crete, Greece.
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12
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Duranton M, Allal F, Valière S, Bouchez O, Bonhomme F, Gagnaire PA. The contribution of ancient admixture to reproductive isolation between European sea bass lineages. Evol Lett 2020; 4:226-242. [PMID: 32547783 PMCID: PMC7293100 DOI: 10.1002/evl3.169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 01/02/2020] [Accepted: 03/05/2020] [Indexed: 12/20/2022] Open
Abstract
Understanding how new species arise through the progressive establishment of reproductive isolation (RI) barriers between diverging populations is a major goal in Evolutionary Biology. An important result of speciation genomics studies is that genomic regions involved in RI frequently harbor anciently diverged haplotypes that predate the reconstructed history of species divergence. The possible origins of these old alleles remain much debated, as they relate to contrasting mechanisms of speciation that are not yet fully understood. In the European sea bass (Dicentrarchus labrax), the genomic regions involved in RI between Atlantic and Mediterranean lineages are enriched for anciently diverged alleles of unknown origin. Here, we used haplotype-resolved whole-genome sequences to test whether divergent haplotypes could have originated from a closely related species, the spotted sea bass (Dicentrarchus punctatus). We found that an ancient admixture event between D. labrax and D. punctatus is responsible for the presence of shared derived alleles that segregate at low frequencies in both lineages of D. labrax. An exception to this was found within regions involved in RI between the two D. labrax lineages. In those regions, archaic tracts originating from D. punctatus locally reached high frequencies or even fixation in Atlantic genomes but were almost absent in the Mediterranean. We showed that the ancient admixture event most likely occurred between D. punctatus and the D. labrax Atlantic lineage, while Atlantic and Mediterranean D. labrax lineages were experiencing allopatric isolation. Our results suggest that local adaptive introgression and/or the resolution of genomic conflicts provoked by ancient admixture have probably contributed to the establishment of RI between the two D. labrax lineages.
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Affiliation(s)
- Maud Duranton
- ISEM Univ Montpellier, CNRS, EPHE, IRD Montpellier France
| | - François Allal
- MARBEC Université de Montpellier, Ifremer-CNRS-IRD-UM Palavas-les-Flots 34250 France
| | - Sophie Valière
- INRA, US 1426, GeT-PlaGe Genotoul Castanet-Tolosan 31326 France
| | - Olivier Bouchez
- INRA, US 1426, GeT-PlaGe Genotoul Castanet-Tolosan 31326 France
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13
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Vandeputte M, Bugeon J, Bestin A, Desgranges A, Allamellou JM, Tyran AS, Allal F, Dupont-Nivet M, Haffray P. First Evidence of Realized Selection Response on Fillet Yield in Rainbow Trout Oncorhynchus mykiss, Using Sib Selection or Based on Correlated Ultrasound Measurements. Front Genet 2019; 10:1225. [PMID: 31921286 PMCID: PMC6933014 DOI: 10.3389/fgene.2019.01225] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 11/05/2019] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,MARBEC, Université de Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | | | | | | | | | | | - François Allal
- MARBEC, Université de Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
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14
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Griot R, Allal F, Brard‐Fudulea S, Morvezen R, Haffray P, Phocas F, Vandeputte M. APIS: An auto‐adaptive parentage inference software that tolerates missing parents. Mol Ecol Resour 2019; 20:579-590. [DOI: 10.1111/1755-0998.13103] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 10/01/2019] [Accepted: 10/09/2019] [Indexed: 12/01/2022]
Affiliation(s)
- Ronan Griot
- SYSAAF Station LPGP/INRA Rennes France
- GABI INRA AgroParisTech Université Paris‐Saclay Jouy-en-Josas France
| | - François Allal
- MARBEC Ifremer CNRS IRD Univ. Montpellier Palavas‐les‐Flots France
| | | | | | | | - Florence Phocas
- GABI INRA AgroParisTech Université Paris‐Saclay Jouy-en-Josas France
| | - Marc Vandeputte
- GABI INRA AgroParisTech Université Paris‐Saclay Jouy-en-Josas France
- MARBEC Ifremer CNRS IRD Univ. Montpellier Palavas‐les‐Flots France
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15
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Besson M, Allal F, Chatain B, Vergnet A, Clota F, Vandeputte M. Combining Individual Phenotypes of Feed Intake With Genomic Data to Improve Feed Efficiency in Sea Bass. Front Genet 2019; 10:219. [PMID: 30984235 PMCID: PMC6449465 DOI: 10.3389/fgene.2019.00219] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 02/27/2019] [Indexed: 11/18/2022] Open
Abstract
Measuring individual feed intake of fish in farms is complex and precludes selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content that were possibly linked to FCR. The 588 fish were derived from a full factorial mating between parental lines divergently selected for high (F+) or low (F–) weight loss at fasting. The pedigree was known back to the great grand-parents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs which allowed to calculate the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable (genomic h2 = 0.47 and 0.76, respectively) and strongly genetically correlated (−0.98) meaning that, under restricted feeding, faster growing fish were more efficient. FCR and growth rate in aquariums were also significantly better for fish with both parents from F– (1.38), worse for fish with two parents F+ (1.51) and intermediate for cross breed fish (F+/F– or F–/F+ at 1.46). Muscle fat content was positively genetically correlated to growth rate in aquarium and during fasting. Thus, selecting for higher growth rate in aquarium, lower weight loss during fasting and fatter fish could improve FCR in aquarium. Improving these traits would also improve FCR of fish in normal group rearing conditions, as we showed experimentally that groups composed of fish with good individual FCR were significantly more efficient. The FCR of groups was also better when the fish composing the groups had, on average, lower estimated breeding values for growth rate during fasting (losing less weight). Thus, improving FCR in aquarium and weight loss during fasting is promising to improve FCR of fish in groups but a selection response experiment needs to be done. Finally, we showed that the reliability of estimated breeding values was higher (from+10% up to +125%) with a genomic-based BLUP model than with a traditional pedigree-based BLUP, showing that genomic data would enhance the accuracy of the prediction of EBV of selection candidates.
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Affiliation(s)
- Mathieu Besson
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - François Allal
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Béatrice Chatain
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Alain Vergnet
- MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Frédéric Clota
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France.,MARBEC, Univ Montpellier, CNRS, Ifremer, IRD, Palavas-les-Flots, France
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16
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Abstract
The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.
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Affiliation(s)
- M Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,MARBEC, Ifremer-CNRS-IRD-UM, Université de Montpellier, 34250, Palavas-les-Flots, France
| | - P-A Gagnaire
- Institut des Sciences de l'Evolution de Montpellier, UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - F Allal
- MARBEC, Ifremer-CNRS-IRD-UM, Université de Montpellier, 34250, Palavas-les-Flots, France
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17
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Faggion S, Vandeputte M, Chatain B, Gagnaire PA, Allal F. Population-specific variations of the genetic architecture of sex determination in wild European sea bass Dicentrarchus labrax L. Heredity (Edinb) 2018; 122:612-621. [PMID: 30356226 DOI: 10.1038/s41437-018-0157-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 09/10/2018] [Accepted: 09/28/2018] [Indexed: 12/22/2022] Open
Abstract
Polygenic sex determination (PSD) may show variations in terms of genetic and environmental components between populations of fish species exposed/adapted to different environments. The European sea bass (Dicentrarchus labrax) is an interesting model, combining both a PSD system and a genetic subdivision into an Atlantic and a Mediterranean lineage, with genetic substructures within the Mediterranean Sea. Here, we produced experimental progeny crosses (N = 927) from broodstock sampled in four wild populations (North Atlantic, NAT; Western Mediterranean, WEM; North-Eastern Mediterranean, NEM; South-Eastern Mediterranean, SEM). We found less females than males in the progeny, both in the global dataset (32.5%) and within each paternal group (from 25.1% for NEM to 39.0% for WEM), with significant variation among populations, dams, and sires. Sex, body weight (BW), and body length (BL) showed moderate heritability (0.52 ± 0.17, 0.46 ± 0.17, 0.34 ± 0.15, respectively) and sex was genetically correlated with BW and BL, with rAsex/BW = 0.69 ± 0.12 and rA sex/BL = 0.66 ± 0.13. A weighted GWAS performed both on the global dataset and within each paternal group revealed a different genetic architecture of sex determination between Atlantic and Mediterranean populations (9 QTLs found in NAT, 7 in WEM, 5 in NEM, and 4 in SEM, with a cumulated variance explained of 27.04%, 21.87%, 15.89%, and 12.10%, respectively) and a more similar genetic architecture among geographically close populations compared to geographically distant populations, consistent with the hypothesis of a population-specific evolution of polygenic sex determination systems in different environments.
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Affiliation(s)
- Sara Faggion
- Department of Comparative Biomedicine and Food Science, University of Padua, Agripolis, Viale dell'Università, 16, 35020, Legnaro, PD, Italy.,MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | - Marc Vandeputte
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France.,GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350, Paris, France
| | - Béatrice Chatain
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France
| | | | - François Allal
- MARBEC, Univ. Montpellier, Ifremer, CNRS, IRD, Palavas-les-Flots, France.
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18
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Anastasiadi D, Vandeputte M, Sánchez-Baizán N, Allal F, Piferrer F. Dynamic epimarks in sex-related genes predict gonad phenotype in the European sea bass, a fish with mixed genetic and environmental sex determination. Epigenetics 2018; 13:988-1011. [PMID: 30265213 PMCID: PMC6284782 DOI: 10.1080/15592294.2018.1529504] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/10/2018] [Accepted: 09/22/2018] [Indexed: 12/13/2022] Open
Abstract
The integration of genomic and environmental influences into methylation patterns to bring about a phenotype is of central interest in developmental epigenetics, but many details are still unclear. The sex ratios of the species used here, the European sea bass, are determined by genetic and temperature influences. We created four families from parents known to produce offspring with different sex ratios, exposed larvae to masculinizing temperatures and examined, in juvenile gonads, the DNA methylation of seven genes related to sexual development by a targeted sequencing approach. The genes most affected by both genetics and environment were cyp19a1a and dmrt1, with contrasting sex-specific methylation and temperature responses. The relationship between cyp19a1a methylation and expression is relevant to the epigenetic regulation of vertebrate sex, and we report the evidence of such relationship only below a methylation threshold, ~ 80%, and that it was sex-specific: negatively correlated in females but positively correlated in males. From parents to offspring, the methylation in gonads was midway between oocytes and sperm, with bias towards oocytes for amh-r2, er-β2, fsh-r and cyp19a1a. In contrast, dmrt1 levels resembled those of sperm. The methylation of individual CpGs from foxl2, er-β2 and nr3c1 were conserved from parents to offspring, whereas those of cyp19a1a, dmrt1 and amh-r2 were affected by temperature. Utilizing a machine-learning procedure based on the methylation levels of a selected set of CpGs, we present the first, to our knowledge, system based on epigenetic marks capable of predicting sex in an animal with ~ 90% accuracy and discuss possible applications.
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Affiliation(s)
- Dafni Anastasiadi
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - Marc Vandeputte
- MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD, Palavas-les-Flots, France
- GABI, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - Núria Sánchez-Baizán
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
| | - François Allal
- MARBEC, Univ. Montpellier, Ifremer-CNRS-IRD, Palavas-les-Flots, France
| | - Francesc Piferrer
- Institut de Ciències del Mar, Consejo Superior de Investigaciones Científicas (CSIC), Barcelona, Spain
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Duranton M, Allal F, Fraïsse C, Bierne N, Bonhomme F, Gagnaire PA. The origin and remolding of genomic islands of differentiation in the European sea bass. Nat Commun 2018; 9:2518. [PMID: 29955054 PMCID: PMC6023918 DOI: 10.1038/s41467-018-04963-6] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Accepted: 05/23/2018] [Indexed: 01/06/2023] Open
Abstract
Speciation is a complex process that leads to the progressive establishment of reproductive isolation barriers between diverging populations. Genome-wide comparisons between closely related species have revealed the existence of heterogeneous divergence patterns, dominated by genomic islands of increased divergence supposed to contain reproductive isolation loci. However, this divergence landscape only provides a static picture of the dynamic process of speciation, during which confounding mechanisms unrelated to speciation can interfere. Here we use haplotype-resolved whole-genome sequences to identify the mechanisms responsible for the formation of genomic islands between Atlantic and Mediterranean sea bass lineages. Local ancestry patterns show that genomic islands first emerged in allopatry through linked selection acting on a heterogeneous recombination landscape. Then, upon secondary contact, preexisting islands were strongly remolded by differential introgression, revealing variable fitness effects among regions involved in reproductive isolation. Interestingly, we find that divergent regions containing ancient polymorphisms conferred the strongest resistance to introgression. The speciation process tends to generate ‘genomic islands’ of increased divergence. Here, the authors use haplotype–resolved whole-genome sequences of European sea bass lineages to infer divergence history and show that linked selection generated genomic islands that resist introgression at secondary contact.
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Affiliation(s)
- Maud Duranton
- Institut des Sciences de l'Evolution de Montpellier - UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France. .,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.
| | - François Allal
- Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France.,MARBEC, Université de Montpellier, Ifremer-CNRS-IRD-UM, 34250, Palavas-les-Flots, France
| | - Christelle Fraïsse
- Institut des Sciences de l'Evolution de Montpellier - UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Nicolas Bierne
- Institut des Sciences de l'Evolution de Montpellier - UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - François Bonhomme
- Institut des Sciences de l'Evolution de Montpellier - UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
| | - Pierre-Alexandre Gagnaire
- Institut des Sciences de l'Evolution de Montpellier - UMR5554 UM-CNRS-IRD-EPHE, Place Eugène Bataillon, 34095, Montpellier, France.,Université de Montpellier, Place Eugène Bataillon, 34095, Montpellier, France
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20
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Palaiokostas C, Cariou S, Bestin A, Bruant JS, Haffray P, Morin T, Cabon J, Allal F, Vandeputte M, Houston RD. Genome-wide association and genomic prediction of resistance to viral nervous necrosis in European sea bass (Dicentrarchus labrax) using RAD sequencing. Genet Sel Evol 2018; 50:30. [PMID: 29884113 PMCID: PMC5994081 DOI: 10.1186/s12711-018-0401-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Accepted: 05/31/2018] [Indexed: 12/15/2022] Open
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 < 1e06). Weighted genomic best linear unbiased predictor provided additional support for the QTL on chromosome 3 and suggested that it explained 4% of the additive genetic variation. Genomic prediction approaches were tested to investigate the potential of using genome-wide SNP data to estimate breeding values for resistance to VNN and showed that genomic prediction resulted in a 13% increase in successful classification of resistant and susceptible animals compared to pedigree-based methods, with Bayes A and Bayes B giving the highest predictive ability. CONCLUSIONS Genome-wide significant QTL were identified but each with relatively small effects on the trait. Tests of genomic prediction suggested that incorporating genome-wide SNP data is likely to result in higher accuracy of estimated breeding values for resistance to VNN. RAD sequencing is an effective method for generating such genome-wide SNPs, and our findings highlight the potential of genomic selection to breed farmed European sea bass with improved resistance to VNN.
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Affiliation(s)
- Christos Palaiokostas
- The Roslin Institute¸Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
| | - Sophie Cariou
- Ferme Marine De Douhet, BP 4, 17840 La Brée Les Bains, France
| | - Anastasia Bestin
- SYSAAF, LPGP-INRA, Campus de Beaulieu, 35042 Rennes Cedex, France
| | | | - Pierrick Haffray
- SYSAAF, LPGP-INRA, Campus de Beaulieu, 35042 Rennes Cedex, France
| | - Thierry Morin
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Ploufragan-Plouzané Laboratory, Viral Fish Pathology Unit, National Reference Laboratory for Regulated Fish Diseases, Bretagne Loire University, Technopôle Brest-Iroise, BP 70, 29280 Plouzané, France
| | - Joëlle Cabon
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Ploufragan-Plouzané Laboratory, Viral Fish Pathology Unit, National Reference Laboratory for Regulated Fish Diseases, Bretagne Loire University, Technopôle Brest-Iroise, BP 70, 29280 Plouzané, France
| | - François Allal
- MARBEC, Université de Montpellier, Ifremer-CNRS-IRD-UM, Palavas-les-Flots, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Ross D. Houston
- The Roslin Institute¸Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG Scotland, UK
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Doan QK, Vandeputte M, Chatain B, Morin T, Allal F. Viral encephalopathy and retinopathy in aquaculture: a review. J Fish Dis 2017; 40:717-742. [PMID: 27633881 DOI: 10.1111/jfd.12541] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Revised: 06/23/2016] [Accepted: 06/27/2016] [Indexed: 05/22/2023]
Abstract
Viral encephalopathy and retinopathy (VER), otherwise known as viral nervous necrosis (VNN), is a major devastating threat for aquatic animals. Betanodaviruses have been isolated in at least 70 aquatic animal species in marine and in freshwater environments throughout the world, with the notable exception of South America. In this review, the main features of betanodavirus, including its diversity, its distribution and its transmission modes in fish, are firstly presented. Then, the existing diagnosis and detection methods, as well as the different control procedures of this disease, are reviewed. Finally, the potential of selective breeding, including both conventional and genomic selection, as an opportunity to obtain resistant commercial populations, is examined.
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Affiliation(s)
- Q K Doan
- Ifremer, UMR 9190 MARBEC, Palavas-les-Flots, France
- TNU, Thai Nguyen University of Agriculture and Forestry (TUAF), Quyet Thang Commune, Thai Nguyen City, Vietnam
| | - M Vandeputte
- Ifremer, UMR 9190 MARBEC, Palavas-les-Flots, France
- INRA, GABI, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, France
| | - B Chatain
- Ifremer, UMR 9190 MARBEC, Palavas-les-Flots, France
| | - T Morin
- Anses, Ploufragan-Plouzané Laboratory, Unit Viral Diseases of Fish, Plouzané, France
| | - F Allal
- Ifremer, UMR 9190 MARBEC, Palavas-les-Flots, France
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22
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Ferrari S, Horri K, Allal F, Vergnet A, Benhaim D, Vandeputte M, Chatain B, Bégout ML. Heritability of Boldness and Hypoxia Avoidance in European Seabass, Dicentrarchus labrax. PLoS One 2016; 11:e0168506. [PMID: 27992517 PMCID: PMC5167369 DOI: 10.1371/journal.pone.0168506] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/01/2016] [Indexed: 11/19/2022] Open
Abstract
To understand the genetic basis of coping style in European seabass, fish from a full factorial mating (10 females x 50 males) were reared in common garden and individually tagged. Individuals coping style was characterized through behavior tests at four different ages, categorizing fish into proactive or reactive: a hypoxia avoidance test (at 255 days post hatching, dph) and 3 risk-taking tests (at 276, 286 and 304 dph). We observed significant heritability of the coping style, higher for the average of risk-taking scores (h2 = 0.45 ± 0.14) than for the hypoxia avoidance test (h2 = 0.19 ± 0.10). The genetic correlations between the three risk-taking scores were very high (rA = 0.96–0.99) showing that although their repeatability was moderately high (rP = 0.64–0.72), successive risk-taking tests evaluated the same genetic variation. A mild genetic correlation between the results of the hypoxia avoidance test and the average of risk-taking scores (0.45 ± 0.27) suggested that hypoxia avoidance and risk-taking tests do not address exactly the same behavioral and physiological responses. Genetic correlations between weight and risk taking traits showed negative values whatever the test used in our population i.e. reactive individual weights were larger. The results of this quantitative genetic analysis suggest a potential for the development of selection programs based on coping styles that could increase seabass welfare without altering growth performances. Overall, it also contributes to a better understanding of the origin and the significance of individual behavioral differences.
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Affiliation(s)
- Sébastien Ferrari
- Ifremer, Fisheries laboratory, Place Gaby Coll, L’Houmeau, France
- * E-mail: (SF); (MLB)
| | - Khaled Horri
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - François Allal
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - Alain Vergnet
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - David Benhaim
- Laboratoire universitaire des sciences appliquées de Cherbourg, Normandie Univ, UNICAEN, LUSAC, Cherbourg, France
- Conservatoire National des Arts et Métiers. Intechmer, Cherbourg, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay Jouy-en-Josas, France
- Ifremer, L3AS, Chemin de Maguelone, Palavas-les-Flots, France
| | - Béatrice Chatain
- Ifremer, MARBEC UMR9190, Chemin de Maguelone, Palavas-les-Flots, France
| | - Marie-Laure Bégout
- Ifremer, Fisheries laboratory, Place Gaby Coll, L’Houmeau, France
- * E-mail: (SF); (MLB)
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Hubert JN, Allal F, Hervet C, Ravakarivelo M, Jeney Z, Vergnet A, Guyomard R, Vandeputte M. How could fully scaled carps appear in natural waters in Madagascar? Proc Biol Sci 2016; 283:rspb.2016.0945. [PMID: 27559059 DOI: 10.1098/rspb.2016.0945] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Accepted: 08/01/2016] [Indexed: 01/02/2023] Open
Abstract
The capacity of organisms to rapidly evolve in response to environmental changes is a key feature of evolution, and studying mutation compensation is a way to evaluate whether alternative routes of evolution are possible or not. Common carps (Cyprinus carpio) carrying a homozygous loss-of-function mutation for the scale cover gene fgfr1a1, causing the 'mirror' reduced scale cover, were introduced in Madagascar a century ago. Here we show that carps in Malagasy natural waters are now predominantly covered with scales, though they still all carry the homozygous mutation. We also reveal that the number of scales in mutated carps is under strong polygenic genetic control, with a heritability of 0.49. As a whole, our results suggest that carps submitted to natural selection could evolve a wild-type-like scale cover in less than 40 generations from standing polygenic genetic variation, confirming similar findings mainly retrieved from model organisms.
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Affiliation(s)
- Jean-Noël Hubert
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - François Allal
- Ifremer, UMR 9190 MARBEC, 34250 Palavas-les-Flots, France
| | - Caroline Hervet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | | | | | | | - René Guyomard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France
| | - Marc Vandeputte
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350 Jouy-en-Josas, France Ifremer, 34250 Palavas-les-Flots, France
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Allal F, Vaillant A, Sanou H, Kelly B, Bouvet JM. Isolation and characterization of new microsatellite markers in shea tree (Vitellaria paradoxa C. F. Gaertn). Mol Ecol Resour 2013; 8:822-4. [PMID: 21585902 DOI: 10.1111/j.1755-0998.2007.02079.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vitellaria paradoxa is one of the major components of African parkland agroforestry systems. In order to assess the genetic diversity and population structure of this species, we isolated and characterized 14 polymorphic nuclear microsatellite loci. Primers developed to amplify these loci were used to analyse 200 individuals of a shea tree population in Mali. Loci have shown a high number of alleles ranging from four to 26, and display an observed level of heterozygosity between 0.37 and 0.85. These new very polymorphic microsatellite markers will be useful for genetic and ecological studies of V. paradoxa.
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Affiliation(s)
- François Allal
- CIRAD - BIOS, Unité Propre de Recherche de Génétique Forestière, Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France, IER (Institut d'Economie Rurale), Programme Ressources Forestières, Centre Régional de la Recherche Agronomique de Sotuba, BP 258, Bamako, Mali, IER (Institut d'Economie Rurale), Programme Ressources Forestières, Centre Régional de la Recherche Agronomique de Sikasso, BP 178, Sikasso, Mali
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Allal F, Sanou H, Millet L, Vaillant A, Camus-Kulandaivelu L, Logossa ZA, Lefèvre F, Bouvet JM. Erratum: Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa. Heredity (Edinb) 2011. [DOI: 10.1038/hdy.2011.112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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Logossa ZA, Camus-Kulandaivelu L, Allal F, Vaillant A, Sanou H, Kokou K, Bouvet JM. Molecular data reveal isolation by distance and past population expansion for the shea tree (Vitellaria paradoxa C.F. Gaertn) in West Africa. Mol Ecol 2011; 20:4009-27. [PMID: 21914014 DOI: 10.1111/j.1365-294x.2011.05249.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
While the genetic structure of many tree species in temperate, American and Asian regions is largely explained by climatic oscillations and subsequent habitat contractions and expansions, little is known about Africa. We investigated the genetic diversity and structure of shea tree (Vitellaria paradoxa,) in Western Africa, an economically important tree species in the Sudano-Sahelian zone. Eleven nuclear microsatellites (nuc) were used to genotype 673 trees selected in 38 populations. They revealed moderate to high within-population diversity: allelic richness ranged from R(nuc) = 3.99 to 5.63. This diversity was evenly distributed across West Africa. Populations were weakly differentiated (F(STnuc) = 0.085; P < 0.0001) and a pattern of isolation by distance was noted. No phylogeographic signal could be detected across the studied sample. Additionally, two chloroplast microsatellite loci, leading to 11 chlorotypes, were used to analyse a sub-set of 370 individuals. Some variation in chloroplast allelic richness among populations could be detected (R(cp) = 0.00 to 4.36), but these differences were not significant. No trend with latitude and longitude were observed. Differentiation was marked (G(STcp) = 0.553; P < 0.0001), but without a significant phylogeographical signal. Population expansion was detected considering the total population using approximate Bayesian computation (nuclear microsatellites) and mismatch distribution (chloroplast microsatellites) methods. This expansion signal and the isolation by distance pattern could be linked to the past climatic conditions in West Africa during the Pleistocene and Holocene which should have been favourable to shea tree development. In addition, human activities through agroforestry and domestication (started 10,000 bp) have probably enhanced gene flow and population expansion.
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Farikou O, Thevenon S, Njiokou F, Allal F, Cuny G, Geiger A. Genetic diversity and population structure of the secondary symbiont of tsetse flies, Sodalis glossinidius, in sleeping sickness foci in Cameroon. PLoS Negl Trop Dis 2011; 5:e1281. [PMID: 21886849 PMCID: PMC3160304 DOI: 10.1371/journal.pntd.0001281] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2011] [Accepted: 07/03/2011] [Indexed: 11/17/2022] Open
Abstract
Background Previous studies have shown substantial differences in Sodalis glossinidius and trypanosome infection rates between Glossina palpalis palpalis populations from two Cameroonian foci of human African trypanosomiasis (HAT), Bipindi and Campo. We hypothesized that the geographical isolation of the two foci may have induced independent evolution in the two areas, resulting in the diversification of symbiont genotypes. Methodology/Principal Findings To test this hypothesis, we investigated the symbiont genetic structure using the allelic size variation at four specific microsatellite loci. Classical analysis of molecular variance (AMOVA) and differentiation statistics revealed that most of the genetic diversity was observed among individuals within populations and frequent haplotypes were shared between populations. The structure of genetic diversity varied at different geographical scales, with almost no differentiation within the Campo HAT focus and a low but significant differentiation between the Campo and Bipindi HAT foci. Conclusions/Significance The data provided new information on the genetic diversity of the secondary symbiont population revealing mild structuring. Possible interactions between S. glossinidius subpopulations and Glossina species that could favor tsetse fly infections by a given trypanosome species should be further investigated. Human African trypanosomiasis remains a threat to the poorest people in Africa. The trypanosomes causing the disease are transmitted by tsetse flies. The drugs currently used are unsatisfactory: some are toxic and all are difficult to administer. Furthermore, drug resistance is increasing. Therefore, investigations for novel disease control strategies are urgently needed. Previous analyses showed the association between the presence of Glossina symbiont, Sodalis glossinidius, and the fly infection by trypanosomes in a south-western region in Cameroon: flies harbouring symbionts had a threefold higher probability of being infected by trypanosomes than flies devoid of symbionts. But the study also showed substantial differences in S. glossinidius and trypanosome infection rates between Glossina populations from two Cameroonian foci of sleeping sickness. We hypothesized that the geographical isolation of the two foci may have induced the independent evolution of each one, leading to the diversification of symbiont genotypes. Microsatellite markers were used and showed that genetic diversity structuring of S. glossinidius varies at different geographical scales with a low but significant differentiation between the Campo and Bipindi HAT foci. This encourages further work on interactions between S. glossinidius subpopulations and Glossina species that could favor tsetse fly infections by a given trypanosome species.
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Affiliation(s)
- Oumarou Farikou
- UMR 177, IRD-CIRAD, CIRAD TA A-17/G, Campus International de Baillarguet, Montpellier, France
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Fischer I, Camus-Kulandaivelu L, Allal F, Stephan W. Adaptation to drought in two wild tomato species: the evolution of the Asr gene family. New Phytol 2011; 190:1032-1044. [PMID: 21323928 DOI: 10.1111/j.1469-8137.2011.03648.x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Wild tomato species are a valuable system in which to study local adaptation to drought: they grow in diverse environments ranging from mesic to extremely arid conditions. Here, we investigate the evolution of members of the Asr (ABA/water stress/ripening induced) gene family, which have been reported to be involved in the water stress response. We analysed molecular variation in the Asr gene family in populations of two closely related species, Solanum chilense and Solanum peruvianum. We concluded that Asr1 has evolved under strong purifying selection. In contrast to previous reports, we did not detect evidence for positive selection at Asr2. However, Asr4 shows patterns consistent with local adaptation in an S. chilense population that lives in an extremely dry environment. We also discovered a new member of the gene family, Asr5. Our results show that the Asr genes constitute a dynamic gene family and provide an excellent example of tandemly arrayed genes that are of importance in adaptation. Taking the potential distribution of the species into account, it appears that S. peruvianum can cope with a great variety of environmental conditions without undergoing local adaptation, whereas S. chilense undergoes local adaptation more frequently.
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Affiliation(s)
- Iris Fischer
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
| | - Létizia Camus-Kulandaivelu
- CIRAD, Biological System Department - Research Unit 39 'Genetic Diversity and Breeding of Forest Tree Species', Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France
| | - François Allal
- CIRAD, Biological System Department - Research Unit 39 'Genetic Diversity and Breeding of Forest Tree Species', Campus international de Baillarguet TA A-39/C, 34398 Montpellier Cedex 5, France
| | - Wolfgang Stephan
- Section of Evolutionary Biology, Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany
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Allal F, Sanou H, Millet L, Vaillant A, Camus-Kulandaivelu L, Logossa ZA, Lefèvre F, Bouvet JM. Past climate changes explain the phylogeography of Vitellaria paradoxa over Africa. Heredity (Edinb) 2011; 107:174-86. [PMID: 21407253 DOI: 10.1038/hdy.2011.5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The evolution of the savanna biome has been deeply marked by repeated contraction/expansion phases due to climate perturbations during the Quaternary period. In this study, we investigated the impact of the last glacial maximum (LGM) on the present genetic pattern of Vitellaria paradoxa (shea tree), a major African savanna tree. A range-wide sampling of the species enabled us to sample 374 individuals from 71 populations distributed throughout sub-Sahelian Africa. Trees were genotyped using 3 chloroplasts and 12 nuclear microsatellites, and were sequenced for 2 polymorphic chloroplast intergenic spacers. Analyses of genetic diversity and structure were based on frequency-based and Bayesian methods. Potential distributions of V. paradoxa at present, during the LGM and the last interglacial period, were examined using DIVA-GIS ecological niche modelling (ENM). Haplotypic and allelic richness varied significantly across the range according to chloroplast and nuclear microsatellites, which pointed to higher diversity in West Africa. A high but contrasted level of differentiation was revealed among populations with a clear phylogeographic signal, with both nuclear (F(ST) = 0.21; R(ST) = 0.28; R(ST) > R(ST) (permuted)) and chloroplast simple sequence repeats (SSRs) (G(ST) = 0.81; N(ST) = 0.90; N(ST) > N(ST) (permuted)). We identified a strong geographically related structure separating western and eastern populations, and a substructure in the eastern part of the area consistent with subspecies distinction. Using ENM, we deduced that perturbations during the LGM fragmented the potential eastern distribution of shea tree, but not its distribution in West Africa. Our main results suggest that climate variations are the major factor explaining the genetic pattern of V. paradoxa.
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Affiliation(s)
- F Allal
- Cirad-Bios Department, Research Unit, Genetic Diversity and Breeding of Forest Tree Species, International Campus of Baillarguet, Montpellier, France.
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Davrieux F, Allal F, Piombo G, Kelly B, Okulo JB, Thiam M, Diallo OB, Bouvet JM. Near infrared spectroscopy for high-throughput characterization of Shea tree (Vitellaria paradoxa) nut fat profiles. J Agric Food Chem 2010; 58:7811-7819. [PMID: 20518501 DOI: 10.1021/jf100409v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
The Shea tree (Vitellaria paradoxa) is a major tree species in African agroforestry systems. Butter extracted from its nuts offers an opportunity for sustainable development in Sudanian countries and an attractive potential for the food and cosmetics industries. The purpose of this study was to develop near-infrared spectroscopy (NIRS) calibrations to characterize Shea nut fat profiles. Powders prepared from nuts collected from 624 trees in five African countries (Senegal, Mali, Burkina Faso, Ghana and Uganda) were analyzed for moisture content, fat content using solvent extraction, and fatty acid profiles using gas chromatography. Results confirmed the differences between East and West African Shea nut fat composition: eastern nuts had significantly higher fat and oleic acid contents. Near infrared reflectance spectra were recorded for each sample. Ten percent of the samples were randomly selected for validation and the remaining samples used for calibration. For each constituent, calibration equations were developed using modified partial least squares (MPLS) regression. The equation performances were evaluated using the ratio performance to deviation (RPD(p)) and R(p)(2) parameters, obtained by comparison of the validation set NIR predictions and corresponding laboratory values. Moisture (RPD(p) = 4.45; R(p)(2) = 0.95) and fat (RPD(p) = 5.6; R(p)(2) = 0.97) calibrations enabled accurate determination of these traits. NIR models for stearic (RPD(p) = 6.26; R(p)(2) = 0.98) and oleic (RPD(p) = 7.91; R(p)(2) = 0.99) acids were highly efficient and enabled sharp characterization of these two major Shea butter fatty acids. This study demonstrated the ability of near-infrared spectroscopy for high-throughput phenotyping of Shea nuts.
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Affiliation(s)
- Fabrice Davrieux
- CIRAD, Performance of Tropical Production and Processing Systems Department, UMR QUALISUD, TA B-95/16, 73, avenue Jean Francois Breton, 34398 Montpellier Cedex 5, France.
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