Linkage disequilibrium and population structure in wild and cultivated populations of rubber tree (Hevea brasiliensis)

de Souza Lívia Moura, dos Santos Luciano H. B., Rosa João Ricardo Bachega Feijó, Da Silva Carla Cristina, Mantello Camilia Campos, Conson Andre R.O., Scaloppi Junior Erivaldo José, Fialho Josefino de F., de Moraes Mario Luiz T., Gonçalves Paulo De Souza, Margarido Gabriel R. A., Garcia Antonio Augusto Franco, Le Guen Vincent, de Souza Anete Pereira. 2018. Linkage disequilibrium and population structure in wild and cultivated populations of rubber tree (Hevea brasiliensis). Frontiers in Plant Science, 9:815, 10 p.

Journal article ; Article de recherche ; Article de revue à facteur d'impact Revue en libre accès total
Published version - Anglais
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Quartile : Q1, Sujet : PLANT SCIENCES

Abstract : Among rubber tree species, which belong to the Hevea genus of the Euphorbiaceae family, Hevea brasiliensis (Willd. ex 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.

Mots-clés Agrovoc : Hevea brasiliensis, Ressource génétique, Génotype, Polymorphisme génétique, Marqueur génétique, Carte génétique

Mots-clés géographiques Agrovoc : Brésil

Classification Agris : F30 - Plant genetics and breeding
K10 - Forestry production
F01 - Crops

Champ stratégique Cirad : Axe 1 (2014-2018) - Agriculture écologiquement intensive

Auteurs et affiliations

  • de Souza Lívia Moura, UNICAMP (BRA)
  • dos Santos Luciano H. B., UNICAMP (BRA)
  • Rosa João Ricardo Bachega Feijó, Universidade de São Paulo (BRA)
  • Da Silva Carla Cristina, UNICAMP (BRA)
  • Mantello Camilia Campos, UNICAMP (BRA)
  • Conson Andre R.O., UNICAMP (BRA)
  • Scaloppi Junior Erivaldo José, IAC (BRA)
  • Fialho Josefino de F., IAC (BRA)
  • de Moraes Mario Luiz T., UNESP (BRA)
  • Gonçalves Paulo De Souza, IAC (BRA)
  • Margarido Gabriel R. A., Universidade de São Paulo (BRA)
  • Garcia Antonio Augusto Franco, Universidade de São Paulo (BRA)
  • Le Guen Vincent, CIRAD-BIOS-UMR AGAP (FRA)
  • de Souza Anete Pereira, UNICAMP (BRA) - auteur correspondant

Source : Cirad-Agritrop (

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