Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes
Abstract Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populat...
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Springer Science and Business Media LLC
2021
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Online Access: | http://dx.doi.org/10.1186/s12711-021-00680-9 https://link.springer.com/content/pdf/10.1186/s12711-021-00680-9.pdf https://link.springer.com/article/10.1186/s12711-021-00680-9/fulltext.html |
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crspringernat:10.1186/s12711-021-00680-9 2023-05-15T18:15:53+02:00 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 L. Houston, Ross D. Prchal, Martin Bargelloni, Luca Tzokas, Kostas Haffray, Pierrick Bruant, Jean-Sebastien Villanueva, Beatriz 2021 http://dx.doi.org/10.1186/s12711-021-00680-9 https://link.springer.com/content/pdf/10.1186/s12711-021-00680-9.pdf https://link.springer.com/article/10.1186/s12711-021-00680-9/fulltext.html en eng Springer Science and Business Media LLC https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 CC-BY Genetics Selection Evolution volume 53, issue 1 ISSN 1297-9686 Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics journal-article 2021 crspringernat https://doi.org/10.1186/s12711-021-00680-9 2022-01-04T12:22:21Z Abstract Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot ( Scophthalmus maximus ), gilthead seabream ( Sparus aurata ), European seabass ( Dicentrarchus labrax ) and common carp ( Cyprinus carpio ) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. Article in Journal/Newspaper Scophthalmus maximus Turbot Springer Nature (via Crossref) Genetics Selection Evolution 53 1 |
institution |
Open Polar |
collection |
Springer Nature (via Crossref) |
op_collection_id |
crspringernat |
language |
English |
topic |
Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics |
spellingShingle |
Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics 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 L. Houston, Ross D. 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 |
Genetics Animal Science and Zoology General Medicine Ecology, Evolution, Behavior and Systematics |
description |
Abstract Background The high fecundity of fish species allows intense selection to be practised and therefore leads to fast genetic gains. Based on this, numerous selective breeding programmes have been started in Europe in the last decades, but in general, little is known about how the base populations of breeders have been built. Such knowledge is important because base populations can be created from very few individuals, which can lead to small effective population sizes and associated reductions in genetic variability. In this study, we used genomic information that was recently made available for turbot ( Scophthalmus maximus ), gilthead seabream ( Sparus aurata ), European seabass ( Dicentrarchus labrax ) and common carp ( Cyprinus carpio ) to obtain accurate estimates of the effective size for commercial populations. Methods Restriction-site associated DNA sequencing data were used to estimate current and historical effective population sizes. We used a novel method that considers the linkage disequilibrium spectrum for the whole range of genetic distances between all pairs of single nucleotide polymorphisms (SNPs), and thus accounts for potential fluctuations in population size over time. Results Our results show that the current effective population size for these populations is small (equal to or less than 50 fish), potentially putting the sustainability of the breeding programmes at risk. We have also detected important drops in effective population size about five to nine generations ago, most likely as a result of domestication and the start of selective breeding programmes for these species in Europe. Conclusions Our findings highlight the need to broaden the genetic composition of the base populations from which selection programmes start, and suggest that measures designed to increase effective population size within all farmed populations analysed here should be implemented in order to manage genetic variability and ensure the sustainability of the breeding programmes. |
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 L. Houston, Ross D. 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 L. Houston, Ross D. 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 |
Springer Science and Business Media LLC |
publishDate |
2021 |
url |
http://dx.doi.org/10.1186/s12711-021-00680-9 https://link.springer.com/content/pdf/10.1186/s12711-021-00680-9.pdf https://link.springer.com/article/10.1186/s12711-021-00680-9/fulltext.html |
genre |
Scophthalmus maximus Turbot |
genre_facet |
Scophthalmus maximus Turbot |
op_source |
Genetics Selection Evolution volume 53, issue 1 ISSN 1297-9686 |
op_rights |
https://creativecommons.org/licenses/by/4.0 https://creativecommons.org/licenses/by/4.0 |
op_rightsnorm |
CC-BY |
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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1766189142702555136 |