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Genetic variation and structure of rubber population based on microsatellites

By: Aldrin Y. Cantila, Rene Rafael C. Espino, Emma K. Sales

Key Words: Genetic variation, Microsatellites, Population structure, Rubber clones

Int. J. Biosci. 10(3), 107-117, March 2017.



Information towards genetic variation and structure of rubber leads to a proper utility of rubber clones for a varietal development. Rubber population represented by nine Asian, 10 South American and nine West African clones was described by indices for genetic variation such as number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), unbiased heterozygosity (uHe), fixation index (F), Shannon’s information index (I) and gene diversity (GD); and population structure such as analysis of molecular variance (AMOVA), structure analysis and principal component analysis (PCA) based on 13 microsatellites. Microsatellites derived 60 alleles in all with means Na, Ne, Ho, uHe, F, I and GDof4.615, 2.997, 0.619, 0.686, 0.051, 1.174 and 0.647 per microsatellite, respectively. AMOVA revealed 4%, 16% and 80% genetic variation among groups, among and within clones, respectively. The initial three groups based on geographical origin were reassigned into four based on the structure analysis.PCA supported the grouping through the distribution of clones on the scatterplot’s projection. PCA also detectedPC1 clones: GW5, IAN873, IRCA22, PB311, RRIM600 and USM1as the most variable clones based on squared cosines. Microsatellite data showed a rich genetic variation is within clones and confirmed rubber is genetically heterogenous. PCA result suggested PC1 clones can be effective parents while unbiased structure grouping will serve as heterotic groups as basis for the hybridization and development of new rubber varieties.

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Genetic variation and structure of rubber population based on microsatellites

Anderson JA, Churchill GA, Autrique JE, Sorells ME, Tanksley SD. 1993. Optimizing parental selection for genetic-linkage maps. Genome 36, 181–186.

Baudouin L, Baril C, Clément-Demange A, Leroy T, Paulin D. 1997. Recurrent selection of tropical tree crops. Euphytica 96, 101-114.

Botstein D, White RL, Skolnick M, Davis RW. 1980. Construction of a genetic map in man using restriction fragment length polymorphism. American Journal of Human Genetics 32, 314-331.

Cantila AY, Espino RRE, Sales EK. 2015. Utilization of simple sequence repeats markers in the genetic characterization of Philippine rubber, Hevea brasiliensis (Willd. ex A. Juss) Muell. Arg., germplasm. Philippine Journal of Crop Science 40(3), 33-39.

Cantila AY, Espino RRE, Sales EK. 2016. Assessing Genetic Diversity of Asian-based Rubber Populations using SSR and Multivariate Statistics in the Philippines. Journal of Biology, Agriculture and Healthcare 6(16), 108-117.

Cataldo F. 2000. Guayule rubber: a new possible world scenario for the production of natural rubber. Progress in Rubber and Plastics Technology 16, 31-59.

Chesnokov YV, Artemyeva AM. 2015. Evaluation

of the Measure of Polymorphism Information of  Genetic Diversity. ISSN 2412-0324 (English Ed.

Online). Agricultural Biology 50(5), 571-578.

Cornish K. 2001.Similarities and differences in rubber biochemistry among plant species. Phytochemistry 57, 1123–1134.

De Souza LM, Le Guen V, Cerqueira-Silva CBM, Silva CC, Mantello CC, Conson ARO, Vianna JPG, Zucchi MI, Junior EJS, Fialho JF, de Moraes MLT, Gonçalves PS, de Souza AP. 2015. Genetic Diversity Strategy for the Management and Use of Rubber Genetic Resources: More than 1,000 Wild and Cultivated Accessions in a100-Genotype Core Collection. PLoS ONE 10(7), e0134607.

Department of Trade and Industry-Regional Operations Development Group (DTI-RODG). 2012. Rubber Industry. Retrieved June 2012 from

Earl DA, vonHoldt BM. 2012. STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetic Resources 4, 359-361.

Evanno G, Regnaut S, Goudet J. 2005. Detecting the number of clusters of individuals using the software STRUCTURE: A simulation study.Molecular Ecology14: 2611-2620.

Excoffier L, Smouse PE, Quattro M. 1992. Analysis of molecular variance inferred from metric distances among DNA haplotypes: Application to human mitochondrial DNA restriction sites. Genetics 131, 479-491.

Fukunaga K, Hill J, Vigouroux Y, Matsuoka Y, Sanchez JG, Liu K, Buckler EK, Doebley J. 2005. Genetic diversity and population structure of

teosinte. Genetics 169, 2241-2254.

Garris AJ, Tai TH, Coburn J, Kresovich S, McCouch S. 2005. Genetic structure and diversity in Oryza sativa L. Genetics 169, 1631-1638.

Gupta PK, Varshney RK. 2000. The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread

wheat. Euphytica 113, 163-185.

Hartl DL, Clark AG. 1989. Principles of population genetics. 2nd Ed. Sinauer Associates, Sunderland, MA.

Hartl DL, Clark AG. 1997. Principles of Population Genetics 3rd Ed. Sunderland, Massachusetts: Sinauer Associates, Inc.

Kinnarat P, Rattanawong R. 2002. Improvement of rubber tree. Academic Matter of Rubber Tree Conference 1st. Rubber Research Institute, Department of Agriculture, Nongkhai, Thailand. February 20-22, 2002.

Le Guen V, Gay C, Xiong TC, Souza LM, Rodier-Goud M, Seguin M. 2011. Development and characterization of 296 new polymorphic microsatellite markers for rubber tree (Hevea brasiliensis). Plant Breeding 130, 294-296.

Luo H, Van Coppenolle B, Seguin M, Boutry M. 1995. Mitochondrial DNA polymorphism and phylogenetic relationships in Hevea brasiliensis. Molecular Breeding 1, 51–63.

Mooibroek H, Cornish K. 2000.Alternative sources of natural rubber. Applied Microbiology and Biotechnology 53, 355–365.

Morgante M, Olivieri AM. 1993. PCR-amplified

microsatellite as markers in plant genetics. Plant

Journal 3, 175-182.

Nei M, Roychoudhury AK. 1974. Sampling

variances of heterozygosity and genetic distance. Genetics 76, 379-390.

Nouy B, Nicolas D. 1985. Hevea brasiliensis in Ivory Coast – 10 years of pollination. Revue Générale du Caoutchoucet des Plastiques, 656 p.

Oktavia F, Kuswanhadi ML. 2011. Selection of parent trees for Rubber (Hevea brasiliensis) breeding based on RAPD analysis. NUSANTARA Bioscience 3(3), 124-129.

Peakall R, Smouse PE. 2012. Gen AlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics 28, 2537-2539.

Perseguini J, Romão L, Briñez B, Scaloppi EJr, Gonçalves P, Benchimol LL. 2012. Genetic diversity of cultivated accessions and wild species of rubber tree using EST-SSR markers.Pesquisa Agropecuária Brasileira 47(8), 1087-1094.

Pritchard JK, Stephens M, Donnelly P. 2000. Inference of population structure using multi locus genotype data. Genetics 155, 945–959.

Priyadarshan PM, Gonçalves P. 2002. Use of Hevea gene pool in rubber tree (Hevea brasiliensis Muell. Arg) breeding. The Planter 78, 123-138.

Rao CR. 1982. Diversity and dissimilarity coefficients: a unified approach. Theoretical Population Biology 21, 24-43.

Seguin M, Gay C, Chen XT, Rodier-Goud M. 2002. Microsatellite markers for genome analysis of rubber tree (Hevea spp.). The IRRDB Symposium 2001 Biotechnology & Rubber Tree, 25-28 September 2001.Montpellier, France. Retrieved from

Sherwin WB, Jabot F, Rush R, Rossetto M.  2006. Measurement of biological information with applications from genes to landscapes. Molecular Ecology 15, 2857-2869.

Triwitayakorn K, Chatkulkawin P, Kanjanawattanawong S, Sraphet S, Yoocha T, Sangsrakru D, Chanprasert J, Ngamphiw C, Jomchai N, Therawattanasuk K, Tangphatsornruang S. 2011. Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers & construction of a genetic linkage map. DNA Research 18, 471-482.

Wang ML, Barkley NA, Jenkins TM. 2009. Microsatellite Markers in Plants & Insects. Part I: Applications of Biotechnology. Genes, Genomes and Genomics 3(1), x-y ©2009 Global Science Books: 14p.

Wright S. 1951.The genetical structure of populations. Annals of Eugenics 15, 323-354.

Yu F, Wang BH, Feng SP, Wang JY, Li WG, Wu YT. 2011. Development, characterization, and cross‑species/genera transferability of SSR markers for rubber tree (Hevea brasiliensis). Plant Cell Reports 30, 335-344.

Aldrin Y. Cantila, Rene Rafael C. Espino, Emma K. Sales. 2017. Genetic variation and structure of rubber population based on microsatellites. Int. J. Biosci. 10(3), 107-117.
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