Physiology and Molecular Biology of Plants

, Volume 25, Issue 3, pp 753–764 | Cite as

Molecular analysis of genetic diversity and population genetic structure in Ephedra foliata: an endemic and threatened plant species of arid and semi-arid regions of India

  • Baleshwar Meena
  • Niraj Singh
  • Kamalesh Singh Mahar
  • Yogesh Kumar Sharma
  • Tikam Singh RanaEmail author
Research Article


Studies on the genetic diversity and structure in endangered and threatened species are of utmost importance to design and promote effective conservation and management programs. Ephedra foliata, an endemic and threatened species growing naturally in arid and semi-arid regions of north western India, was investigated to estimate genetic variability and population structure using inter-simple sequence repeats (ISSR) and directed amplification of mini-satellite DNA (DAMD) markers. Twenty-five (ISSR 15; DAMD 10) markers produced 449 fragments, of which 382 were polymorphic in nature, revealing 84.59% polymorphism. ISSR markers revealed higher levels of polymorphism, polymorphic information content, marker index, diversity index and effective multiplex ratio than DAMD markers. Higher values of polymorphism, genetic diversity and Shannon information index at species level than at population level revealed that E. foliata possess high genetic diversity. AMOVA revealed much higher variance within populations than among the populations. The three clustering approaches viz., UPGMA, PCoA, and STRUCTURE, grouped the eleven investigated populations into two clusters revealing two genetic populations and the patterns of clustering of populations was in accordance with their geographic distribution, suggesting that these populations have evolved in response to their local environments. The high level of genetic differentiation (GST = 0.31) and moderate gene flow (Nm = 1.11) among populations could be due to geographic isolation, regional climatic conditions, over-exploitation and improper seed setting. To the best of our knowledge, this study is the first endeavour to estimate genetic diversity and population structure of E. foliata using molecular markers.


Arid regions Ephedra foliata Genetic variability Molecular markers Population genetic structure 



The financial support from Council of Scientific and Industrial Research (CSIR), New Delhi, India (OLP-101) is duly acknowledged.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

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Copyright information

© Prof. H.S. Srivastava Foundation for Science and Society 2019

Authors and Affiliations

  • Baleshwar Meena
    • 1
  • Niraj Singh
    • 1
  • Kamalesh Singh Mahar
    • 3
  • Yogesh Kumar Sharma
    • 2
  • Tikam Singh Rana
    • 1
    Email author
  1. 1.Molecular Systematics LaboratoryCSIR-National Botanical Research InstituteLucknowIndia
  2. 2.Department of BotanyUniversity of LucknowLucknowIndia
  3. 3.CSIR-Central Institute of Medicinal and Aromatic PlantsLucknowIndia

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