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Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection.

de Souza LM, Le Guen V, Cerqueira-Silva CB, Silva CC, Mantello CC, Conson AR, Vianna JP, Zucchi MI, Scaloppi Junior EJ, Fialho Jde F, de Moraes ML, Gonçalves Pde S, Souza AP - PLoS ONE (2015)

Bottom Line: The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018.Rubber tree breeders can effectively utilize this core collection for cultivar improvement.Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.

ABSTRACT
The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.

No MeSH data available.


Related in: MedlinePlus

Genetic structure of the Hevea germplasm accessions.The genetic structure was inferred through Bayesian analyses of the most probable number of groups (K) estimated based on the mean log probability [A] using the method described by Evanno et al. (2005) [B]. Each column (histogram) [C] represents the genotyping data from one accession, and the colors used in the histogram represent the most likely ancestry of the cluster from which the accessions were derived.
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pone.0134607.g003: Genetic structure of the Hevea germplasm accessions.The genetic structure was inferred through Bayesian analyses of the most probable number of groups (K) estimated based on the mean log probability [A] using the method described by Evanno et al. (2005) [B]. Each column (histogram) [C] represents the genotyping data from one accession, and the colors used in the histogram represent the most likely ancestry of the cluster from which the accessions were derived.

Mentions: To examine the relatedness among the 1,117 accessions, the data for 13 markers were analyzed using the STRUCTURE program. A strict interpretation of our results using the method of Evanno et al. (2005) suggested that two genetic clusters (K = 2) were sufficient to interpret our data (Fig 3A and 3B); the results are also presented as K = 3 and K = 7 in S3 Fig. Based on a membership probability threshold of 0.70, 277 accessions were assigned to cluster 1 and 783 accessions were assigned to cluster 2. The remaining 57 accessions were classified into a mixed subgroup. The membership probability was <0.70 in any given subgroup (Table 3).


Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a 100-Genotype Core Collection.

de Souza LM, Le Guen V, Cerqueira-Silva CB, Silva CC, Mantello CC, Conson AR, Vianna JP, Zucchi MI, Scaloppi Junior EJ, Fialho Jde F, de Moraes ML, Gonçalves Pde S, Souza AP - PLoS ONE (2015)

Genetic structure of the Hevea germplasm accessions.The genetic structure was inferred through Bayesian analyses of the most probable number of groups (K) estimated based on the mean log probability [A] using the method described by Evanno et al. (2005) [B]. Each column (histogram) [C] represents the genotyping data from one accession, and the colors used in the histogram represent the most likely ancestry of the cluster from which the accessions were derived.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4520663&req=5

pone.0134607.g003: Genetic structure of the Hevea germplasm accessions.The genetic structure was inferred through Bayesian analyses of the most probable number of groups (K) estimated based on the mean log probability [A] using the method described by Evanno et al. (2005) [B]. Each column (histogram) [C] represents the genotyping data from one accession, and the colors used in the histogram represent the most likely ancestry of the cluster from which the accessions were derived.
Mentions: To examine the relatedness among the 1,117 accessions, the data for 13 markers were analyzed using the STRUCTURE program. A strict interpretation of our results using the method of Evanno et al. (2005) suggested that two genetic clusters (K = 2) were sufficient to interpret our data (Fig 3A and 3B); the results are also presented as K = 3 and K = 7 in S3 Fig. Based on a membership probability threshold of 0.70, 277 accessions were assigned to cluster 1 and 783 accessions were assigned to cluster 2. The remaining 57 accessions were classified into a mixed subgroup. The membership probability was <0.70 in any given subgroup (Table 3).

Bottom Line: The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018.Rubber tree breeders can effectively utilize this core collection for cultivar improvement.Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.

View Article: PubMed Central - PubMed

Affiliation: Molecular Biology and Genetic Engineering Center (CBMEG), University of Campinas (UNICAMP), Campinas, SP, Brazil.

ABSTRACT
The rubber tree [Hevea brasiliensis (Willd. ex Adr. de Juss.) Muell. Arg.] is the only plant species worldwide that is cultivated for the commercial production of natural rubber. This study describes the genetic diversity of the Hevea spp. complex that is available in the main ex situ collections of South America, including Amazonian populations that have never been previously described. Genetic data were analyzed to determine the genetic structure of the wild populations, quantify the allelic diversity and suggest the composition of a core collection to capture the maximum genetic diversity within a minimal sample size. A total of 1,117 accessions were genotyped with 13 microsatellite markers. We identified a total of 408 alleles, 319 of which were shared between groups and 89 that were private in different groups of accessions. In a population structure and principal component analysis, the level of clustering reflected a primary division into the following two subgroups: cluster 1, which consisted of varieties from the advanced breeding germplasm that originated from the Wickham and Mato Grosso accessions; and cluster 2, which consisted of the wild germplasm from the Acre, Amazonas, Pará and Rondônia populations and Hevea spp. The analyses revealed a high frequency of gene flow between the groups, with the genetic differentiation coefficient (GST) estimated to be 0.018. Additionally, no distinct separation among the H. brasiliensis accessions and the other species from Amazonas was observed. A core collection of 99 accessions was identified that captured the maximum genetic diversity. Rubber tree breeders can effectively utilize this core collection for cultivar improvement. Furthermore, such a core collection could provide resources for forming an association panel to evaluate traits with agronomic and commercial importance. Our study generated a molecular database that should facilitate the management of the Hevea germplasm and its use for subsequent genetic and genomic breeding.

No MeSH data available.


Related in: MedlinePlus