Genetic Diversity Analysis of 28 Cacao Collections (Theobroma cacao L.) Based on SSR Markers

Ilham Nur ardhi Wicaksono, Rubiyo Rubiyo, Dewi Sukma, Sudarsono Sudarsono

Abstract


Analysis of genetic diversity of cacao germplasm collections using molecular markers has an important role in the assembly of new superior clones. The availability of commercial and superior local clones could increase the success of new superior clones’ assembly. Hence, the genetic diversity analysis of these materials needs to be done. The study was aimed to analyze genetic diversity of 28 cacao collections based on SSR markers that would be useful for selection of parental lines. The research was conducted in the Integrated Laboratory, Indonesian Industrial and Beverage Crops Research Institute, Sukabumi, and Plant Molecular Biology laboratory, Bogor Agricultural University, from November 2015 to May 2016. Analysis of genetic diversity was conducted using 28 cacao clones (13 superior local clones and 15 commercial clones). DNA was extraction using CTAB method, which then amplified by PCR technique using 20 SSR primers. The result showed that all SSR markers used in this study were polymorphic with an average value of PIC was high (57%). Phylogenetic tree constructed using DARwin program version 6.05 is divided into 3 major groups, which placed commercial and superior local clones together in each group. Superior local clones observed herein might have close relationships with commercial clones that have long been cultivated in Indonesia. Furthermore, some cacao clones could potentially be parental lines because they had high genetic distance. The results showed that SSR markers are powerful tools to determine potential parental lines, which is expected to increase the chances of heterosis in their progenies.

Keywords


Cacao; genetic diversity; SSR markers; superior local clones; commercial clones

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References


Allen, G.C., Vergara, M.A., Krasynanski, S., Kumar, S., & Thompson, W.F. (2006). A modified protocol for rapid DNA isolation from plant tissues using cetyl trimethylammonium bromide. Nat, Prot., 1, 2320–2325.

Azrai, M. (2005). Pemanfaatan marka molekuler dalam proses seleksi pemuliaan tanaman. Jurnal Agro Biogen, 1(1), 26–27.

Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314–31.

Izzah, N.K. (2014). Peran marka molekuler dalam perbaikan genetik tanaman kakao. In Rubiyo, R. Harni, B. Martono, E. Wardiana, N.K. Izzah, & A.M. Hasibuan (Eds.), Bunga Rampai Inovasi Teknologi Bioindustri Kakao (pp. 47–56). Bogor: IAARD Press.

Kalia, R.K., Rai, M.K., Kalia, S., Singh, R., & Dhawan, A.K. (2011). Microsatellite markers: An overview of the recent progress in plants. Euphytica, 177, 309–334.

Kalinowski, S.T., Taper, M.L., & Marshall, T.C. (2007). Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol, Ecol, 16, 1099–1106.

Kurniasih, S., Rubiyo, Setiawan, A., Purwantara, A., & Sudarsono. (2011). Analisis keragaman genetik plasma nutfah kakao (Theobroma cacao L,) berdasarkan marka SSR. Jurnal Littri., 17(4), 156–162.

Lanaud, C., Risterucci, A.M., Pieretti, I., Falque, M., Bouet, A., & Lagoda P.J.L. (1999). Isolation and characterization of microsatellites in Theobroma cacao L. Mol Ecol, 8, 2142–2152.

Parida, S.K., Yadava, D.K., & Mohapatra, T. (2010). Microsatellites in Brassica unigenes: Relative abundance, marker design, and use in comparative physical mapping and genome analysis. Genome, 53, 55–67.

Peakall, R., & Smouse, P. (2012). GenAlEx 6,5: Genetic analysis in Excel, Population genetic software for teaching and research. Bioinformatics, 28, 2537–2539.

Perrier, X., & Jacquemoud-Collet J.P. (2010). DARwin software. Retrieved from http://darwin,cirad,fr/.

Pourabed, E., Noushabadi, M. R. J., Jamali, S. H., Alipour, N. M., Zareyan, A., & Sadeghi, L. (2015). Identification and DUS testing of rice varieties through microsatellite markers. Int. J. Plant Genomics. doi: http://dx.doi.org/10.1155/2015/965073.

Rubiyo, Purwantara, Suhendi, Trikusumaningtyas, Ilyas, I., & Sudarsono. (2008). Uji ketahanan kakao (Theobroma cacao L,) terhadap penyakit busuk buah dan efektivitas metode inokulasi. Pelita Perkebunan, 24, 95–113.

Rubiyo. (2013). Inovasi teknologi perbaikan bahan tanam kakao di Indonesia. Buletin RISTRI, 4(3), 199–214.

Rubiyo, Izzah, N.K., Sulistiyorini, I., & Tresniawati, C. (2015). Evaluation of genetic diversity in cacao collected from Kolaka, Southeast Sulawesi, using SSR markers. Indonesian Journal of Agricultural Science, 16(2), 71–78.

Santos, R.M.F., Lopes, U.V., Clement, D., Pires, J.L., Lima, E.M., Messias, T.B., & Gramacho, K.P. (2014). A protocol for large scale genomic DNA isolation for cacao genetics analysis. African Journal of Biotechnology, 13(7), 814–820.

Silva, C.R.S., Albuquerque, P.S.B., Ervedosa, F.R., Mota, J.W.S., Figueira, A., & Sebben, A.M. (2011). Understanding the genetic diversity, spatial genetic structure and mating system at the hierarchical levels of fruits and individuals of a continuous Theobroma cacao population from the Brazilian Amazon. Heredity, 106, 973–985.

Sitaresmi, T., Yunani, N., Zakki, K.A.F., Mulsanti, I.W., Utomo, S.T.W., & Daradjat, A.A. (2013). Identifikasi varietas contoh untuk karakter penciri spesifik sebagai penunjang harmonisasi pengujian BUSS padi. Penelitian Pertanian Tanaman Pangan, 32(3), 148–158.

Susilo, A.W. (2007). Akselerasi program pemuliaan kakao (Theobroma cacao L.) melalui pemanfaatan penanda molekuler dalam proses seleksi. Warta Pusat Penelitian Kopi dan Kakao Indonesia, 23(1), 11–24.

Thiel, T., Michalek, W., Varshney, R.K., & Graner, A. (2013). Exploiting EST database for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor. Appl. Genet., 106, 411–42.

Zhang, D., Mischke, S., Johnson, E.S., Phillips-Mora, W., & Meinhardt, L. (2009). Molecular characterization of an international cacao collection using microsatellite markers. Tree genetic & Genomic, 5, 1–10.




DOI: http://dx.doi.org/10.21082/jtidp.v4n1.2017.p13-22

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This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.


 

P-ISSN: 2356-1297
E-ISSN: 2528-7222
Accredited No.30/E/KPT/2018 on Oktober 24, 2018 by Ministry of Research, Technology and Higher Education of the Republic of Indonesia

                    


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