Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

Fetrina Oktavia, Kuswanhadi Kuswanhadi, Dini Dinarty, Widodo Widodo, Sudarsono Sudarsono


The accession of the IRDB 1981 (PN’81) population is a newly introduced and an important rubber tree germplasm while the Wickham clone is a commercial variety one. The objectives of this study were to assess the genetic diversity and the population structure of PN’81 populations and the Wickham clones using 15 EST-SSR loci. Results of the analysis showed that the evaluated SSR primers yielded polymorphic markers. The gSSR 268 primer pairs yielded the most informative markers while HBE 280 primers generated the lowest ones. Results of the genetic diversity analysis supported that the PN’81 population belonged to a single large natural population of rubber trees while the Wickham clones belonged to a different group than that of PN’81. The population structure analysis of the rubber accessions was also in agreement with the results of the genetic diversity analysis. The experiment also indicated that PN’81 populations would be useful for future rubber breeding in Indonesia, especially as the sources of parent clones for rubber tree hybridization programs and rubber tree genetic resource conservation.


Amazon germplasm; Hevea brasiliensis; IRRDB 1981; rubber breeding; Wickham population

Full Text:



Aidi,-D. (2009). Genotipe terpilih sebagai penghasil kayu lateks dari plasma nutfah karet IRRDB 1981 [The selected of genotypes of IRRDB rubber germplasm for a latex timber producer]. In Siagian, N., Anwar, C., Gunawan, A., & Rachmawan, A. (Eds.), Prospek dan pengembangan kayu karet [Prospect and development or rubber timber] (pp. 75-84). Medan, ID: Pusat Penelitian Karet.

An, Z.-W., Li, Y.-C., Zhai, Q.-L., Xie, L.-L., Zhao, Y.-H., & Huang, H.-S. (2013). Development and characterization of novel expressed sequence tag-derived simple sequence repeat markers in Hevea brasiliensis (rubber tree). Genetics and Molecular Research, 2(4), 5905-5910. crossref

An, Z.-W., Zhao, Y.-H., Cheng, H., Li, W.-G., & Huang, H.-S. (2009). Development and application of EST-SSR markers in Hevea brasiliensis Muell. Arg. Hereditas (Beijing), 31(3), 311-319. crossref

Besse, P., Seguin, M., Lebrun, P., Chevallier, M. H., Nicolas, D., & Lanaud, C. (1994). Genetic diversity among wild and cultivated populations of Hevea brasiliensis assessed by nuclear RFLP analysis. Theoretical and Applied Genetics, 88(2), 199-207. crossref

Bhargava, A., & Fuentes, F. F. (2010). Mutational dynamics of microsatellites. Molecular Biotechnology, 44(3), 250–266. crossref

Chow, K. S., Wan, K. L., Isa, M. N. M., Bahari, A., Tan, S. H., Harikrishna, K., & Yeang, H. Y. (2007). Insights into rubber biosynthesis from transcriptome analysis of Hevea brasiliensis latex. Journal of Experimental Botany, 58(10), 2429–2440. crossref

Cubry, P., Pujade‐Renaud, V., Garcia, D., Espeout, S., Le Guen, V., Granet, F., ... Ordon, F. (2014). Development and characterization of a new set of 164 polymorphic EST-SSR markers for diversity and breeding studies in rubber tree (Hevea brasiliensis Müll. Arg.). Plant Breeding, 133(3), 419-426. crossref

de Souza, L. M., Le Guen, V., Cerqueira-Silva, C. B. M., Silva, C. C., Mantello, C. C., Conson, A. R. O., ... de Souza, A. P. (2015). 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. PLoS One, 10(7), e0134607. crossref

Earl, D. A., & vonHoldt, B. M. (2012). STRUCTURE HARVESTER: A website and program for visualizing STRUCTURE output and implementing the Evanno method. Conservation Genetics Resources, 4(2), 359-361. crossref

Ellstrand, N. C., & Elam, D. R. (1993). Population genetic consequences of small population size: Implications for plant conservation. Annual Review of Ecology and Systematics, 24, 217–242. crossref

Evanno, G., Regnaut, S., & Goudet, J. (2005). Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Molecular Ecology, 14(8), 2611-2620. crossref

Feng, S.-P., Li, W.-G., Huang, H.-S., Wang, J.-Y., & Wu, Y.-T. (2009). Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis). Molecular Breeding, 23(1), 85-97. crossref

García-R, I. A., González-S, S. M., Montoya-C, D., & Aristizabal, F. (2011). Identification in silico of SSR markers for genotyping Hevea sp. clone gardens in Colombia. Agronomía Colombiana, 29(3), 359-366. Retrieved from website

Gouvêa, L. R. L., Rubiano, L. B., Chioratto, A. F., Zucchi, M. I., & de Souza Gonçalves, P. (2010). Genetic divergence of rubber tree estimated by multivariate techniques and microsatellite markers. Genetics and Molecular Biology, 33(2), 308–318. crossref

Guichoux, E., Lagache, L., Wagner, S., Chaumeil, P., Léger, P., Lepais, O., … Petit, R. J. (2011). Current trends in microsatellite genotyping. Molecular Ecology Resources, 11(4), 591–611. crossref

Huat, O.-S., Othman, R., & Benong, M. (1995). Status report on the 1981 Hevea germplasm collection. Paper presented at Proceedings of Symposium on Physiological and Molecular Aspects of the Breeding of Hevea. Kuala Lumpur: IRRDB.

Kalinowski, S. T., Taper, M. L., & Marshall, T. C. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Molecular Ecology, 16(5), 1099–1066. crossref

Ko, J.-H., Chow, K.-S, & Han, K.-H. (2003). Transcriptome analysis reveals novel features of the molecular events occurring in the laticifers of Hevea brasiliensis (para rubber tree). Plant Molecular Biology, 53, 479-492. Retrieved from

Lam, L. V., Thanh, T., Chi, V. T. Q., & Tuy, L. M. (2009). Genetic diversity of Hevea IRRDB’81 collection assessed by RAPD markers. Molecular Biotechnology, 42(3), 292–298. crossref

Larekeng, S. H., Maskromo, I., Purwito, A., Matjik, N. A., & Sudarsono. (2015). Pollen dispersal and pollination patterns studies in Pati kopyor coconut using molecular markers. International Journal on Coconut R & D, 31(1), 46-60. Retrieved from website

Le Guen, V., Doaré, F., Weber, C., & Seguin, M. (2009). Genetic structure of Amazonian populations of Hevea brasiliensis is shaped by hydrographical network and isolation by distance. Tree Genetics and Genomes, 5(4), 673–683. crossref

Le Guen, V., Garcia, D., Mattos, C. R. R., & Clément-Demange, A. (2002). Evaluation of field resistance to Microcyclus ulei of a collection of Amazonian rubber tree (Hevea brasiliensis) germplasm.. Crop Breeding and Applied Biotechnology, 2(1), 141-148. crossref

Lekawipat, N., Teerawatanasuk, K., Rodier-Goud, M., Seguin, M., Vanavichit, A., Toojinda, T., & Tragoonrung, S. (2003). Genetic diversity analysis of wild germplasm and cultivated clones of Hevea brasiliensis Muell. Arg. by using microsatellite markers. Journal of Rubber Research, 6(1), 36-47. Retrieved from website

Li, D., Deng, Z., Qin, B., Liu, X., & Men, Z. (2012). De novo assembly and characterization of bark transcriptome using Illumina sequencing and development of EST-SSR markers in rubber tree (Hevea brasiliensis Muell. Arg.). BMC Genomics, 13, 192. crossref

Li, D.-J., Deng, Z., Guo, H.-N., Xia, Z.-H. (2014). Development and characterizations of EST-SSR markers in rubber tree (Hevea brasiliensis). Agricultural Science & Technology, 15(5), 733-737.

Lopes, U. V., & Marques, J. R. B. (2015). Diversity, inbreeding and inbreeding depression in rubber tree (Hevea spp.). Agrotrópica, 27(1), 33-44. Retrieved from

Mantello, C. C., Cardoso-Silva, C. B., da Silva, C. C., de Souza, L. M., Scaloppi Jr, E. J., de Souza Gonçalves, P., … de Souza, A. P. (2014). De Novo assembly and transcriptome analysis of the rubber tree (Hevea brasiliensis) and SNP markers development for rubber biosynthesis pathways. PLoS ONE, 9(7), e102665. crossref

Mantello, C. C., Suzuki, F. I., Souza, L. M., Gonçalves, P. S., & Souza, A. P. (2012). Microsatellite marker development for the rubber tree (Hevea brasiliensis): Characterization and cross-amplification in wild Hevea species. BMC Research Notes, 5, 329. crossref

Maskromo, I., Tenda, E. T., Tulalo, M. A., Novarianto, H., Sukma, D., Sukendah, & Sudarsono. (2015). Keragaman fenotipe dan genetik tiga varietas kelapa genjah kopyor asal Pati Jawa Tengah [Phenotypic and genotypic variabilities among kopyor dwarf coconut varieties originated from Pati Central Java]. Jurnal Penelitian Tanaman Industri, 21(1), 1-8. Retrieved from website

Mercy, M. A. (2001). Genotypic evaluation and screening for drought tolerance in wild Hevea germplasm (Unpublished Ph.D. Thesis). Kerala Agricultural University, Trichur, Kerala.

Mydin, K. K., Reju, M. J., Narayanan, C., & Abraham, T. (2012). Incorporation of the 1981 IRRDB wild amazonian germplasm in Hevea breeding in India. Paper presented at The IRRDB – IRRI International Seminar On Rubber Plant Breeding, Medan. Kuala Lumpur: IRRDB.

Oktavia, F., & Kuswanhadi, M. L. (2011). Genetic relationship of Wickham and IRRDB 1981 rubber population based on RAPD markers analysis. HAYATI Journal of Biosciences, 18(1), 27-32. crossref

Orozco-Castillo, C., Chalmers, K. J., Waugh, R., & Powell, W. (1994). Detection of genetic diversity and selective gene introgression in coffee using RAPD markers. Theoretical and Applied Genetics, 87(8), 934–940. crossref

Peakall, R., & Smouse, P. E. (2012). GenAlEx 6.5: Genetic analysis in Excel. Population genetic software for teaching and research – an update. Bioinformatics, 28(11), 2537–2539. crossref

Perseguini, J. M. K. C., de Castro Romão, L. R., Briñez, B., Scaloppi Jr, E. J., de Souza Gonçalves, P., & Benchimol, L. L. (2012). Genetic diversity of cultivated accessions and wild species of rubber tree using EST-SSR markers. Pesquisa Agropecuária Brasileira, 47(8), 1087–1094. crossref

Phumichai, T., Teerawattanasuk, K., Kongsiri, N., Sansing, K., & Phumichai, C. (2011). Genetic analysis and population structure of rubber tree for association mapping. Paper presented at IRRDB International Rubber Conference, 15-16 December 2011, Chiang Mai, Thailand. Kuala Lumpur: IRRDB.

Pootakham, W., Chanprasert, J., Jomchai, N., Sangsrakru, D., Yoocha, T., Tragoonrung, S., & Tangphatsornruang, S. (2012). Development of genomic-derived simple sequence repeat markers in Hevea brasiliensis from 454 genome shotgun sequences. Plant Breeding, 131(4), 555–562. crossref

Priyadarshan, P. M. (2016). Genetic diversity and erosion in hevea rubber. In Ahuja, M. R., & Jain, S. M. (Eds.), Genetic diversity and erosion in plants: case histories (pp. 233-267). Switzerland: Springer.

Priyadarshan, P. M., & de S. Goncalves, P. (2003). Hevea gene pool for breeding. Genetic Resources and Crop Evolution, 50(1), 101–114. crossref

Reghu, C. P., Mercy, M. A., & Lakshmanan, R. (2012). Further evaluation and selection of 1981 IRRDB wild Hevea germplasm collection in India. Natural Rubber Research, 25(1), 31-38. Retrieved from website

Saha, T., Roy, C. B., & Nazeer, M. A. (2005). Microsatellite variability and its use in the characterization of cultivated clones of Hevea brasiliensis. Plant Breeding, 124(1), 86-92. crossref

Seguin, M., Gay, C., Xiong, T.-C., & Rodier-Goud, M. (2001). Microsatellite markers for genome analysis of rubber tree (Hevea spp.). In Sainte-Beuve, J. (Ed.), Biotechnology and rubber tree. Paper presented at Proceedings of IRRDB symposium, 25-28 September 2001, Montpellier, France. Montpellier: CIRAD.

Silva, C. C., Mantello, C. C., Campos, T., Souza, L. M., Gonçalves, P. S., & Souza, A. P. (2014). Leaf-, panel- and latex-expressed sequenced tags from the rubber tree (Hevea brasiliensis) under cold-stressed and suboptimal growing conditions: The development of gene-targeted functional markers for stress response. Molecular Breeding, 34(3), 1035–1053. crossref

Tinche, Asmono, D., Dinarti, D., & Sudarsono. (2014). Keragaman genetik kelapa sawit (Elaeis guineensis Jacq.) populasi Nigeria berdasarkan analisis marka SSR (Simple Sequence Repeats) [Genetic diversity of oil palm originated from Nigeria based on SSR (Simple Sequence Repeats) markers]. Buletin Palma, 15(1), 14-23. Retrieved from website

Triwitayakorn, K., Chatkulkawin, P., Kanjanawattanawong, S., Sraphet, S., Yoocha, T., Sangsrakru, D., … Tangphatsornruang, S. (2011). Transcriptome sequencing of Hevea brasiliensis for development of microsatellite markers and construction of a genetic linkage map. DNA Research, 18(6), 471–482. crossref

Varshney, R. K., Graner, A., & Sorrells, M. E. (2005). Genomics-assisted breeding for crop improvement. Trends in Plant Science, 10(12), 621–630. crossref

Xia, Z., Xu, H., Zhai, J., Li, D., Luo, H., He, C., & Huang, X. (2011). RNA-Seq analysis and de novo transcriptome assembly of Hevea brasiliensis. Plant Molecular Biology, 77, 299. crossref



License URL: