Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera

Detalhes bibliográficos
Autor(a) principal: Parejo, Melanie
Data de Publicação: 2018
Outros Autores: Henriques, Dora, Pinto, M. Alice, Soland-Reckeweg, Gabriele, Neuditschko, Markus
Tipo de documento: Artigo
Idioma: eng
Título da fonte: Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
Texto Completo: http://hdl.handle.net/10198/18739
Resumo: The genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees.
id RCAP_28bb9f577a5eedcb4abd1b9fb78ed46c
oai_identifier_str oai:bibliotecadigital.ipb.pt:10198/18739
network_acronym_str RCAP
network_name_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository_id_str 7160
spelling Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera melliferaApis mellifera melliferaConservationIntrogressionMicrosatellitesSNPsThe genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees.This work was supported by the Swiss Federal Office for Agriculture FOAG, the Fondation Sur-la-Croix, Basel, and by the 2013–2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders “Fundac¸ão para a Ciência e Tecnologia” (Portugal), “Agence Nationale de la Recherche” (France), and “Ministerio de Economía y Competividad” (Spain).Biblioteca Digital do IPBParejo, MelanieHenriques, DoraPinto, M. AliceSoland-Reckeweg, GabrieleNeuditschko, Markus2018-01-19T10:00:00Z20182018-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10198/18739engParejo, Melanie; Henriques, Dora; Pinto, M. Alice; Soland-Reckeweg, Gabriele; Neuditschko, Markus (2018). Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera. Journal of Apicultural Research. ISSN 0021-8839. 57, p. 504-5060021-883910.1080/00218839.2018.1494894info:eu-repo/semantics/openAccessreponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãoinstacron:RCAAP2023-11-21T10:42:55Zoai:bibliotecadigital.ipb.pt:10198/18739Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T23:09:04.699958Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informaçãofalse
dc.title.none.fl_str_mv Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
title Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
spellingShingle Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
Parejo, Melanie
Apis mellifera mellifera
Conservation
Introgression
Microsatellites
SNPs
title_short Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
title_full Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
title_fullStr Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
title_full_unstemmed Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
title_sort Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
author Parejo, Melanie
author_facet Parejo, Melanie
Henriques, Dora
Pinto, M. Alice
Soland-Reckeweg, Gabriele
Neuditschko, Markus
author_role author
author2 Henriques, Dora
Pinto, M. Alice
Soland-Reckeweg, Gabriele
Neuditschko, Markus
author2_role author
author
author
author
dc.contributor.none.fl_str_mv Biblioteca Digital do IPB
dc.contributor.author.fl_str_mv Parejo, Melanie
Henriques, Dora
Pinto, M. Alice
Soland-Reckeweg, Gabriele
Neuditschko, Markus
dc.subject.por.fl_str_mv Apis mellifera mellifera
Conservation
Introgression
Microsatellites
SNPs
topic Apis mellifera mellifera
Conservation
Introgression
Microsatellites
SNPs
description The genetic identity of the dark European honey bee, Apis mellifera mellifera is currently under pressure throughout most of its native range due to large scale commercial trade and replacement with honey bees of mainly Eastern European ancestry (C-lineage: Apis mellifera carnica and Apis mellifera ligustica). To counteract this process, numerous conservation efforts for the protection of native honey bees are sprouting across Europe. For the management of such protected areas and conservation breeding purposes, honey bee subspecies have been routinely identified through wing morphology and through DNA-hybrid tests using microsatellite markers. Currently, new methods are evolving including rapid innovations in single-nucleotide polymorphism (SNP) array technology and high-throughput sequencing. Here, we aim to quantify potential marker-specific biases of hybrid tests and give recommendations for applications in honey bee conservation management. Using an empirical dataset, we first assessed the accuracy of a recently developed reduced SNP panel to estimate C-lineage introgression in A. m. mellifera compared to whole-genome sequence (WGS) data. Using another independent data set, we estimated the differences in admixture proportions between the currently applied hybrid test based on microsatellites and the novel SNP test. We demonstrate that the SNP-based test which contains highly ancestry-informative markers is very efficient to estimate genome-wide ancestry. Furthermore, we report discrepancies between microsatellite and SNP-based admixture proportions. For conservation management, we, therefore, recommend the implementation of SNP-based hybrid tests to maintain high genetic variation within the breeding population, while minimizing influence of introduced honey bees.
publishDate 2018
dc.date.none.fl_str_mv 2018-01-19T10:00:00Z
2018
2018-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/article
format article
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10198/18739
url http://hdl.handle.net/10198/18739
dc.language.iso.fl_str_mv eng
language eng
dc.relation.none.fl_str_mv Parejo, Melanie; Henriques, Dora; Pinto, M. Alice; Soland-Reckeweg, Gabriele; Neuditschko, Markus (2018). Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera. Journal of Apicultural Research. ISSN 0021-8839. 57, p. 504-506
0021-8839
10.1080/00218839.2018.1494894
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
instname:Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron:RCAAP
instname_str Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
instacron_str RCAAP
institution RCAAP
reponame_str Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
collection Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos)
repository.name.fl_str_mv Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) - Agência para a Sociedade do Conhecimento (UMIC) - FCT - Sociedade da Informação
repository.mail.fl_str_mv
_version_ 1799135350879158272