High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool
Autor(a) principal: | |
---|---|
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/1822/65925 |
Resumo: | The natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation of introgression levels to more effectively monitor and manage A. m. mellifera conservatories. |
id |
RCAP_018e79dadf13f7b37f09e8bae8a424d7 |
---|---|
oai_identifier_str |
oai:repositorium.sdum.uminho.pt:1822/65925 |
network_acronym_str |
RCAP |
network_name_str |
Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
repository_id_str |
7160 |
spelling |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based toolAnimalsBeesGenotyping TechniquesOligonucleotide Array Sequence AnalysisDiploidyHaploidyPolymorphism, Single NucleotideScience & TechnologyThe natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation of introgression levels to more effectively monitor and manage A. m. mellifera conservatories.We are deeply indebted to Joao Costa (Instituto Gulbenkian Ciencia, Oeiras, Portugal), for designing the multiplexes and SNP genotyping. Jose Rufino provided computational resources at the Polytechnic Institute of Braganca, Portugal. DH was supported by a PhD scholarship (SFRH/BD/84195/2012) from the Portuguese Science Foundation (FCT). KAB receives a PhD fellowship from the Irish Research Council. MP was supported by the Swiss Federal Office for Agriculture FOAG and the Fondation Sur-la-Croix, Basel. IM was supported by Saavedra Fajardo fellowship from the Fundacion Seneca (20036/SF/16). MAP is a member of and receives support from the COST Action FA1307 (SUPER-B). Funding for genotyping of Irish honeybees was gratefully received from the Eva Crane Trust, the Native Irish Honeybee Society and the Department of Agriculture, Food and the Marine (16/GR/09). MB and TCF are funded by an Institute Strategic Grant from the Biotechnology and Biological Sciences Research Council (BBSRC) (BB/JO1446X/1). Financial support for this research was provided to MAP and LG by 2013-2014 BiodivERsA/FACCE-JPI joint call for research proposals, with the national funders FCT (Portugal), "Agence Nationale de la Recherche" (France), and "Ministerio de Economia y Competividade" (Spain).Nature ResearchUniversidade do MinhoHenriques, DoraBrowne, Keith ABarnett, Mark WParejo, MelanieKryger, PerFreeman, Tom CMuñoz, IreneGarnery, LionelHighet, FionaJonhston, J SpencerMcCormack, Grace PPinto, M. Alice20182018-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/1822/65925engHenriques, D., Browne, K.A., Barnett, M.W. et al. High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool. Sci Rep 8, 8552 (2018). https://doi.org/10.1038/s41598-018-26932-12045-232210.1038/s41598-018-26932-129867207https://www.nature.com/articles/s41598-018-26932-1.pdfinfo: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:RCAAP2023-07-21T12:18:02Zoai:repositorium.sdum.uminho.pt:1822/65925Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T19:10:45.091487Repositório 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 |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
title |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
spellingShingle |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool Henriques, Dora Animals Bees Genotyping Techniques Oligonucleotide Array Sequence Analysis Diploidy Haploidy Polymorphism, Single Nucleotide Science & Technology |
title_short |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
title_full |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
title_fullStr |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
title_full_unstemmed |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
title_sort |
High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool |
author |
Henriques, Dora |
author_facet |
Henriques, Dora Browne, Keith A Barnett, Mark W Parejo, Melanie Kryger, Per Freeman, Tom C Muñoz, Irene Garnery, Lionel Highet, Fiona Jonhston, J Spencer McCormack, Grace P Pinto, M. Alice |
author_role |
author |
author2 |
Browne, Keith A Barnett, Mark W Parejo, Melanie Kryger, Per Freeman, Tom C Muñoz, Irene Garnery, Lionel Highet, Fiona Jonhston, J Spencer McCormack, Grace P Pinto, M. Alice |
author2_role |
author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade do Minho |
dc.contributor.author.fl_str_mv |
Henriques, Dora Browne, Keith A Barnett, Mark W Parejo, Melanie Kryger, Per Freeman, Tom C Muñoz, Irene Garnery, Lionel Highet, Fiona Jonhston, J Spencer McCormack, Grace P Pinto, M. Alice |
dc.subject.por.fl_str_mv |
Animals Bees Genotyping Techniques Oligonucleotide Array Sequence Analysis Diploidy Haploidy Polymorphism, Single Nucleotide Science & Technology |
topic |
Animals Bees Genotyping Techniques Oligonucleotide Array Sequence Analysis Diploidy Haploidy Polymorphism, Single Nucleotide Science & Technology |
description |
The natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation of introgression levels to more effectively monitor and manage A. m. mellifera conservatories. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
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/1822/65925 |
url |
http://hdl.handle.net/1822/65925 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Henriques, D., Browne, K.A., Barnett, M.W. et al. High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool. Sci Rep 8, 8552 (2018). https://doi.org/10.1038/s41598-018-26932-1 2045-2322 10.1038/s41598-018-26932-1 29867207 https://www.nature.com/articles/s41598-018-26932-1.pdf |
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.publisher.none.fl_str_mv |
Nature Research |
publisher.none.fl_str_mv |
Nature Research |
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_ |
1799132538198818816 |