Diversity of Tidal Swamp Rice (Oryza sativa) Cultivars Indigenously from South Kalimantan, Indonesia

Dindin Hidayatul Mursyidin(1), Muhammad Zia Zul Haq(2), Badruzsaufari Badruzsaufari(3),

DOI: https://doi.org/10.15294/biosaintifika.v14i1.33168


(1) Laboratory of Genetics and Molecular Biology, Faculty of Mathematics and Natural Sciences, Universitas Lambung Mangkurat
(2) Laboratory of Genetics and Molecular Biology, Faculty of Mathematics and Natural Sciences, Universitas Lambung Mangkurat
(3) Laboratory of Genetics and Molecular Biology, Faculty of Mathematics and Natural Sciences, Universitas Lambung Mangkurat

Abstract

Studies on genetic diversity and relationships are necessary for breeders and scientists to increase the effectiveness of future breeding programs. The tidal swamp rice (Oryza sativa L.) is one of the potential germplasms which has a prominent opportunity to be incorporated in the rice breeding program. This study aimed to investigate and reveal the genetic diversity and relationship of tidal swamp rice germplasms indigenously from South Kalimantan, Indonesia, using Random Amplified Polymorphic DNA (RAPD) markers. A total of ten rice samples, consisting of nine from this region and one from South Sumatera (an outgroup), and five selected RAPD markers, i.e., OPB-06, OPAJ-01, OPAB-17, OPAL-09, and OPAL-08, were used in this study. DNA amplifications were performed and programmed for one cycle of initial denaturation (5 min, 94ºC), 45 cycles of denaturation (30 sec, 94ºC), annealing (30 sec, 37ºC), and extension (1.5 min, 72ºC), as well as one cycle of final extension (7 min, 72ºC). The genetic similarity was analyzed using Dice’s coefficient method, whereas their relationship (dendrogram) by the UPGMA. The results showed that these germplasms have a moderate genetic diversity level, indicated by the polymorphism degree of 75.64%. The clustering analysis revealed that they are grouped into three main groups at a similarity coefficient of 0.70. In this case, Siam Unus is distantly related to the other cultivars and forms a solitaire group. Siam Unus also shows the farthest relationship with Sardani, an outgroup. It is a new finding for the genetic insight of tidal swamp rice of South Kalimantan, Indonesia, including their diversity and relationship. Thus, the results obtained from this study is useful in supporting future rice conservation and breeding programs.

Keywords

breeding program, DNA fingerprint, genetic diversity, rice landrace

Full Text:

PDF

References

Acquaah, G. (2012). Principles of plant genetics and breeding. Oxford, UK: Wiley-Blackwell. https://doi.org/10.1002/9781118313718

Adioetomo, S. M., & Mujahid, G. (2014). Indonesia on the threshold of population ageing. In UNFPA Indonesia Monograph Series. https://doi.org/10.1299/kikaic.65.1319

Ali, M. A., Islam, M. S., Mandal, S. K., Nasrin, Z., Rahman, M. M., Kuddus, R. H., & Prodhan, S. H. (2014). Genetic diversity among salt-tolerant rice (Oryza sativa L.) landraces cultivated in the coastal districts of Bangladesh. Journal of Biological Science and Biotechnology, 3(1), 15–22.

Anumalla, M., Roychowdhury, R., Geda, C. K., Mazid, M., & Rathoure, A. K. (2015). Utilization of plant genetic resources and diversity analysis tools for sustainable crop improvement with special emphasis on rice. International Journal of Advanced Research, 3(3), 1155–1175.

Chauhan, R., Jasrai, Y., Pandya, H., Gami, R., & Tiwari, K. (2015). Genetic diversity analysis of six major cereal crops cultivars through RAPD markers. Bioinformatics, Proteomics and Immaging Analysis, 1(1), 20–24. https://doi.org /10.4172/2329-8863.1000191

Cifci, E. A., & Yagdi, K. (2012). Study of genetic diversity in wheat (Triticum aestivum) varities using random amplified polymorphic DNA (RAPD) analysis. Turkish Journal of Field Crop, 17(1), 91–95.

Glaszmann, J. C., Kilian, B., Upadhyaya, H. D., & Varshney, R. K. (2010). Accessing genetic diversity for crop improvement. Current Opinion in Plant Biology, 13, 1–7. https://doi.org/10.1016/j.pbi.2010.01.004

Hasan, M., & Raihan, M.S. (2015). Genetic variability in Bangladeshi aromatic rice through RAPD analysis. Turkish Journal of Agriculture and Food Science Technology, 3, 107–111.https://doi.org/10.24925/turjaf.v3i3.1 07-111.210

Höglund, J. (2009). Evolutionary conservation genetics. Oxford, UK: Oxford University Press. https://doi.org/10.1093/acprof:oso/9780 199214211.001.0001

Islam, M. S., Ali, M. A., Guswami, P., Ullah, S. M. S., Hossain, M. M., Miah, M. F., & Prodhan, S. H. (2013). Assessment of genetic diversity among moderately drought tolerant landraces of rice using RAPD markers. Journal of Biological Science and Biotechnology, 2(3), 207–213.

Jiang, G. (2017). Breeding genetics and biotechnology. In: Brian, T, Murphy, DJ, Murray, BG (Eds.), Encyclopedia of Applied Plant Science. New York, USA: Academic Press.

Kanawapee, N., Sanitchon, J., Srihaban, P., & Theerakulpisut, P. (2011). Genetic diversity analysis of rice cultivars (Oryza sativa L.) differing in salinity tolerance based on RAPD and SSR markers. Electronics Journal of Biotechnology, 14(6), 1–17. https://doi.org/10. 2225/vol14-issue6-fulltext-4

Kiani, G. (2011). Genetic diversity analysis of Iranian improved rice cultivars through RAPD markers. Notulae Scientia Biologicae, 3(3), 135–139. ttps://doi.org/10.15835/nsb.3.3.6131

Mani, P., Bastin, T. M. M. J., Kumar, R. A., & Ahmed, A. B. A. (2010). RAPD-Analysis of genetic variation of four important rice varieties using two OPR primers. ARPN Journal of Agriculture and Biological Science, 5, 12–15.

Mondini, L., Noorani, A., & Pagnotta, M. (2009). Assessing plant genetic diversity by molecular tools. Diversity, 1(1), 19–35. https://doi.org /10.3390/d1010019

Mursyidin, D. H., & Daryono, B. S. (2016). Genetic diversity of local durian (Durio zibethinus Murr.) cultivars of South Kalimantan’s province based on RAPD markers. AIP Conference Proceedings, 1755. https://doi.org/10.1063/1.4958483

Mursyidin, D. H., Nazari, Y. A., & Daryono, B. S. (2017). Tidal swamp rice cultivars of South Kalimantan Province, Indonesia: A case study of diversity and local culture. Biodiversitas, 18(1), 427-432. https://doi.org/10.13057/biodiv /d180156

Muthayya, S., Sugimoto, J. D., Montgomery, S., & Maberly, G. F. (2014). An overview of global rice production, supply, trade, and consumption. Annals of the New York Academy of Sciences, 1324(1), 7–14. https://d oi.org/10.1111/nyas.12540

Nayak, S. N., Singh, V. K., & Varshney, R. K. (2017). Marker-Assisted Selection. In Encyclopedia of applied plant sciences (pp. 183–197). Elsevier. https://doi.org/10.1016/B9 78-0-12-394807-6.00192-1

Pervaiz, Z. H., Rabbani, M. A., Khaliq, I., Pearce, S. R., & Malik, S. A. (2010). Genetic diversity associated with agronomic traits using microsatellite markers in Pakistani rice landraces. Electronic Journal of Biotechno logy, 13(3), 1–12. https://doi.org/10.2225/vol 13-issue3-fulltext-5

Rabbani, M. A., Pervaiz, Z. H., & Masood, M. S. (2008). Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L.) using RAPD markers. Electronic Journal of Biotechnology, 11(3), 1–10. https:// doi.org/10.2225/vol11-issue3-fulltext-3

Rajani, J., Deepu, V., Nair, G. M., & Nair, A. J. (2013). Molecular characterization of selected cultivars of rice, Oryza sativa L using Random Amplified Polymorphic DNA (RAPD) markers. International Food Research Journal, 20(2), 919–923.

Ray, A., Deb, D., Ray, R., & Chattopadhayay, B. (2013). Phenotypic characters of rice landraces reveal independent lineages of short-grain aromatic indica rice. AoB PLANTS, 5, 1–9. https://doi.org/10.1093/aobpla/plt032

Rekha, T., Martin, K. P., Sreekumar, V. B., & Madassery, J. (2011). Genetic diversity assessment of rarely cultivated traditional indica rice (Oryza sativa L.) varieties. Biotechnology Research International, 2011, 1–7. https://doi.org/10.4061/2011/784719

Rohlf, F. J. (2009). NTSYSpc: Numerical Taxonomy and Multivariate Analysis

Systemver. 2.2. In The American Statistician. New York: Applied Biostatistics Inc. https://doi.org /10.2307/2684761

Sitaresmi, T., Wening, R. H., Rakhmi, A. T., Yunani, N., & Susanto, U. (2013). Pemanfaatan plasma nutfah padi varietas lokal dalam perakitan varietas unggul. Iptek Tanaman Pangan, 8(1), 22–30. https://doi.org/ 10.2307/3440134

Sugihardjo, Suntoro, Sutrisno, J., & Setyono, P. (2016). The factors that affect risk of decline in rice productivity at irrigated rice fields due to climate change. International Conference on Climate Change, 235–241. https://doi.org/10.1 5608/iccc.y2016.568

Surapaneni, M., Balakrishnan, D., Mesapogu, S., Raju, A. K., et al. (2016). Genetic characterization and population structure of Indian rice cultivars and wild genotypes using core set markers. 3 Biotech, 6(1), 1–11. https:// doi.org/10.1007/s13205-016-0409-7

Tahir, N. A. (2014). Genetic variability evaluation among Iraqi rice (Oryza sativa L.) varieties using RAPD markers and protein profiling. Jordan Journal of Biological Science, 7(1), 13–18. http://dx.doi.org/10.12816/0008207

Thomson, M. J., Polato, N. R., Prasetiyono, J., Trijatmiko, K. R., Silitonga, T. S., & McCouch, S. R. (2009). Genetic diversity of isolated populations of Indonesian landraces of rice (Oryza sativa L.) collected in East Kalimantan on the Island of Borneo. Rice, 2(1), 80–92. https://doi.org/10.1007/s12284-009-9023-1

Wahdah, R., Langai, B. F., & Sitaresmi, T. (2012). Keragaman karakter varietas lokal padi pasang surut Kalimantan Selatan. Penelitian Pertanian Tanaman Pangan, 31(3), 158–165. http:// dx.doi.org/10.21082/jpptp.v31n3.2012.p158-165

Refbacks

  • There are currently no refbacks.


Bookmark and Share


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