Physiology and Molecular Biology of Plants

, Volume 19, Issue 2, pp 245–250 | Cite as

RAPD, SCAR and conserved 18S rDNA markers for a red-listed and endemic medicinal plant species, Knema andamanica (Myristicaceae)

  • T. E. Sheeja
  • P. R. Anju
  • R. S. Shalini
  • S. Siju
  • K. Dhanya
  • B. Krishnamoorthy
Research Article


Knema andamanica is a red-listed endemic medicinal species of Myristicaceae restricted to Andaman and Nicobar (A&N) Islands, India. This species is used in tribal medicines and has immense bioprospective potential. With a view to generate suitable genomic markers for classification and identification, we have generated RAPD, SCAR and conserved 18S rDNA markers from K. andamanica. A unique 585 bp fragment, that distinguished it from seven other related species of Myristicaceae was first amplified using the random primer OPE 06 and converted to SCAR marker (GenBank accession # JN228256). The conserved sequences of 18S rDNA loci from K. andamanica were also amplified and sequenced (GenBank accession #JN228265). The sequence revealed deviations including 18 variable regions and 15 indels that were unique to K. andamanica. These markers can help in definite identification of K. andamanica even at the juvenile stages.


Knema andamanica RAPD SCAR 18S rDNA and germplasm characterization Genetic differentiation 



Sequence Characterised Amplified Region


Inter Simple Sequence Repeats


Amplified Fragment Length Polymorphism


Simple Sequence Repeats


ribosomal DNA


National Center for Biotechnology Information


Random Amplification of Polymorphic DNA


Single Nucleotide Polymorphism


Basic Local Alignment Search Tool


  1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410PubMedGoogle Scholar
  2. Bachmann K (1997) Nuclear DNA markers in plant biosystematic research. Opera Bot 132:137–148Google Scholar
  3. Bhakuni DS, Dhar ML, Dhar MM, Dhawan BN, Mehrotra BN (1969) Screening of Indian plants for biological activity, Part VIII. Indian J Exp Biol 7(4):250–262PubMedGoogle Scholar
  4. Castells CJ, Rodrguez MG, Rosas BM, Garca CN, Navarrete VB (2008) Population genetics of the endangered Canarian endemic Atractylis arbuscula (Asteraceae): implications for taxonomy and conservation. Plant Syst Evol 274:99–109CrossRefGoogle Scholar
  5. Das M, Bhattacharya S, Pal A (2004) Generation and characterization of SCARs by cloning and sequencing of RAPD products: a strategy for species-specific marker development in bamboo. Ann Bot 95:835–841CrossRefGoogle Scholar
  6. Ding G, Zhang D, Yu Y, Zhang B, Zhao L (2012) Genetic identification and relationship analysis of medicinal Limonium by rDNA ITS sequence, single nucleotide polymorphism (SNP) and amplification refractory mutation system (ARMS). J Med Plants Res 6:4535–4539Google Scholar
  7. Ghosh M, Chezhian P, Ramasamy S, Ramasamy Y (2011) Development of SCAR marker in Casuarina equisetifolia for species authentication. Trees 25:465–472CrossRefGoogle Scholar
  8. Jo SH, Koo DH, Kim JF, Hur CG, Lee S, Yang TJ, Kwon SY, Choi D (2009) Evolution of ribosomal DNA-derived satellite repeat in tomato genome. BMC Plant Biol 9:42PubMedCrossRefGoogle Scholar
  9. Kim CS, Lee CH, Park KW, Kang SJ, Shin IS, Lee GP (2005) Phylogenetic relationships among Pyrus pyrifolia and Pyrus communis detected by randomly amplified polymorphic DNA (RAPD) and conserved rDNA sequences. Sci Hortic 106:491–501CrossRefGoogle Scholar
  10. Lee GP, Lee CH, Kim CS (2004) Molecular markers derived from RAPD, SCAR and the conserved 18S rDNA sequences for classification and identification in Pyrus pyrifolia and P. communis. Theor Appl Genet 108:1487–1491PubMedCrossRefGoogle Scholar
  11. Lee EJ, Hwang IK, Kim NY, Lee KL, Han MS, Lee YH, Kim MY, Yang MS (2010) An assessment of the utility of universal and specific genetic markers for opium poppy identification. J Forensic Sci 55:1202–1208PubMedCrossRefGoogle Scholar
  12. Lee SY, Weber J, Mohamed R (2011) Genetic variation and molecular authentication of selected Aquilaria species from natural populations in Malaysia using RAPD and SCAR markers. Asian J Plant Sci 10:202–211CrossRefGoogle Scholar
  13. Li G, Park YJ (2012) SCAR markers for discriminating species fo two genera of medicinal plants, Liriope and Ophiopogon. Genet Mol Res 18:11Google Scholar
  14. Librado P, Rozas J (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25:1451–1452PubMedCrossRefGoogle Scholar
  15. Maya KM, Zachariah JT, Krishnamurthy KS, Rema J, Krishnamoorthy B (2006) Fatty acids and leaf amino acids in Myristica fragrans Houtt. and related taxa. Indian J Hortic 63:316–318Google Scholar
  16. Mentewab AB, Jacobsen MJ, Flowers RA (2011) Incomplete homogenization of 18 S ribosomal DNA coding regions in Arabidopsis thaliana. BMC Res Notes 4:93PubMedCrossRefGoogle Scholar
  17. Nei M, Rooney AP (2005) Concerted and birth and death evolution of mutligene families. Annu Rev Genet 39:121–152PubMedCrossRefGoogle Scholar
  18. Nickrent DL, Soltis DE (1995) A comparison of angiosperm phylogenies from nuclear 18S rDNA and rbcL sequences. Ann Mo Bot Gard 82:208–234CrossRefGoogle Scholar
  19. Prasad PRC, Reddy CS, Lakshmi RKV, Kumari PV, Raza SH (2009) List of species. Angiosperms of North Andaman, Andaman and Nicobar islands, India. Check List 5:254–269Google Scholar
  20. Rema J, Krishnamoorthy B, Mathew PA (2005) Genetic diversity… Nutmeg (Myristica fragrans Houtt.). Indian Hortic 50:5–6Google Scholar
  21. Rieseberg LH (1996) Homology among RAPD fragments in interspecific comparisons. Mol Ecol 5:99–105CrossRefGoogle Scholar
  22. Roy SC, Chattopadhyay A (2011) Evaluation of genetic diversity in mango germplasm resources using RAPD markers and characterization of cultivar Guti based on 18S rRNA gene sequence. Indian J Genet Plant Breed 71:254–261Google Scholar
  23. Roy S, Krishnan P (2005) Mangrove stands of Andamans vis-à-vis tsunami. Curr Sci 89:1800–1804Google Scholar
  24. Sasaki Y, Fushimi H, Cao H, Cai SQ, Komatsu K (2002) Sequence analysis of Chinese and Japanese Curcuma drugs on the 18S rRNA gene and trnK gene and the application of amplification-refractory mutation system analysis for their authentication. Biol Pharm Bull 25:1593–1599PubMedCrossRefGoogle Scholar
  25. Sharief MU (2007) Plants folk medicine of Negrito tribes of Bay Islands. Indian J Tradit Knowl 6:468–476Google Scholar
  26. Sheeja TE, Rajesh Y, Krishnamoorthy B, Parthasarathy VA (2006) DNA polymorphism in clonal and seedling progenies of an elite nutmeg (Myristica fragrans Houtt.) by RAPD. J Plant Crop 34:558–561Google Scholar
  27. Sheeja TE, George KJ, Jerome J, Varma RS, Syamkumar S, Krishnamoorthy B, Parthasarathy VA (2008) Optimization of DNA isolation and PCR parameters in Myristica sp. and related genera for RAPD and ISSR analysis. J Spices Aromat Crops 17:91–97Google Scholar
  28. Sheeja TE, Sabeesh C, Shabna OV, Shalini RS, Krishnamoorthy B (2013) A comparative analysis of genetic diversity of wild and related genera of Myristica using RAPD and ISSR markers. J. Spices Aromat Crops 22 (in press)Google Scholar
  29. Soltis PS, Douglas ES, Paul GW, Daniel LN, Chaw SM, Russell LC (1999) The phylogeny of land plants inferred from 18S rDNA sequences: pushing the limits of rDNA signal? Mol Biol Evol 16:1774–1784PubMedCrossRefGoogle Scholar
  30. Sun XQ, Wei YL, Zhou YF, Guo JL, Hang YY (2011) Development of species and region specific random amplification of polymorphic DNA- sequence characterized amplified region (RAPD-SCAR) markers for identification of the genuineness of Spica prunellae (Lamiaceae). J Med Plants Res 5:1677–1684Google Scholar
  31. Valderrama J, Martinez C (2000) Distribution of flavonoids in the Myristicaceae. Phytochemistry 55:505–511PubMedCrossRefGoogle Scholar
  32. Yoo YK, Yuan T, Lee JS, Lee AK, Roh MS, Kurita S, Suh JK (2011) Species relationships of Lycoris endemic to Korea evaluated by RAPD and SNPs of nrDNA-ITS regions. Hortic Environ Biotechnol 52:145–151CrossRefGoogle Scholar
  33. Zhang YB, Shaw PC, Sze CW, Wang ZT, Tong Y (2007) Molecular authentication of Chinese herbal materials. J Food Drug Anal 15:1–9Google Scholar

Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2013

Authors and Affiliations

  • T. E. Sheeja
    • 1
  • P. R. Anju
    • 1
  • R. S. Shalini
    • 1
  • S. Siju
    • 1
  • K. Dhanya
    • 1
    • 2
  • B. Krishnamoorthy
    • 1
  1. 1.Division of Crop Improvement and BiotechnologyIndian Institute of Spices ResearchCalicutIndia
  2. 2.Weill Cornell Medical College in Qatar, Qatar Foundation – Education CityDohaQatar

Personalised recommendations