Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)
Autor(a) principal: | |
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Data de Publicação: | 2018 |
Outros Autores: | , , , , , , , , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.3389/fpls.2018.00815 http://hdl.handle.net/11449/164372 |
Resumo: | Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation. |
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Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)linkage mappinggenetic diversitypopulation structurenon-random associationgenome-wide association studyHeveaAmong rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation.Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Univ Estadual Campinas, Ctr Mol Biol, Campinas, SP, BrazilUniv Estadual Campinas, Genet Engn Ctr, Campinas, SP, BrazilUniv Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, Piracicaba, BrazilFTS Sementes SA, Res & Dev Ctr, Ponta Grossa, BrazilNatl Inst Agr Bot, John Bingham Lab, Cambridge, EnglandAgron Inst Campinas, Ctr Rubber Tree & Agroforestry Syst, Votuporanga, BrazilEmpresa Brazileira Pesquisa Agr, Embrapa Cerrados, Cpac, Planaltina, BrazilUniv Estadual Paulista, Facu Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, BrazilCtr Cooperat Int Rech Agron Dev, UMR AGAP, Montpellier, FranceUniv Estadual Campinas, Dept Plant Biol, Biol Inst, Campinas, SP, BrazilUniv Estadual Paulista, Facu Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, BrazilFAPESP: 2007/50392-1FAPESP: 2012/50491-8FAPESP: 2011/50188-0FAPESP: 2014/18755-0FAPESP: 2009/52975-0FAPESP: 2014/11807-5FAPESP: 2017/07908-9FAPESP: 2012/05473-1CNPq: 478701/2012-8CNPq: 402954/2012-2Frontiers Media SaUniversidade Estadual de Campinas (UNICAMP)Universidade de São Paulo (USP)FTS Sementes SANatl Inst Agr BotAgron Inst CampinasEmpresa Brasileira de Pesquisa Agropecuária (EMBRAPA)Universidade Estadual Paulista (Unesp)Ctr Cooperat Int Rech Agron DevSouza, Livia M. deSantos, Luciano H. B. dosRosa, Joao R. B. F.Silva, Carla C. daMantello, Camila C.Conson, Andre R. O.Scaloppi, Erivaldo J.Fialho, Josefino de F.Moraes, Mario Luiz T. de [UNESP]Goncalves, Paulo de S.Margarido, Gabriel R. A.Garcia, Antonio A. F.Le Guen, VincentSouza, Anete P. de2018-11-26T17:54:17Z2018-11-26T17:54:17Z2018-07-03info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article10application/pdfhttp://dx.doi.org/10.3389/fpls.2018.00815Frontiers In Plant Science. Lausanne: Frontiers Media Sa, v. 9, 10 p., 2018.1664-462Xhttp://hdl.handle.net/11449/16437210.3389/fpls.2018.00815WOS:000437122100001WOS000437122100001.pdfWeb of Sciencereponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengFrontiers In Plant Scienceinfo:eu-repo/semantics/openAccess2023-10-21T06:04:44Zoai:repositorio.unesp.br:11449/164372Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462023-10-21T06:04:44Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
title |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
spellingShingle |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) Souza, Livia M. de linkage mapping genetic diversity population structure non-random association genome-wide association study Hevea |
title_short |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
title_full |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
title_fullStr |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
title_full_unstemmed |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
title_sort |
Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) |
author |
Souza, Livia M. de |
author_facet |
Souza, Livia M. de Santos, Luciano H. B. dos Rosa, Joao R. B. F. Silva, Carla C. da Mantello, Camila C. Conson, Andre R. O. Scaloppi, Erivaldo J. Fialho, Josefino de F. Moraes, Mario Luiz T. de [UNESP] Goncalves, Paulo de S. Margarido, Gabriel R. A. Garcia, Antonio A. F. Le Guen, Vincent Souza, Anete P. de |
author_role |
author |
author2 |
Santos, Luciano H. B. dos Rosa, Joao R. B. F. Silva, Carla C. da Mantello, Camila C. Conson, Andre R. O. Scaloppi, Erivaldo J. Fialho, Josefino de F. Moraes, Mario Luiz T. de [UNESP] Goncalves, Paulo de S. Margarido, Gabriel R. A. Garcia, Antonio A. F. Le Guen, Vincent Souza, Anete P. de |
author2_role |
author author author author author author author author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual de Campinas (UNICAMP) Universidade de São Paulo (USP) FTS Sementes SA Natl Inst Agr Bot Agron Inst Campinas Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Universidade Estadual Paulista (Unesp) Ctr Cooperat Int Rech Agron Dev |
dc.contributor.author.fl_str_mv |
Souza, Livia M. de Santos, Luciano H. B. dos Rosa, Joao R. B. F. Silva, Carla C. da Mantello, Camila C. Conson, Andre R. O. Scaloppi, Erivaldo J. Fialho, Josefino de F. Moraes, Mario Luiz T. de [UNESP] Goncalves, Paulo de S. Margarido, Gabriel R. A. Garcia, Antonio A. F. Le Guen, Vincent Souza, Anete P. de |
dc.subject.por.fl_str_mv |
linkage mapping genetic diversity population structure non-random association genome-wide association study Hevea |
topic |
linkage mapping genetic diversity population structure non-random association genome-wide association study Hevea |
description |
Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg. is the main commercial source of natural rubber production worldwide. Knowledge of the population structure and linkage disequilibrium (LD) of this species is essential for the efficient organization and exploitation of genetic resources. Here, we obtained single-nucleotide polymorphisms (SNPs) using a genotyping-by-sequencing (GBS) approach and then employed the SNPs for the following objectives: (i) to identify the positions of SNPs on a genetic map of a segregating mapping population, (ii) to evaluate the population structure of a germplasm collection, and (iii) to detect patterns of LD decay among chromosomes for future genetic association studies in rubber tree. A total of 626 genotypes, including both germplasm accessions (368) and individuals from a genetic mapping population (254), were genotyped. A total of 77,660 and 21,283 SNPs were detected by GBS in the germplasm and mapping populations, respectively. The mapping population, which was previously mapped, was constructed with 1,062 markers, among which only 576 SNPs came from GBS, reducing the average interval between two adjacent markers to 4.4 cM. SNPs from GBS genotyping were used for the analysis of genetic structure and LD estimation in the germplasm accessions. Two groups, which largely corresponded to the cultivated and wild populations, were detected using STRUCTURE and via principal coordinate analysis. LD analysis, also using the mapped SNPs, revealed that non-random associations varied along chromosomes, with regions of high LD interspersed with regions of low LD. Considering the length of the genetic map (4,693 cM) and the mean LD (0.49 for cultivated and 0.02 for wild populations), a large number of evenly spaced SNPs would be needed to perform genome-wide association studies in rubber tree, and the wilder the genotypes used, the more difficult the mapping saturation. |
publishDate |
2018 |
dc.date.none.fl_str_mv |
2018-11-26T17:54:17Z 2018-11-26T17:54:17Z 2018-07-03 |
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://dx.doi.org/10.3389/fpls.2018.00815 Frontiers In Plant Science. Lausanne: Frontiers Media Sa, v. 9, 10 p., 2018. 1664-462X http://hdl.handle.net/11449/164372 10.3389/fpls.2018.00815 WOS:000437122100001 WOS000437122100001.pdf |
url |
http://dx.doi.org/10.3389/fpls.2018.00815 http://hdl.handle.net/11449/164372 |
identifier_str_mv |
Frontiers In Plant Science. Lausanne: Frontiers Media Sa, v. 9, 10 p., 2018. 1664-462X 10.3389/fpls.2018.00815 WOS:000437122100001 WOS000437122100001.pdf |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Frontiers In Plant Science |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
10 application/pdf |
dc.publisher.none.fl_str_mv |
Frontiers Media Sa |
publisher.none.fl_str_mv |
Frontiers Media Sa |
dc.source.none.fl_str_mv |
Web of Science reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
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