In the recent past, realization of massive loss in diversity of medicinal plants at an alarming rate has triggered the efforts for their conservation. Sustainable and effective conservation strategies of germplasm of medicinal plants essentially require the use of ex-situ and in-situ conservation techniques to maximize the potential use of genetic diversity. The key to successful assessment of diversity and conservation relies upon the precise and indisputable characterization and identification of medicinal plants. Application of DNA based molecular techniques is one such promising and widely used approach for the accurate assessment of diversity for conservation. The diversity assessment approach for medicinal plants must consider the selection of molecular techniques that has potential to unravel the chemical diversity; gene specific secondary metabolite features in addition to distribution and magnitude of genetic diversity within and between species. Initially, molecular markers such as RAPD, AFLP and ISSR are profoundly used in the population studies to differentiate closely related genotypes or identification of cultivars because of their high degree of variation. Advanced molecular markers like VNTR, Minisatelliets, SNP are used for closely related genotypes. Similarly, DNA variation in the large number of loci is detected by DAFT, a microarray-based technique. Recent advances in the use of molecular tools will be discussed for the screening and assessment of secondary metabolite and genetic diversity of medicinal plants of India.
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