Linkage Disequilibrium and Population Structure in Wild and Cultivated Populations of Rubber Tree (Hevea brasiliensis)

Author(s):Show less -

de Souza, Livia M. ^{[1, 2]} ; dos Santos, Luciano H. B. ^{[1, 2]} ; Rosa, Joao R. B. F. ^{[3, 4]} ; da Silva, Carla C. ^{[1, 2]} ; Mantello, Camila C. ^{[1, 2, 5]} ; Conson, Andre R. O. ^{[1, 2]} ; Scaloppi, Jr., Erivaldo J. ^[6] ; Fialho, Josefino de F. ^[7] ; de Moraes, Mario Luiz T. ^[8] ; Goncalves, Paulo de S. ^[6] ; Margarido, Gabriel R. A. ^[3] ; Garcia, Antonio A. F. ^[3] ; Le Guen, Vincent ^[9] ; de Souza, Anete P. ^{[1, 2, 10]}

Affiliation

^[1] Univ Estadual Campinas, Ctr Mol Biol, Campinas, SP - Brazil

^[2] Univ Estadual Campinas, Genet Engn Ctr, Campinas, SP - Brazil

^[3] Univ Sao Paulo, Escola Super Agr Luiz de Queiroz, Dept Genet, Piracicaba - Brazil

^[4] FTS Sementes SA, Res & Dev Ctr, Ponta Grossa - Brazil

^[5] Natl Inst Agr Bot, John Bingham Lab, Cambridge - England

^[6] Agron Inst Campinas, Ctr Rubber Tree & Agroforestry Syst, Votuporanga - Brazil

^[7] Empresa Brazileira Pesquisa Agr, Embrapa Cerrados, Cpac, Planaltina - Brazil

^[8] Univ Estadual Paulista, Facu Engn Ilha Solteira, Dept Fitotecnia, Ilha Solteira - Brazil

^[9] Ctr Cooperat Int Rech Agron Dev, UMR AGAP, Montpellier - France

^[10] Univ Estadual Campinas, Dept Plant Biol, Biol Inst, Campinas, SP - Brazil

• Document type: Journal article
• Source: FRONTIERS IN PLANT SCIENCE; v. 9, JUL 3 2018.
• Web of Science Citations: 1

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. (AU)

• FAPESP's process: 12/50491-8 - Evaluation of allelic variability, population structure and linkage desequilibrium in the rubber tree ex situ germoplasm (Hevea brasiliensis)
• Grantee: Anete Pereira de Souza
• Support Opportunities: Regular Research Grants
• FAPESP's process: 14/11807-5 - Use of genotyping-by-sequencing (GBS) for the identification of molecular markers SNP (single nucleotide polymorphism) and construction of the linkage map in Hevea brasiliensis
• Grantee: Luciano Henrique Braz dos Santos
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 17/07908-9 - Genetic and genomic analysis in the Hevea genus aiming to contribute to the genetic improvement of Hevea brasiliensis
• Grantee: Luciano Henrique Braz dos Santos
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)
• FAPESP's process: 14/18755-0 - Analysis of RNA expression profiling by RNA-seq in rubber tree and identification of the genes involved in the response to cold
• Grantee: Camila Campos Mantello
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• FAPESP's process: 12/05473-1 - Evaluation of the linkage desequilibrium and population structure in rubber tree ex situ germplasm (Hevea brasiliensis) using SNPs (Single Nucleotide Polymorphism)
• Grantee: Livia Moura de Souza
• Support Opportunities: Scholarships in Brazil - Post-Doctoral