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...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	María Saura, Armando Caballero, Enrique Santiago, Almudena Fernández, Elisabeth Morales-González, Jesús Fernández, Santiago Cabaleiro, Adrián Millán, Paulino Martínez, Christos Palaiokostas, Martin Kocour, Muhammad L. Aslam, Ross D. Houston, Martin Prchal, Luca Bargelloni, Kostas Tzokas, Pierrick Haffray, Jean-Sebastien Bruant, Beatriz Villanueva
Formato:	article
Lenguaje:	DE EN FR
Publicado:	BMC 2021
Materias:	Animal culture SF1-1100 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/a92bcc0ea4f1472ab5d47c96962872db
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:a92bcc0ea4f1472ab5d47c96962872db
record_format	dspace
spelling	oai:doaj.org-article:a92bcc0ea4f1472ab5d47c96962872db2021-11-08T10:58:32ZEstimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes10.1186/s12711-021-00680-91297-9686https://doaj.org/article/a92bcc0ea4f1472ab5d47c96962872db2021-11-01T00:00:00Zhttps://doi.org/10.1186/s12711-021-00680-9https://doaj.org/toc/1297-9686Abstract 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.María SauraArmando CaballeroEnrique SantiagoAlmudena FernándezElisabeth Morales-GonzálezJesús FernándezSantiago CabaleiroAdrián MillánPaulino MartínezChristos PalaiokostasMartin KocourMuhammad L. AslamRoss D. HoustonMartin PrchalLuca BargelloniKostas TzokasPierrick HaffrayJean-Sebastien BruantBeatriz VillanuevaBMCarticleAnimal cultureSF1-1100GeneticsQH426-470DEENFRGenetics Selection Evolution, Vol 53, Iss 1, Pp 1-8 (2021)
institution	DOAJ
collection	DOAJ
language	DE EN FR
topic	Animal culture SF1-1100 Genetics QH426-470
spellingShingle	Animal culture SF1-1100 Genetics QH426-470 María Saura Armando Caballero Enrique Santiago Almudena Fernández Elisabeth Morales-González Jesús Fernández Santiago Cabaleiro Adrián Millán Paulino Martínez Christos Palaiokostas Martin Kocour Muhammad L. Aslam Ross D. Houston Martin Prchal Luca Bargelloni Kostas Tzokas Pierrick Haffray Jean-Sebastien Bruant Beatriz Villanueva Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes
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
author	María Saura Armando Caballero Enrique Santiago Almudena Fernández Elisabeth Morales-González Jesús Fernández Santiago Cabaleiro Adrián Millán Paulino Martínez Christos Palaiokostas Martin Kocour Muhammad L. Aslam Ross D. Houston Martin Prchal Luca Bargelloni Kostas Tzokas Pierrick Haffray Jean-Sebastien Bruant Beatriz Villanueva
author_facet	María Saura Armando Caballero Enrique Santiago Almudena Fernández Elisabeth Morales-González Jesús Fernández Santiago Cabaleiro Adrián Millán Paulino Martínez Christos Palaiokostas Martin Kocour Muhammad L. Aslam Ross D. Houston Martin Prchal Luca Bargelloni Kostas Tzokas Pierrick Haffray Jean-Sebastien Bruant Beatriz Villanueva
author_sort	María Saura
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	BMC
publishDate	2021
url	https://doaj.org/article/a92bcc0ea4f1472ab5d47c96962872db
work_keys_str_mv	AT mariasaura estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT armandocaballero estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT enriquesantiago estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT almudenafernandez estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT elisabethmoralesgonzalez estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT jesusfernandez estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT santiagocabaleiro estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT adrianmillan estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT paulinomartinez estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT christospalaiokostas estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT martinkocour estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT muhammadlaslam estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT rossdhouston estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT martinprchal estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT lucabargelloni estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT kostastzokas estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT pierrickhaffray estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT jeansebastienbruant estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes AT beatrizvillanueva estimatesofrecentandhistoricaleffectivepopulationsizeinturbotseabreamseabassandcarpselectivebreedingprogrammes
_version_	1718442455277240320

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

Ejemplares similares