Empirical comparison of microsatellite and SNP markers to estimate introgression in Apis mellifera mellifera
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , |
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. |
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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 |
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1799135350879158272 |