The genetic relationships among four species of Pterocarpus (P. dalbergioides, P. indicus, P. marsupium and P. santalinus) with sixteen accessions and one accession of Tipuana tipu (Fabaceae) were assessed using RAPD and ISSR markers. Twelve RAPD and fourteen ISSR primers were used for analysis of genetic diversity among the species and accessions studied and high degrees of polymorphism was observed with most of the primers used. All the species and accessions had an average similarity of 52% among themselves. Highest similarity (95%) was observed between two accession of Pterocarpus dalbergioides and lowest (28%) between Tipuana tipu and Pterocarpus marsupium. The lone accession of Tipuana tipu got separated from the Pterocarpus group in the dendrograms constructed using both RAPD and ISSR primers which justify their generic distinctness. Among the four species of Pterocarpus, P. indicus was distantly related to rest three species and P. marsupium and P. santalinus were genetically very close to each other exhibiting a similarity of 88.80%.
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