Development of Chloroplast Microsatellite Markers for Phylogenetic Analysis in Brassicaceae


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.


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Financial assistance provided by institutional CSIR grants in deeply acknowledged.

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Correspondence to Sumit G. Gandhi.

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Awasthi, P., Ahmad, I., Gandhi, S.G. et al. Development of Chloroplast Microsatellite Markers for Phylogenetic Analysis in Brassicaceae. BIOLOGIA FUTURA 63, 463–473 (2012).

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  • Simple Sequence Repeat
  • SSRs
  • chloroplast DNA
  • universal primers
  • in silico