Study on Diversity of Sapodilla (Manilkara zapota) by Molecular Marker in the Special Region of Yogyakarta

Vega Kartika Sari, Rani Agustina Wulandari, Rudi Hari Murti


The objective of this research was to determine the diversity and relationship of sapodilla accession derived from districts in DIY based on DNA profiles. From the screening of 20 total primers, five primers (OPA 20, OPB 5, OPB 6, OPB 8, and OPC 19) producing polymorphic bands in RAPD analysis were selected. Different-shaped samples of sapodilla randomly collected from Bantul, Gunungkidul, Kulonprogo, Sleman and Yogyakarta city were used in this research. The analysis of molecular data was performed by using NTSys pc-2.02 and GenAlex 6.1 program. The clustering indicated that the accessions tend to group by their locations. However, there was no corelation between DNA marker and the fruit shape. The first group comprised samples from Yogyakarta city (Keraton Yogyakarta), Bantul and Kulonprogo while the second group consisted of samples from Sleman and Gunungkidul with genetic similarity of 53% and 37% respectively. The genetic diversity was high (PLP = 98.85% of 87 loci and H=0.280±0.14) comprising the genetic diversity within population (53%) which was greater than genetic diversity between populations (47%). Having the highest genetic diversity, Gunungkidul should be potential for conservation and selection of sapodilla in DIY.


diversity; fruit shape; polymorphic; RAPD; sapodilla

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Aukar, A. P. de A., Lemos, E. G. de M., & Oliveira, J. C. (2002). Genetic variations among passion fruit species using rapd markers. Revista Brasileira de Fruticultura, 24(3), 738–740. crossref

Bayazit, S., Imrak, B., Küden, A., & Kemal Güngör, M. (2011). RAPD analysis of genetic relatedness among selected quince (Cydonia oblonga Miil.) accessions from different parts of Turkey. Horticultural Science, 38(4), 134–141. Retrieved from PDF

Chanda, S. V., & Nagani, K. V. (2010). Antioxidant capacity of Manilkara zapota L. leaves extracts evaluated by four in vitro methods. Nature and Science, 8(10), 260-266. Retrieved from PDF

Doyle, J. J., & Doyle, J. L. (1990). Isolation of plant DNA from fresh tissue. Focus, 12, 13–15. Retrieved from PDF

Finkeldey, R. (2005). Pengantar genetika hutan tropis [An introduction to tropical forest genetics]. (E. Djamhuri, I. Z. Siregar & U. J. Siregar, Trans.). Gottingen, DE: Institute of Forest Genetics and Forest Tree Breeding, Georg-August-University-Gottingen. (Original work published 1998)

Gaudeul, M., Till-Bottraud, I., Barjon, F., & Manel, S. (2004). Genetic diversity and differentiation in Eryngium alpinum L. (Apiaceae): Comparison of AFLP and microsatellite markers. Heredity, 92(6), 508–518. crossref

Hapsoro, D., Warganegara, H. A., Utomo, S. D., Sriyani, N., & Yusnita. (2015). Genetic diversity among sugarcane (Saccharum officinarum L.) genotypes as shown by randomly amplified polymorphic DNA (RAPD). AGRIVITA Journal of Agricultural Science, 37(3), 247–257. crossref

Hartati, D., Rimbawanto, A., Taryono, Sulistyaningsih, E., & Widyatmoko, A. (2007). Pendugaan keragaman genetik di dalam dan antar provenan pulai (Alstonia scholaris (L.) R. Br.) menggunakan penanda RAPD [Estimation of genetic diversity within and among pulai (Alstonia scholaris (L.) R. Br.) provenance realed by RAPD marker. Jurnal Pemuliaan Tanaman Hutan, 1(2), 89–98. Retrieved from website

Heaton, H. J., Whitkus, R., & Gomez-Pompa, A. (1999). Extreme ecological and phenotypic differences in the tropical tree chicozapote (Manilkara zapota (L.) P. Royen) are not matched by genetic divergence: A random amplified polymorphic DNA (RAPD) analysis. Molecular Ecology, 8(4), 627–632. crossref

Holsinger, K. E., & Mason-Gamer, R. J. (1996). Hierarchical analysis of nucleotide diversity in geographically structured populations. Genetics, 142(2), 629–639. Retrieved from website

Hu, Y., Xie, X., Wang, L., Zhang, H., Yang, J., & Li, Y. (2014). Genetic variation in cultivated Rheum tanguticum populations. Genetics and Molecular Biology, 37(3), 540–548. crossref

Inoue, E., Kasumi, M., Sakuma, F., Anzai, H., Amano, K., & Hara, H. (2006). Identification of RAPD marker linked to fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). Scientia Horticulturae, 107(3), 254–258. crossref

Khatun, M. M., Hossain, K. M., & Mahbubur Rahman, S. M. (2012). Molecular characterization of selected local and exotic cattle using RAPD marker. Asian-Australasian Journal of Animal Sciences, 25(6), 751–757. crossref

Laserna, M. P., Maddonni, G. A., & López, C. G. (2012). Phenotypic variations between non-transgenic and transgenic maize hybrids. Field Crops Research, 134, 175–184. crossref

Lowe, A., Harris, S., & Ashton, P. (2004). Ecological genetics: Design, analysis and application. Oxford, UK: Blackwell Publishing.

Medhi, K., Sarmah, D. K., Deka, M., & Bhau, B. S. (2014). High gene flow and genetic diversity in three economically important Zanthoxylum Spp. of Upper Brahmaputra Valley Zone of NE India using molecular markers. Meta Gene, 2, 706–721. crossref

Meghala, R., Ravishankar, K. V, Anand, L., & Rekha, A. (2005). Genetic diversity of Indian sapota (Manilkara zapota) cultivars characterized by RAPD markers. Plant Genetic Resources Newsletter, 142, 43–46. Retrieved from website

Peiris, K. (2007). Chapter 6: sapodilla Manilkara zapota L. van Royen. In D. K. N. G. Pushpakumara, H. P. M. Gunasena, & V. P. Singh (Eds.), Underutilized fruit trees in Sri Lanka (pp. 183-224). New Delhi, IN: World Agroforestry Centre, South Asia Office.

Rahayu, S. E., & Handayani, S. (2010). Keragaman genetik pandan asal Jawa Barat berdasarkan penanda inter simple sequence repeat [Genetic diversity of Pandanus from West Java based on ISSR markers]. Makara Journal of Science, 14(2), 158-162. crossref

Robi'ah, H. R., Sobir, & Surahman, M. (2005). Analisis pembandingan pola keanekaragaman pisang introduksi berdasarkan penanda fenotipik dengan penanda RAPD dan pendugaan korelasi antara keduanya terhadap komposisi genomiknya [Comparison analysis for diversity pattern of introduction banana based on phenotypic and RAPD markers and estimating correlation between both of them totheir genomic composition]. Jurnal Agronomi Indonesia, 33(3), 55-61. Retrieved from website

Rozika, Murti, R. H., Purwanti, & Setyastuti. (2013). Esplorasi dan karakterisasi sawo (Manilkara zapota (L.) van Royen) di Daerah Istimewa Yogyakarta [Exploration and characterization of Sapodilla (Manilkara zapota (L.) van Royen) in Daerah Istimewa Yogyakarta]. Vegetalika, 2(4), 101–114. Retrieved from website

Salinas-Peba, L., & Parra-Tabla, V. (2007). Phenology and pollination of Manilkara zapota in forest and homegardens. Forest Ecology and Management, 248(3), 136–142. crossref

Sari, V. K., & Murti, R. H. (2015). An effective method for DNA extraction of mature leaf of Sapodilla (Manilkara zapota (L.) van Royen). AGRIVITA Journal of Agricultural Science, 37(1), 18–23. crossref

Sera, T., Ruas, P. M., Ruas, C. D. F., Diniz, L. E. C., Carvalho, V. D. P., Rampim, L., … Silveira, S. R. Da. (2003). Genetic polymorphism among 14 elite Coffea arabica L. cultivars using RAPD markers associated with restriction digestion. Genetics and Molecular Biology, 26(1), 59–64. crossref

Soerianegara, I., & Lemmens, R. H. M. J. (2002). Sumber daya nabati Asia Tenggara: Pohon penghasil kayu perdagangan utama [Southeast Asia's vegetable resource: The main timber-producing tree]. Prosea, 5(1). Bogor, ID: Balai Penelitian Teknologi Perbenihan.

Sultana, R. S., & Rahman, M. M. (2013). Biotechnological approaches of watermelon to meet the future challenges for next decades. Advances in Bioscience and Bioengineering, 1(2), 40–48. crossref

Susantidiana, Wijaya, A., Lakitan, B., & Surahman, M. (2009). Identifikasi beberapa aksesi jarak pagar (Jatropha curcas L.) melalui analisis RAPD dan morfologi [The identification of some accessions of Jatropha curcas L. using morphological and RAPD analysis]. Jurnal Agronomi Indonesia, 37(524), 167–173. Retrieved from website

Taheri, S., Abdullah, T. L., Abdullah, N. A. P., & Ahmad, Z. (2013). Use of intersimple sequence repeat assay for detection of DNA polymorphism induced by gamma rays in Curcuma alismatifolia. HortScience, 48(11), 1346–1351. Retrieved from website

Widyatmoko, AYPBC., Rimbawanto, A., & Chasani, A. (2013). Hubungan kekerabatan antar populasi jati (Tectona grandis Linn. F.) berdasarkan penanda RAPD (Random Amplified Polymorphic DNA). Jurnal Pemuliaan Tanaman Hutan, 7(3), 151-166. Retrieved from website

Widyatmoko, AYPBC., Rimbawanto, A., & Suharyanto. (2005). Keragaman genetik Araucaria cunninghamii menggunakan penanda RAPD [The genetic diversity of Araucaria cunninghamii using the RAPD marker]. In E. B. Hardiyanto (Ed.). Paper presented at Proceedings of the National Seminar of Increase Productivity of Forests: The Role of Conservation of Gene, Breeding and Silviculture Resources in Supporting Forest Rehabilitation, Yogyakarta, 26-27 May (pp. 397-408). Yogyakarta, ID: UGM and ITTO.



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