Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population
Autor(a) principal: | |
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Data de Publicação: | 2022 |
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/10451/55813 |
Resumo: | Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak. |
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Repositório Científico de Acesso Aberto de Portugal (Repositórios Cientìficos) |
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spelling |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) PopulationCork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak.MDPIRepositório da Universidade de LisboaMendes, BrunaSampaio, TeresaAntunes, MartaMagalhães, HugoCosta e Silva, FilipeBorges, CarlaSimões, FernandaUsié, AnaAlmeida, Maria HelenaRamos, António Marcos2023-01-10T20:19:07Z2022-022022-02-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttp://hdl.handle.net/10451/55813engMendes, B.; Sampaio, T.; Antunes, M.A.; Magalhães, H.; Costa e Silva, F.; Borges, C.; Simões, F.; Usié, A.; Almeida, M.H.; Ramos, A.M. Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population. Forests 2022, 13, 226. https://doi.org/10.3390/f1302022610.3390/f13020226info: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:RCAAP2023-11-08T17:02:58Zoai:repositorio.ul.pt:10451/55813Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireopendoar:71602024-03-19T22:06:22.908428Repositório 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 |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
title |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
spellingShingle |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population Mendes, Bruna |
title_short |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
title_full |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
title_fullStr |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
title_full_unstemmed |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
title_sort |
Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population |
author |
Mendes, Bruna |
author_facet |
Mendes, Bruna Sampaio, Teresa Antunes, Marta Magalhães, Hugo Costa e Silva, Filipe Borges, Carla Simões, Fernanda Usié, Ana Almeida, Maria Helena Ramos, António Marcos |
author_role |
author |
author2 |
Sampaio, Teresa Antunes, Marta Magalhães, Hugo Costa e Silva, Filipe Borges, Carla Simões, Fernanda Usié, Ana Almeida, Maria Helena Ramos, António Marcos |
author2_role |
author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Repositório da Universidade de Lisboa |
dc.contributor.author.fl_str_mv |
Mendes, Bruna Sampaio, Teresa Antunes, Marta Magalhães, Hugo Costa e Silva, Filipe Borges, Carla Simões, Fernanda Usié, Ana Almeida, Maria Helena Ramos, António Marcos |
description |
Cork oak (Quercus suber L.) is a valuable forest species in the western Mediterranean Basin due to its ecological value and the production of cork (a renewable natural material). Cork quality depends on the genetic background and cork oak environment, which has long been recognized. As no cork oak genetic trials with pedigree information were available, the inference of the genetic relatedness between individuals from molecular markers can potentially be applied to natural populations. This work aimed to investigate the potential of performing kinship prediction and pedigree reconstruction by SNP genotyping a natural cork oak population. A total of 494 trees located in Portugal were genotyped with 8K SNPs. The raw SNP set was filtered differently, producing four SNP sets that were further filtered by missing data, genotype frequency, and minor allele frequency. For each set, an identity by descent (IBD) matrix was generated to perform the relationship prediction, revealing from 22,114 to 23,859 relationships. Familial categories from the first to the third degree were able to be assigned. The feasibility of SNP genotyping for future studies on the kinship analysis and pedigree reconstruction of cork oak populations was demonstrated. The information produced may be used in further breeding and conservation programs for cork oak. |
publishDate |
2022 |
dc.date.none.fl_str_mv |
2022-02 2022-02-01T00:00:00Z 2023-01-10T20:19:07Z |
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/10451/55813 |
url |
http://hdl.handle.net/10451/55813 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Mendes, B.; Sampaio, T.; Antunes, M.A.; Magalhães, H.; Costa e Silva, F.; Borges, C.; Simões, F.; Usié, A.; Almeida, M.H.; Ramos, A.M. Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population. Forests 2022, 13, 226. https://doi.org/10.3390/f13020226 10.3390/f13020226 |
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 |
MDPI |
publisher.none.fl_str_mv |
MDPI |
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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