The present study aimed to characterize finger millet (Eleusine coracana L.) varieties on the basis of their phosphate transporter gene which is considered a reliable gene marker for the identification and discrimination in various genotypes. The analysis had 7 different phosphate transporter based SSR markers which were developed and tested against 47 finger millet varieties. Fingerprint analysis showed that germplasm VHC3752 and PRM1 Ragi, PRM 6118 Ragi and PRM 6122 Ragi and, Ragi local

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... ra and PRM 5103 were closely located where as VHC 3611 and VHC3972 were very distantly located in the phylogenetic tree. Principle Component Analysis (PCA) of the obtained fingerprint also confirmed genetic diversity among various finger millet varieties. Therefore, this study could be proposed as a reliable tool for characterization of different finger millet varieties in a precise and standard manner.