Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)
dc.contributor.author | Souza, Livia M. de | |
dc.contributor.author | Santos, Luciano H. B. dos | |
dc.contributor.author | Rosa, Joao R. B. F. | |
dc.contributor.author | Silva, Carla C. da | |
dc.contributor.author | Mantello, Camila C. | |
dc.contributor.author | Conson, Andre R. O. | |
dc.contributor.author | Scaloppi, Erivaldo J. | |
dc.contributor.author | Fialho, Josefino de F. | |
dc.contributor.author | Moraes, Mario Luiz T. de [UNESP] | |
dc.contributor.author | Goncalves, Paulo de S. | |
dc.contributor.author | Margarido, Gabriel R. A. | |
dc.contributor.author | Garcia, Antonio A. F. | |
dc.contributor.author | Le Guen, Vincent | |
dc.contributor.author | Souza, Anete P. de | |
dc.contributor.institution | Universidade Estadual de Campinas (UNICAMP) | |
dc.contributor.institution | Universidade de São Paulo (USP) | |
dc.contributor.institution | FTS Sementes SA | |
dc.contributor.institution | Natl Inst Agr Bot | |
dc.contributor.institution | Agron Inst Campinas | |
dc.contributor.institution | Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) | |
dc.contributor.institution | Universidade Estadual Paulista (Unesp) | |
dc.contributor.institution | Ctr Cooperat Int Rech Agron Dev | |
dc.date.accessioned | 2018-11-26T17:54:17Z | |
dc.date.available | 2018-11-26T17:54:17Z | |
dc.date.issued | 2018-07-03 | |
dc.description.abstract | 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. | en |
dc.description.affiliation | Univ Estadual Campinas, Ctr Mol Biol, Campinas, SP, Brazil | |
dc.description.affiliation | Univ Estadual Campinas, Genet Engn Ctr, Campinas, SP, Brazil | |
dc.description.affiliation | Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, Piracicaba, Brazil | |
dc.description.affiliation | FTS Sementes SA, Res & Dev Ctr, Ponta Grossa, Brazil | |
dc.description.affiliation | Natl Inst Agr Bot, John Bingham Lab, Cambridge, England | |
dc.description.affiliation | Agron Inst Campinas, Ctr Rubber Tree & Agroforestry Syst, Votuporanga, Brazil | |
dc.description.affiliation | Empresa Brazileira Pesquisa Agr, Embrapa Cerrados, Cpac, Planaltina, Brazil | |
dc.description.affiliation | Univ Estadual Paulista, Facu Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, Brazil | |
dc.description.affiliation | Ctr Cooperat Int Rech Agron Dev, UMR AGAP, Montpellier, France | |
dc.description.affiliation | Univ Estadual Campinas, Dept Plant Biol, Biol Inst, Campinas, SP, Brazil | |
dc.description.affiliationUnesp | Univ Estadual Paulista, Facu Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira, Brazil | |
dc.description.sponsorship | Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) | |
dc.description.sponsorship | Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) | |
dc.description.sponsorship | Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) | |
dc.description.sponsorshipId | FAPESP: 2007/50392-1 | |
dc.description.sponsorshipId | FAPESP: 2012/50491-8 | |
dc.description.sponsorshipId | FAPESP: 2011/50188-0 | |
dc.description.sponsorshipId | FAPESP: 2014/18755-0 | |
dc.description.sponsorshipId | FAPESP: 2009/52975-0 | |
dc.description.sponsorshipId | FAPESP: 2014/11807-5 | |
dc.description.sponsorshipId | FAPESP: 2017/07908-9 | |
dc.description.sponsorshipId | FAPESP: 2012/05473-1 | |
dc.description.sponsorshipId | CNPq: 478701/2012-8 | |
dc.description.sponsorshipId | CNPq: 402954/2012-2 | |
dc.format.extent | 10 | |
dc.identifier | http://dx.doi.org/10.3389/fpls.2018.00815 | |
dc.identifier.citation | Frontiers In Plant Science. Lausanne: Frontiers Media Sa, v. 9, 10 p., 2018. | |
dc.identifier.doi | 10.3389/fpls.2018.00815 | |
dc.identifier.file | WOS000437122100001.pdf | |
dc.identifier.issn | 1664-462X | |
dc.identifier.uri | http://hdl.handle.net/11449/164372 | |
dc.identifier.wos | WOS:000437122100001 | |
dc.language.iso | eng | |
dc.publisher | Frontiers Media Sa | |
dc.relation.ispartof | Frontiers In Plant Science | |
dc.rights.accessRights | Acesso aberto | |
dc.source | Web of Science | |
dc.subject | linkage mapping | |
dc.subject | genetic diversity | |
dc.subject | population structure | |
dc.subject | non-random association | |
dc.subject | genome-wide association study | |
dc.subject | Hevea | |
dc.title | Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) | en |
dc.type | Artigo | |
dcterms.rightsHolder | Frontiers Media Sa | |
unesp.department | Fitotecnia, Tecnologia de Alimentos e Socioeconomia - FEIS | pt |
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