The objective of the present work is to study the chemical variation in Calophyllum inophyllum growing along the Western Ghats of India. Contents of dipyranocoumarins (inophyllums) in C. inophyllum were determined to assess whether they could be used as a taxonomic marker for C. inophyllum. This study also aims to establish inter simple sequence repeat (ISSR) markers that can be used to study genetic variation within the species and explore correlation between ISSR and chemical markers. The contents of dipyranocoumarins were estimated in seeds collected from 20 locations. Leaves from plants at the same 20 locations were assayed for ISSR variation. A dendrogram based on Nei's genetic distance as well as principal component analysis based on dipyranocoumarins and ISSR variation clustered plants from these 20 locations into three groups that indicated close relationship among ISSR, dipyranocoumarins contents, and geographical position (variation) of locations. Based on this study, two locations of elite plants were identified.

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