Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) Population

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 g...

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Autores: Mendes, Bruna, Sampaio, Teresa, Antunes, Marta A., Magalhães, Hugo, Costa e Silva, Filipe, Borges, Carla, Simões, Fernanda, Usié Chimenos, Anabel, Almeida, Maria Helena, Marcos Ramos, António
Tipo de recurso: artículo
Estado:Versión publicada
Fecha de publicación:2022
País:España
Institución:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
Repositorio:Recercat. Dipósit de la Recerca de Catalunya
OAI Identifier:oai:recercat.cat:10459.1/469072
Acceso en línea:https://doi.org/10.3390/f13020226
https://hdl.handle.net/10459.1/469072
http://hdl.handle.net/10459.1/469072
Access Level:acceso abierto
Palabra clave:Cork oak
Pedigree reconstruction
SNP
Kinship
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spelling Kinship Analysis and Pedigree Reconstruction of a Natural Regenerated Cork Oak (Quercus suber) PopulationMendes, BrunaSampaio, TeresaAntunes, Marta A.Magalhães, HugoCosta e Silva, FilipeBorges, CarlaSimões, FernandaUsié Chimenos, AnabelAlmeida, Maria HelenaMarcos Ramos, AntónioCork oakPedigree reconstructionSNPKinshipCork 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.MDPI2022info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttps://doi.org/10.3390/f13020226https://hdl.handle.net/10459.1/469072http://hdl.handle.net/10459.1/469072reponame:Recercat. Dipósit de la Recerca de Catalunyainstname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)InglésReproducció del document publicat a https://doi.org/10.3390/f13020226Forests, 2022, vol. 13, núm. 2, 226cc-by, (c) Bruna Mendes et al., 2022Attribution 4.0 Internationalinfo:eu-repo/semantics/openAccesshttp://creativecommons.org/licenses/by/4.0/oai:recercat.cat:10459.1/4690722026-05-29T05:05:01Z
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
Cork oak
Pedigree reconstruction
SNP
Kinship
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
dc.creator.none.fl_str_mv Mendes, Bruna
Sampaio, Teresa
Antunes, Marta A.
Magalhães, Hugo
Costa e Silva, Filipe
Borges, Carla
Simões, Fernanda
Usié Chimenos, Anabel
Almeida, Maria Helena
Marcos Ramos, António
author Mendes, Bruna
author_facet Mendes, Bruna
Sampaio, Teresa
Antunes, Marta A.
Magalhães, Hugo
Costa e Silva, Filipe
Borges, Carla
Simões, Fernanda
Usié Chimenos, Anabel
Almeida, Maria Helena
Marcos Ramos, António
author_role author
author2 Sampaio, Teresa
Antunes, Marta A.
Magalhães, Hugo
Costa e Silva, Filipe
Borges, Carla
Simões, Fernanda
Usié Chimenos, Anabel
Almeida, Maria Helena
Marcos Ramos, António
author2_role author
author
author
author
author
author
author
author
author
dc.subject.none.fl_str_mv Cork oak
Pedigree reconstruction
SNP
Kinship
topic Cork oak
Pedigree reconstruction
SNP
Kinship
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
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://doi.org/10.3390/f13020226
https://hdl.handle.net/10459.1/469072
http://hdl.handle.net/10459.1/469072
url https://doi.org/10.3390/f13020226
https://hdl.handle.net/10459.1/469072
http://hdl.handle.net/10459.1/469072
dc.language.none.fl_str_mv Inglés
language_invalid_str_mv Inglés
dc.relation.none.fl_str_mv Reproducció del document publicat a https://doi.org/10.3390/f13020226
Forests, 2022, vol. 13, núm. 2, 226
dc.rights.none.fl_str_mv cc-by, (c) Bruna Mendes et al., 2022
Attribution 4.0 International
info:eu-repo/semantics/openAccess
http://creativecommons.org/licenses/by/4.0/
rights_invalid_str_mv cc-by, (c) Bruna Mendes et al., 2022
Attribution 4.0 International
http://creativecommons.org/licenses/by/4.0/
eu_rights_str_mv openAccess
dc.publisher.none.fl_str_mv MDPI
publisher.none.fl_str_mv MDPI
dc.source.none.fl_str_mv reponame:Recercat. Dipósit de la Recerca de Catalunya
instname:Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
instname_str Varias* (Consorci de Biblioteques Universitáries de Catalunya, Centre de Serveis Científics i Acadèmics de Catalunya)
reponame_str Recercat. Dipósit de la Recerca de Catalunya
collection Recercat. Dipósit de la Recerca de Catalunya
repository.name.fl_str_mv
repository.mail.fl_str_mv
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