Pongamia pinnata has received much attention in recent years as a source of seed oil that
can provide a substitute for diesel fuel. Very little molecular work has been reported on this
species. This paper reports our studies on the diversity amongst the CPTs (candidate plus
trees) of P. pinnata previously identified on the basis of morphometric traits, particularly
pod and seed traits. For this RAPD (random amplified polymorphic DNA) markers were
used to determine the genetic diversity among 10 genotypes of P. pinnata CPTs selected for
suitability for energy production. For further investigation, 18 primers generating stable
band patterns from 40 tested arbitrary primers were selected. A total of 210 amplification
products were obtained of which 10.48% were polymorphic. The genetic similarity index
ranged from 0.11 to 0.87. Genetic distance values were used to generate a dendrogram
(UPGMA) between the genotypes. The Mantel method used for comparing the similarity
matrixes produced correlation coefficients that were statistically significant for the RAPD
marker. This genomic analysis allows a cost effective characterization of CPTs of P. pinnata.
The present investigation supports in future the development of genetic map in Pongamia
which are a highly useful tool in breeding and may provide information on the inheritance
of features crucial for increase seed yield, oil content and the resistance to key insects and
pests. Thus this study warrants Pongamia producers to realize its full potential and
contributes for its sustainable production and improvement.