Acta Biologica Hungarica

, Volume 63, Issue 4, pp 463–473 | Cite as

Development of Chloroplast Microsatellite Markers for Phylogenetic Analysis in Brassicaceae

  • Praveen Awasthi
  • Irshad Ahmad
  • Sumit G. GandhiEmail author
  • Yashbir S. Bedi


By employing in silico tools, we devised new chloroplast microsatellite primers for inferring phyloge-netic relationships within Brassicaceae. Microsatellite repeats were scanned in 12 chloroplast genomes of Brassicaceae, regions flanking these repeats were aligned and 19 universal primers were designed. Fifteen of these primer pairs are predicted to yield polymorphic amplicons, that are more or less evenly distributed throughout the chloroplast genomes. Finally, using PCR, we have validated three primer pairs on a limited ‘test set’ of plants, different from those used in computational analysis.


Simple Sequence Repeat SSRs chloroplast DNA universal primers in silico 


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Financial assistance provided by institutional CSIR grants in deeply acknowledged.


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© Akadémiai Kiadó, Budapest 2012

This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (, which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.

Authors and Affiliations

  • Praveen Awasthi
    • 1
  • Irshad Ahmad
    • 1
  • Sumit G. Gandhi
    • 1
    Email author
  • Yashbir S. Bedi
    • 1
  1. 1.Plant Biotechnology Division, Indian Institute of Integrative Medicine (Council of Scientific and Industrial Research)JammuIndia

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