Estimates of recent and historical effective population size in turbot, seabream, seabass and carp selective breeding programmes.
Journal
Genetics, selection, evolution : GSE
ISSN: 1297-9686
Titre abrégé: Genet Sel Evol
Pays: France
ID NLM: 9114088
Informations de publication
Date de publication:
06 Nov 2021
06 Nov 2021
Historique:
received:
01
02
2021
accepted:
22
10
2021
entrez:
7
11
2021
pubmed:
8
11
2021
medline:
26
11
2021
Statut:
epublish
Résumé
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. 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. 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. 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.
Sections du résumé
BACKGROUND
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
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
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
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.
Identifiants
pubmed: 34742227
doi: 10.1186/s12711-021-00680-9
pii: 10.1186/s12711-021-00680-9
pmc: PMC8572424
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
85Subventions
Organisme : Seventh Framework Programme
ID : KBBE.2013.1.2-659 10 under grant agreement n° 613611 FISHBOOST project
Organisme : Horizon 2020
ID : 727315 MedAID project
Organisme : Ministerio de Ciencia e Innovación (ES)
ID : CGL2016-75904-C2
Organisme : Xunta de Galicia (ES)
ID : ED431C 2020-05
Organisme : Ministry of Education, Youth and Sports (CZ)
ID : Project Biodiverzity (CZ.02.1.01/0.0/0.0/16_025/0007370)
Organisme : MCIN/ AEI /10.13039/501100011033
ID : PID2020-114426GB-C22
Organisme : MCIN/ AEI /10.13039/501100011033
ID : PID2020-114426GB-C2
Informations de copyright
© 2021. The Author(s).
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