Development of chloroplast microsatellite markers for phylogenetic analysis in Brassicaceae

Awasthi, Praveen and Ahmad, Irshad and Gandhi, Sumit and Bedi, Yashbir (2012) Development of chloroplast microsatellite markers for phylogenetic analysis in Brassicaceae. Acta Biologica Hungarica, 63 (4). pp. 463-473. ISSN 0236-5383

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Abstract

By employing in silico tools, we devised new chloroplast microsatellite primers for inferring phylogenetic 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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