Physiology and Molecular Biology of Plants

, Volume 16, Issue 4, pp 375–378 | Cite as

Development of EST-based new SSR markers in seabuckthorn

  • Ankit Jain
  • Rajesh Ghangal
  • Atul Grover
  • Saurabh Raghuvanshi
  • Prakash C. SharmaEmail author
Short Communication


EST-based SSR markers were developed by screening a collection of 1584 clustered ESTs of seabuckthorn (Hippophae rhamnoides). PCR primers were designed for the amplification of 30 microsatellite loci. Two to five allelic bands were displayed by nine primer pairs in H. rhamnoides genotypes and by eleven primer pairs in H. salicifolia genotypes. None of the thirty primer pairs detected polymorphism in H. tibetana genotypes. Considering the high polymorphism detected in the tested genotypes and their direct origin from the genic regions, these EST-SSR markers hold immense promise in seabuckthorn genome analysis, molecular breeding and population genetics.


Hippophae rhamnoides Expressed sequence tags Simple sequence repeats (SSRs) Cross-amplification 



This research and AJ was supported by Defense Research and Development Organization (DRDO), India through a sponsored project (Project No. LSRB-146/FS/2008). RG thanks Indian Council of Medical Research (ICMR), India for financial support. Authors wish to thank Defense Institute of High Altitude Research (DIHAR), Leh, India for providing genotypes used in this study.


  1. Chauhan AS, Negi PS, Rarnteke RS (2007) Antioxidant and antibacterial activities of aqueous extract of seabuckthorn (Hippophae rhamnoides) seeds. Fitoterapia 78:590–592CrossRefPubMedGoogle Scholar
  2. Doyle JJ, Doyle JL (1988) A rapid total DNA preparation procedure for fresh plant tissue. Am J Bot 75:1238CrossRefGoogle Scholar
  3. Fujimori S, Washio T, Higo K, Ohtomo Y, Murakami K, Matsubara K, Kawai J, Carninci P, Hayashizaki Y, Kikuchi S, Tomita M (2003) A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett 554:17–22CrossRefPubMedGoogle Scholar
  4. Geetha S, Ram MS, Sharma SK, Ilavazhagan G, Banerjee PK, Sawhney RC (2009) Cytoprotective and antioxidant activity of seabuckthorn (Hippophae rhamnoides L.) flavones against tert-butyl hydroperoxide-induced cytotoxicity in lymphocytes. J Med Food 12:151–158CrossRefPubMedGoogle Scholar
  5. Ghangal R, Raghuvanshi S, Sharma PC (2009) Isolation of good quality RNA from a medicinal plant seabuckthorn, rich in secondary metabolites. Plant Physiol Biochem 47:1113–1115CrossRefPubMedGoogle Scholar
  6. Grover A, Sharma PC (2004) Occurrence of simple sequence repeats in potato ESTs is not random: An in silico study on distribution and length of simple sequence repeats. Potato J 31:95–102Google Scholar
  7. Grover A, Sharma PC (2007) Microsatellite motifs with moderate GC content are clustered around genes on Arabidopsis thaliana chromosome 2. In Silico Biol 7:0021Google Scholar
  8. Grover A, Aishwarya V, Sharma PC (2007) Biased distribution of microsatellite motifs in the rice genome. Mol Genet Genomics 277:469–480CrossRefPubMedGoogle Scholar
  9. Grover A, Jain A, Sharma PC (2010) Microsatellite markers: potential and opportunities in Medicinal plants. In: Arora R (ed) Medicinal plant biotechnology. (CAB International, Oxon, United Kingdom) (in press)Google Scholar
  10. Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877CrossRefPubMedGoogle Scholar
  11. Jain M, Ganju L, Katiyal A, Padwad Y, Mishra KP, Chanda S, Karan D, Yogendra KM, Sawhney RC (2008) Effect of Hippophae rhamnoides leaf extract against Dengue virus infection in human blood-derived macrophages. Phytomedicine 15:793–799CrossRefPubMedGoogle Scholar
  12. Mishra KP, Chanda S, Karan D, Ganju L, Sawhney RC (2008) Effect of seabuckthorn (Hippophae rhamnoides) flavone on immune system: an in-vitro approach. Phytother Res 22:1490–1495CrossRefPubMedGoogle Scholar
  13. Rozen S, Skaletsky H (2000) Primer3 on the WWW for general users and for biologist programmers. In: Krawetz S, Misener S (eds) Bioinformatics methods and protocols in the series methods in molecular biology. Humana, Totowa, pp 365–386Google Scholar
  14. Shi Z, Su B, Guo Y (1987) Mixed afforestation with Chinese pine and sea-buckthorn. Ningxia Agric Forest Sci Technol 5:54Google Scholar
  15. Thiel T, Michalek W, Varshney RK, Graner A (2003) Exploiting EST databases for the development of cDNA derived microsatellite markers in barley (Hordeum vulgare L.). Theor Appl Genet 106:411–422PubMedGoogle Scholar
  16. Varshney RK, Graner A, Sorrells ME (2005) Genic microsatellite markers in plants: features and applications. Trends Biotechnol 23:48–55CrossRefPubMedGoogle Scholar
  17. Wang A, Zhang Q, Wan D, Yang Y, Liu J (2008) Nine microsatellite DNA primers for Hippophae rhamnoides ssp. sinensis (Elaeagnaceae). Conserv Genet 9:969–971CrossRefGoogle Scholar
  18. Zane L, Bargelloni L, Patarnello T (2002) Strategies for microsatellite isolation: a review. Mol Ecol 11:1–16CrossRefPubMedGoogle Scholar
  19. Zeb A (2004) Chemical and nutritional constituents of sea buckthorn juice. Pak J Nutr 3:99–106CrossRefGoogle Scholar
  20. Zeb A (2006) Anticarcinogenic potential of lipids from Hippophae—evidence from the recent literature. Asian Pac J Cancer Prev 7:32–35PubMedGoogle Scholar

Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2010

Authors and Affiliations

  • Ankit Jain
    • 1
  • Rajesh Ghangal
    • 1
  • Atul Grover
    • 1
    • 3
  • Saurabh Raghuvanshi
    • 2
  • Prakash C. Sharma
    • 1
    Email author
  1. 1.University School of Biotechnology, Guru Gobind Singh Indraprastha UniversityDelhiIndia
  2. 2.Interdisciplinary Center for Plant Genomics, Department of Plant Molecular BiologyUniversity of DelhiNew DelhiIndia
  3. 3.Defense Institute of Bio-Energy ResearchHaldwaniIndia

Personalised recommendations