Journal of Crop Science and Biotechnology

, Volume 22, Issue 1, pp 55–63 | Cite as

Genetic Diversity Analysis of Indonesian Aromatic Rice Varieties (Oryza sativa L.) Using RAPD

  • Nur Meili Zakiyah
  • Tri Handoyo
  • Kyung-Min KimEmail author
Research Article


In this research, we investigated genetic diversity of 21 rice genotypes (Oryza sativa L.) assessed using 38 decamer RAPD primers. A total of 405 bands were produced from 38 primers, which revealed that 84.44% was polymorphic and 15.56% was monomorphic. From the first cluster, Batang Gadis separated from 14 other genotypes. The second cluster consisted of six genotypes which all had awn in the seed except Gogo Fatuk Masin. The high number of amplified polymorphism bands showed that the markers can be used to distinguish the rice genotype well. RAPD markers can show differences in individual fingerprint patterns, since genetic variation is important for the maintenance and development of the organism's potential. The information about the genetic diversity in this study was useful for plant breeders in the selection of elders and processing of plant cultivation.

Key words

Aromatic rice genetic diversity polymorphism RAPD 


Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.


  1. Abuzayed M, El-Dabba N, Frary A, Doganlar S. 2017. GDdom: an online tool for calculation of dominant marker gene diversity. Biochem. Genet. 55: 155–157CrossRefGoogle Scholar
  2. Ampapathi RS, Creath AL, Lou, Jr Craft JW, Blanke SR, Legge GB. 2008. Order-disorder-order transitions mediate the activation of cholera toxin. J. Mol. Biol. 377: 748–760CrossRefGoogle Scholar
  3. Baishya S, Sachdev A, Johari RP, Mehta SL. 2000. RAPD analysis of aromatic and non-aromatic rice (Oryza sativa L.). J. Plant Biochem. Biotechnol. 9: 23–26CrossRefGoogle Scholar
  4. Bolaric S, Melchinger AE, Posselt UK. 2005. Genetic diversity in European perennial ryegrass cultivars investigated with RAPD markers. Plant Breed. 124: 161–166CrossRefGoogle Scholar
  5. Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE. 2005. The gene for fragrance in rice. Plant Biotechnol.J. 3: 363–370CrossRefGoogle Scholar
  6. Chesnokov YV, Artemyeva AM. 2015. Evaluation of the measure of polymorphism information of genetic diversity. Sel’skokhozyaistvennaya Biologiya. 50: 571–578CrossRefGoogle Scholar
  7. Choudhury PR, Kohli S, Srinivasan K, Mohapatra T, Sharma RP. 2001. Identification and classification of aromatic rices based on DNA fingerprinting. Euphytica 118: 243–251CrossRefGoogle Scholar
  8. De Riek J, Calsyn E, Everaert I, Van Bockstaele E, De Loose M. 2001. AFLP based alternatives for the assessment of distinctness, uniformity and stability of sugar beet varieties. Theor. Appl. Genet. 103: 1254–1265CrossRefGoogle Scholar
  9. Fukuoka S, Tran SD, Ebana K, Luu TN, Nagamine T, Okuno K. 2006. Genetic organization of aromatic rice as revealed by RAPD markers: A case study in conserving crop genetic resources on farm. Euphytica 149: 61–71CrossRefGoogle Scholar
  10. Giraud G. 2013. The world market of fragrant rice, main issues and perspectives. Int Food Agribus. Manag. Rev. 16: 1–20Google Scholar
  11. Grattapaglia D, Sederoff R. 1994. Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudotestcross: mapping strategy and RAPD markers. Genetics 137: 1121–1137Google Scholar
  12. Haig SM, Rhymer JM, Heckel DG. 1994. Population differentiation in randomly amplified polymorphic DNA of red-cockaded woodpeckers Picoides borealis. Mol. Ecol. 1994: 581–595CrossRefGoogle Scholar
  13. Hasan M, Raihan MS. 2015. Genetic variability in Bangladeshi aromatic rice through RAPD analysis. Turk. J. Agric. - Food Sci. Technol. 3: 107–111Google Scholar
  14. Henry RJ. 1997. Practical aplications of plant molecular biology. Chapman & Hall. London.CrossRefGoogle Scholar
  15. IRRI. 2013. Standard Evaluation System for Rice. International Rice Research Instiitute. P.O. Box 933, 1099 Manila, PhilippinesGoogle Scholar
  16. Jonah PM, Bello LL, Lucky O, Midau A, Moruppa SM, Moruppa SM. 2011. Review: The importance of molecular markers in plant breeding programmes. Global Journal of Sci. Front. Res. 11: 5–12Google Scholar
  17. 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. Electron. J. Biotechnol. 14: 1–18Google Scholar
  18. Kearney J. 2010. Food consumption trends and drivers. Philos. Trans. R. Soc. Lond. B. Biol. Sci. 365: 2793–2807CrossRefGoogle Scholar
  19. Kibria K, Nur F, Begum SN, Islam MM, Paul SK, Rahman KS, Azam SMM. 2009. Molecular marker based genetic diversity in aromatic rice genotypes using SSR and RAPD markers. Int. J. Sustain. Crop Prod. 4: 23–34Google Scholar
  20. Kumari P, Ahuja U, Jain S, Jain RK. 2012. Fragrance analysis using molecular and biochemical methods in recombinant inbred lines of rice. Afr. J. Biotechnol. 11: 15784–15789CrossRefGoogle Scholar
  21. Mathure S, Jawali N, Nadaf A. 2010. Diversity analysis in selected non-basmati scented rice collection. Rice Sci. 17: 35–42CrossRefGoogle Scholar
  22. McCluskey JJ. 2015. Changing Food Demand and Consumer Preferences. Federal Reserve Bank of Kansas CityGoogle Scholar
  23. Michelmore RW, Paran I, Kesseli RV. 1991. Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc. Natl. Acad. Sci. USA 88: 9828–9832CrossRefGoogle Scholar
  24. Nagy S, Poczai P, Cernák I, Gorji AM, Hegedus G, Taller J. 2012. PICcalc: An online program to calculate polymorphic information content for molecular genetic studies. Biochem. Genet. 50: 670–672CrossRefGoogle Scholar
  25. Nei M. 1973. Analysis of gene diversity in subdivided populations. Proc. Natl. Acad. Sci. USA. 70: 3321–3323CrossRefGoogle Scholar
  26. Patwardhan A, Ray S, Roy A. 2014. Molecular markers in phylogenetic studies-A review. J. Phylogenetics Evol. Biol. 2: 131Google Scholar
  27. Rabbani MA, Pervaiz ZH, Masood MS. 2008. Genetic diversity analysis of traditional and improved cultivars of Pakistani rice (Oryza sativa L.) using RAPD markers. Electron J. Biotechnol. 11(3)Google Scholar
  28. Raghunathachari P, Khanna VK, Singh US, Singh NK. 2000. RAPD analysis of genetic variability in Indian scented rice germplasm (Oryza sativa L.). Curr. Sci. 79: 994–998Google Scholar
  29. Rahman SN, Islam S, Alam S, Nasiruddin KM. 2007. Genetic polymorphism in rice ( Oryza sativa L.) through RAPD analysis. Ind. J. Biotechnol. 6: 224–229Google Scholar
  30. Ray A, Pattanaik A, Samal KC, Kshirsagar SS, Rout GR. 2012. Variety diagnostic PCR-RAPD markers for aromatic rice varieties grown in Eastern Part of India. J. Plant Sci. Res. 28: 91–100Google Scholar
  31. Shete S, Tiwari H, Elston RC. 2000. On Estimating the Heterozygosity and Content Value. Theor. Popul. Biol. 57: 265–271CrossRefGoogle Scholar
  32. Suprihatno B, Daradjat AA, Satoto, Baehaki SE, Suprihanto, Setyono A, Sembiring H. 2010. Description of Rice Varieties. Jakarta: Indonesian Center for Rice Research, Indonesia Agency for Agricultural Research and Development. Ministry of AgricultureGoogle Scholar
  33. Tahmina I, Rahman MIS, Hoqueand RH, Sarker. 2017. Genetic diversity assessment in ten aromatic rice varieties of Bangladesh. Plant Tiss. Cul. Biotechnol. 27: 217–225CrossRefGoogle Scholar
  34. Thomas G, Mohapatra T, Rao AR, Sharma RP. 2006. Distinguishing Indian commercial wheat varieties using RAPD based DNA fingerprints. Ind. J. Biotechnol. 5: 200–206Google Scholar
  35. Timmer CP. 2010. The Changing Role of Rice in Asia’s Food Security. ADB Sustainable Development Working Paper Series. 15Google Scholar
  36. Veatch-Blohm, Maren E. 2007. Principles of plant genetics and breeding. Crop Sci. 47: 1763–1763CrossRefGoogle Scholar
  37. Verma SK, Khanna V, Singh N. 1999. Random amplified polymorphic DNA analysis of Indian scented basmati rice (Orzya sativa L.) germplasm for identification of variability and duplicate accessions. Electrophoresis 20: 1786–1789CrossRefGoogle Scholar
  38. Wahab MS, Satoto, Rahmini, Zarkawi LM, Suprihatno, Guswara A, Suharna. 2018. Description of New Hybrid Rice Varieties. Jakarta: Indonesian Center for Rice Research, Indonesia Agency for Agricultural Research and Development. Ministry of AgricultureGoogle Scholar
  39. Wright S. 1943. Isolation by distance. Genetics 28: 114–138Google Scholar

Copyright information

© Korean Society of Crop Science and Springer 2019

Authors and Affiliations

  • Nur Meili Zakiyah
    • 1
  • Tri Handoyo
    • 2
    • 3
  • Kyung-Min Kim
    • 4
    Email author
  1. 1.Graduate School of BiotechnologyUniversity of JemberJemberIndonesia
  2. 2.Faculty of AgricultureUniversity of JemberJemberIndonesia
  3. 3.Center For Devolopment of Advanced Sciences and TechnologyUniversity of JemberJemberIndonesia
  4. 4.Division of Plant Biosciences, School of Applied Biosciences, College of Agriculture & Life ScienceKyungpook National UniversityDaeguRepublic of Korea

Personalised recommendations