DNA fingerprinting and phylogenetic study of some indica rice varieties using SSR markers

The genetic relationship and DNA fingerprinting of commercially available seven indica rice varieties were investigated by using 28 Simple Sequence Repeats (SSR) primers. The seven recombinant inbred lines (RILs) used in this investigation have been categorized under three distinct groups depending on their seed morphological similarities which are not differentiable to the naked eye. Thus, the objective was to develop a genetic fingerprint for the seven varieties basically in order to differentiate these three groups of rice varieties which exhibit similar morphological characters and to elicit the genetic relationship between the RILs. Theresults revealed that 20 SSR primers out of 28 primers showed polymorphism indicating the robust nature of SSR in eliciting the polymorphism. The information obtained from the DNA fingerprinting studies help to distinctly identify and characterize seven varieties. The cluster analysis grouped the seven varieties into four classes in which the varieties having similar morphological characters were clustered together, thus revealed the close genetic relationship among them.Keywords: SSR primers, DNA fingerprinting, Genetic Relationship, Polymorphism, Monomorphism,Dendrogram