Genetic Diversity Analysis of Hedychium Species Based on RAPD and ISSR Markers

Research Article


The present study reports for the first time the genetic diversity assessment of Hedychium species collected from different parts of Manipur using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeats (ISSR) markers. Eleven RAPD and five ISSR markers produced 271 polymorphic fragments with an average polymorphism of 96.95% between the eleven Hedychium species and similarity coefficients ranged from 0.19 to 0.44 with an average of 0.30, which in turn, indicates high genetic diversity. Cophenetic correlation coefficients between the dendrogram and the combined similarity matrices were moderately significant (r = 0.67). UPGMA clustering based on Jaccard’s similarity coefficient using the combined RAPD and ISSR markers placed the accessions into three distinct clusters with respect to their morphological characteristics and geographical location. Both RAPD and ISSR markers were efficient in distinguishing the eleven Hedychium species, however, ISSR markers were observed to be better in displaying average polymorphism (99%) than RAPD (96.03%). The study has contributed in understanding the genetic diversity and gene pool conservation of Hedychium species.


Genetic diversity Hedychium RAPD ISSR Principal Component Analysis (PCA) 



The authors are thankful to the Department of Biotechnology, New Delhi (DBT) for financial assistance (vide No. BT/Bio-CARE/05/880/2010-11).

Compliance with Ethical Standards

Conflict of interest

The authors declare that there is no conflict of interest or involvement in any organization or entity with any financial interest, to publish this manuscript.

Supplementary material

40011_2018_976_MOESM1_ESM.doc (41 kb)
Supplementary material 1 (DOC 41 kb)
40011_2018_976_MOESM2_ESM.doc (42 kb)
Supplementary material 2 (DOC 41 kb)
40011_2018_976_MOESM3_ESM.doc (38 kb)
Supplementary material 3 (DOC 37 kb)


  1. 1.
    Srimal RC, Sharma SC, Tandon JS (1984) Synthesis of (+)-coronarin. E Indian J Phamacol 16:143Google Scholar
  2. 2.
    Prakash A, Singh KK (2001) Eukaryotic translation synthesis DNA polymerases. J Med Aroma Plant Sci 519:22–23Google Scholar
  3. 3.
    Shrotriya S, Ali MS, Saha A, Bachar SC, Islam MS (2007) Anti-inflammatory and analgesic effects of Hedychium coronarium Koen. Pak J Pharm Sci 20(1):47–51PubMedGoogle Scholar
  4. 4.
    Gopanraj G, Dan M, Shiburaj S, Sethuraman MG, George V (2005) Chemical composition and antibacterial activity of the rhizome oil of Hedychium larsenii. Acta Pharm 55(3):315–320PubMedGoogle Scholar
  5. 5.
    Saleh MM, Kamal RM, Abdulla WA (1982) A contribution to the molluscicidal activity of Hedychium gardinarum. Planta Med 45(7):166CrossRefPubMedGoogle Scholar
  6. 6.
    Warren KS, Peters PA (1968) Cercariae of Schistosoma mansoni and plants: attempt to penetrate Phaseolus vulgaris and Hedychium coronarium produces a cercaricide. Nature 217(5129):647–648CrossRefPubMedGoogle Scholar
  7. 7.
    Facciola S (1990) Cornucopia-a source book of edible plants. Kampong Publications, VistaGoogle Scholar
  8. 8.
    Sarangthem N, Talukdar NC, Thongam B (2013) Collection and evaluation of Hedychium species of Manipur, Northeast India. Genet Resour Crop Evol 60:13–21CrossRefGoogle Scholar
  9. 9.
    Wood TH, Whitten WM, Williams NH (2000) Phylogeny of Hedychium and related genera (Zingiberaceae) based on ITS sequence data. Edinb J Bot 57(2):217–261CrossRefGoogle Scholar
  10. 10.
    Jatoi S, Kikuchi A, Mimura M, San SY, Watanabe KN (2008) Relationships of Zingiber species, and genetic variability assessment in ginger (Zingiber officinale) germplasms from ex situ gene bank on-farm and rural markets. Breed Sci 58:261–270CrossRefGoogle Scholar
  11. 11.
    Kizhakkayil J, Sasikumar B (2010) Genetic diversity analysis of ginger (Zingiber officinale Rosc) germplasm based on RAPD and ISSR markers. Sci Hortic 125:73–76CrossRefGoogle Scholar
  12. 12.
    Basak S, Ramesh AM, Kesari V, Parida A, Mitra S, Rangan L (2014) Genetic diversity and relationship of Hedychium from Northeast India as dissected using PCA analysis and hierarchical clustering. Meta Gene 2:459–468CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Ashraf K, Ahmad A, Chaudhary A, Mujeeb M, Ahmad S, Amir M, Mallick N (2014) Genetic diversity analysis of Zingiber Officinale Roscoe by RAPD collected from subcontinent of India. Saudi J Biol Sci 21:159–165CrossRefPubMedGoogle Scholar
  14. 14.
    Milbourne D, Meyer R, Bradshaw JE, Baird E, Bonar N, Provan J, Powell W, Waugh (1997) Comparison of PCR based marker systems for the analysis of genetic relationships in cultivated potato. Mol Breed 3:127–136CrossRefGoogle Scholar
  15. 15.
    Anderson JA, Churchill GA, Autrique JE, Tanksley SD, Sorrells ME (1993) Optimizing parental selection for genetic linkage maps. Genome 36:181–186CrossRefPubMedGoogle Scholar
  16. 16.
    Prevost A, Wilkinson MJ (1999) A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars. Theor Appl Genet 98:107–112CrossRefGoogle Scholar
  17. 17.
    Syamkumar S, Sasikumar B (2017) Molecular marker based genetic diversity analysis of Curcuma species from India. Sci Hortic 112:235–241CrossRefGoogle Scholar
  18. 18.
    Sajeev S, Roy AR, Langrai B, Pattanayak A, Deka BCC (2011) Genetic diversity analysis in traditional and improved ginger (Zingiber officinale Rosc.) clones cultivated in North- East India. Sci Hortic 128:182–188CrossRefGoogle Scholar
  19. 19.
    Pandotra P, Gupta AP, Husain MK, Gupta SG (2013) Evaluation of genetic diversity and chemical profile of ginger cultivars in north- western Himalayas. Biochem Syst Ecol. 48:281–287CrossRefGoogle Scholar
  20. 20.
    Pandotra P, Gupta AP, Khan S, Ram G, Gupta S (2015) A comparative assessment of ISSR, RAPD, IRAP, & REMAP molecularmarkers in Zingiber officinale germplasm characterization. Sci Hortic 194:201–207CrossRefGoogle Scholar
  21. 21.
    Jugran A, Bhatt ID, Rawat S, Giri L, Rawal RS, Dhar U (2011) Genetic diversity and differentiation in Hedychium spicatum, a valuable medicinal plant of Indian Himalaya. Biochem Genet 49(11):806–818CrossRefPubMedGoogle Scholar

Copyright information

© The National Academy of Sciences, India 2018

Authors and Affiliations

  1. 1.Department of BiotechnologyManipur UniversityCanchipur, ImphalIndia

Personalised recommendations