Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes
International audience 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 popu...
Published in: | Genetics Selection Evolution |
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Main Authors: | , , , , , , , , , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2021
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Online Access: | https://hal.inrae.fr/hal-03832279 https://hal.inrae.fr/hal-03832279/document https://hal.inrae.fr/hal-03832279/file/saura_GenetSelEvol_2021.pdf https://doi.org/10.1186/s12711-021-00680-9 |
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Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) |
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[SDV]Life Sciences [q-bio] |
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[SDV]Life Sciences [q-bio] Saura, María Caballero, Armando Santiago, Enrique Fernández, Almudena Morales-González, Elisabeth Fernández, Jesús Cabaleiro, Santiago Millán, Adrián Martínez, Paulino Palaiokostas, Christos Kocour, Martin Aslam, Muhammad Houston, Ross Prchal, Martin Bargelloni, Luca Tzokas, Kostas Haffray, Pierrick Bruant, Jean-Sebastien Villanueva, Beatriz Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
topic_facet |
[SDV]Life Sciences [q-bio] |
description |
International audience 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. |
author2 |
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 |
format |
Article in Journal/Newspaper |
author |
Saura, María Caballero, Armando Santiago, Enrique Fernández, Almudena Morales-González, Elisabeth Fernández, Jesús Cabaleiro, Santiago Millán, Adrián Martínez, Paulino Palaiokostas, Christos Kocour, Martin Aslam, Muhammad Houston, Ross Prchal, Martin Bargelloni, Luca Tzokas, Kostas Haffray, Pierrick Bruant, Jean-Sebastien Villanueva, Beatriz |
author_facet |
Saura, María Caballero, Armando Santiago, Enrique Fernández, Almudena Morales-González, Elisabeth Fernández, Jesús Cabaleiro, Santiago Millán, Adrián Martínez, Paulino Palaiokostas, Christos Kocour, Martin Aslam, Muhammad Houston, Ross Prchal, Martin Bargelloni, Luca Tzokas, Kostas Haffray, Pierrick Bruant, Jean-Sebastien Villanueva, Beatriz |
author_sort |
Saura, María |
title |
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
title_short |
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
title_full |
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
title_fullStr |
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
title_full_unstemmed |
Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
title_sort |
estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes |
publisher |
HAL CCSD |
publishDate |
2021 |
url |
https://hal.inrae.fr/hal-03832279 https://hal.inrae.fr/hal-03832279/document https://hal.inrae.fr/hal-03832279/file/saura_GenetSelEvol_2021.pdf https://doi.org/10.1186/s12711-021-00680-9 |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
ISSN: 0999-193X EISSN: 1297-9686 Genetics Selection Evolution https://hal.inrae.fr/hal-03832279 Genetics Selection Evolution, 2021, 53 (1), pp.85. ⟨10.1186/s12711-021-00680-9⟩ |
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info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-021-00680-9 info:eu-repo/grantAgreement/EC/FP7/613611/EU/Improving European aquaculture by advancing selective breeding to the next level for the six main finfish species/FISHBOOST info:eu-repo/grantAgreement//727315/EU/Mediterranean Aquaculture Integrated Development/MedAID hal-03832279 https://hal.inrae.fr/hal-03832279 https://hal.inrae.fr/hal-03832279/document https://hal.inrae.fr/hal-03832279/file/saura_GenetSelEvol_2021.pdf doi:10.1186/s12711-021-00680-9 WOS: 000715028100002 |
op_rights |
http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1186/s12711-021-00680-9 |
container_title |
Genetics Selection Evolution |
container_volume |
53 |
container_issue |
1 |
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ftccsdartic:oai:HAL:hal-03832279v1 2023-12-31T10:22:52+01:00 Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes Saura, María Caballero, Armando Santiago, Enrique Fernández, Almudena Morales-González, Elisabeth Fernández, Jesús Cabaleiro, Santiago Millán, Adrián Martínez, Paulino Palaiokostas, Christos Kocour, Martin Aslam, Muhammad Houston, Ross Prchal, Martin Bargelloni, Luca Tzokas, Kostas Haffray, Pierrick Bruant, Jean-Sebastien Villanueva, Beatriz 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 2021-12 https://hal.inrae.fr/hal-03832279 https://hal.inrae.fr/hal-03832279/document https://hal.inrae.fr/hal-03832279/file/saura_GenetSelEvol_2021.pdf https://doi.org/10.1186/s12711-021-00680-9 en eng HAL CCSD BioMed Central info:eu-repo/semantics/altIdentifier/doi/10.1186/s12711-021-00680-9 info:eu-repo/grantAgreement/EC/FP7/613611/EU/Improving European aquaculture by advancing selective breeding to the next level for the six main finfish species/FISHBOOST info:eu-repo/grantAgreement//727315/EU/Mediterranean Aquaculture Integrated Development/MedAID hal-03832279 https://hal.inrae.fr/hal-03832279 https://hal.inrae.fr/hal-03832279/document https://hal.inrae.fr/hal-03832279/file/saura_GenetSelEvol_2021.pdf doi:10.1186/s12711-021-00680-9 WOS: 000715028100002 http://creativecommons.org/licenses/by/ info:eu-repo/semantics/OpenAccess ISSN: 0999-193X EISSN: 1297-9686 Genetics Selection Evolution https://hal.inrae.fr/hal-03832279 Genetics Selection Evolution, 2021, 53 (1), pp.85. ⟨10.1186/s12711-021-00680-9⟩ [SDV]Life Sciences [q-bio] info:eu-repo/semantics/article Journal articles 2021 ftccsdartic https://doi.org/10.1186/s12711-021-00680-9 2023-12-02T23:47:53Z International audience 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. Article in Journal/Newspaper Scophthalmus maximus Turbot Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) Genetics Selection Evolution 53 1 |