Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)
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...
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Frontiers Media S.A.
2018-07-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/article/10.3389/fpls.2018.00815/full |
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| author | Livia M. de Souza Luciano H. B. dos Santos João R. B. F. Rosa João R. B. F. Rosa Carla C. da Silva Camila C. Mantello Camila C. Mantello André R. O. Conson Erivaldo J. Scaloppi Josefino de F. Fialho Mario Luiz T. de Moraes Paulo de S. Gonçalves Gabriel R. A. Margarido Antonio A. F. Garcia Vincent Le Guen Anete P. de Souza Anete P. de Souza |
| author_facet | Livia M. de Souza Luciano H. B. dos Santos João R. B. F. Rosa João R. B. F. Rosa Carla C. da Silva Camila C. Mantello Camila C. Mantello André R. O. Conson Erivaldo J. Scaloppi Josefino de F. Fialho Mario Luiz T. de Moraes Paulo de S. Gonçalves Gabriel R. A. Margarido Antonio A. F. Garcia Vincent Le Guen Anete P. de Souza Anete P. de Souza |
| author_sort | Livia M. de Souza |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-12-16T08:53:59Z |
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| last_indexed | 2024-12-16T08:53:59Z |
| publishDate | 2018-07-01 |
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| spelling | doaj.art-f5a7deeb704a4dc88c0510af1b34c6762022-12-21T22:37:20ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2018-07-01910.3389/fpls.2018.00815342901Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)Livia M. de Souza0Luciano H. B. dos Santos1João R. B. F. Rosa2João R. B. F. Rosa3Carla C. da Silva4Camila C. Mantello5Camila C. Mantello6André R. O. Conson7Erivaldo J. Scaloppi8Josefino de F. Fialho9Mario Luiz T. de Moraes10Paulo de S. Gonçalves11Gabriel R. A. Margarido12Antonio A. F. Garcia13Vincent Le Guen14Anete P. de Souza15Anete P. de Souza16Center of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, BrazilCenter of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, BrazilDepartamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, BrazilFTS Sementes S.A., Research and Development Center, Ponta Grossa, BrazilCenter of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, BrazilCenter of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, BrazilThe John Bingham Laboratory, National Institute of Agricultural Botany, Cambridge, United KingdomCenter of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, BrazilCenter of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, BrazilCentro de Pesquisa Agropecuária dos Cerrados (Cpac), Embrapa Cerrados, Empresa Brazileira de Pesquisa Agropecuária, Planaltina, BrazilDepartamento de Fitotecnia, Faculdade de Engenharia de Ilha Solteira, Universidade Estadual Paulista, Ilha Solteira, BrazilCenter of Rubber Tree and Agroforestry Systems, Agronomic Institute of Campinas, Votuporanga, BrazilDepartamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, BrazilDepartamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Universidade de São Paulo, Piracicaba, BrazilCentre de Coopération Internationale en Recherche Agronomique pour le Développement, UMR AGAP, Montpellier, FranceCenter of Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, BrazilDepartment of Plant Biology, Biology Institute, University of Campinas, Campinas, BrazilAmong 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.https://www.frontiersin.org/article/10.3389/fpls.2018.00815/fulllinkage mappinggenetic diversitypopulation structurenon-random associationgenome-wide association studyHevea |
| spellingShingle | Livia M. de Souza Luciano H. B. dos Santos João R. B. F. Rosa João R. B. F. Rosa Carla C. da Silva Camila C. Mantello Camila C. Mantello André R. O. Conson Erivaldo J. Scaloppi Josefino de F. Fialho Mario Luiz T. de Moraes Paulo de S. Gonçalves Gabriel R. A. Margarido Antonio A. F. Garcia Vincent Le Guen Anete P. de Souza Anete P. de Souza Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis) Frontiers in Plant Science linkage mapping genetic diversity population structure non-random association genome-wide association study Hevea |
| title | 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_short | 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 |
| topic | linkage mapping genetic diversity population structure non-random association genome-wide association study Hevea |
| url | https://www.frontiersin.org/article/10.3389/fpls.2018.00815/full |
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