Amplified fragment length polymorphism (AFLP) was employed to assess the diversity in the elite germplasm collection of Jatropha curcas, which has gained tremendous significance as a biofuel plant in India and many other countries recently. Forty-eight accessions, collected from six different states of India, were used with seven AFLP primer combinations that generated a total of 770 fragments with an average of 110 fragments per primer combination. A total of 680 (88%) fragments showed polymorphism in the germplasm analyzed, of which 59 (8.7%) fragments were unique (accession specific) and 108 (15.9%) fragments were rare (present in less than 10% accessions). In order to assess the discriminatory power of seven primer combinations used, a variety of marker attributes like polymorphism information content (PIC), marker index (MI) and resolving power (RP) values were calculated. Although the PIC values ranged from 0.20 (E-ACA/M-CAA) to 0.34 (E-ACT/M-CTT) with an average of 0.26 per primer combination and the MI values were observed in the range of 17.60 (E-ACA/M-CAA) to 32.30 (E-ACT/M-CTT) with an average of 25.13 per primer combination, the RP was recognized the real attribute for AFLP to determine the discriminatory power of the primer combination. The RP values for different primer combinations varied from 23.11 (E-ACA/M-CAA) to 46.82 (E-ACT/M-CTT) with an average of 35.21. Genotyping data obtained for all 680 polymorphic fragments were used to group the accessions analyzed using the UPGMA-phenogram and principal component analysis (PCA). Majority of groups obtained in phenogram and PCA contained accessions as per geographical locations. In general, accessions coming from Andhra Pradesh were found diverse as these were scattered in different groups, whereas accessions coming from Chhattisgarh showed occurrence of higher number of unique/rare fragments. Molecular diversity estimated in the present study combined with the datasets on other morphological/agronomic traits will be very useful for selecting the appropriate accessions for plant improvement through conventional as well as molecular breeding approaches.

In recent years, Pongamia has been considered as important renewable source of biodiesel, however not much molecular information is available in this species. Molecular characterization of this legume tree will enhance our understanding in improving the optimal yields of oil through breeding and enable us to meet the future demands for biodiesel. To assess the molecular genetic diversity in 48 Pongamia pinnata accessions collected from six different states of India, amplified fragment length polymorphism (AFLP) marker system was employed. Five AFLP primer combinations produced 520 discernible fragments, of which 502 (96.5%) were polymorphic. AFLP primer informativeness was estimated evaluating four parameters namely polymorphism information content (PIC), effective multiplex ratio (EMR), marker index (MI) and resolving power (RP). In total, 51 unique fragments were detected of which 19 unique fragments were observed with primer combination E-ACG / M-CTA. Although neighbour joining (NJ) method did not group accessions strictly according to their region of collection, a good level of genetic diversity was observed in examined germplasm. However, accessions collected from Karnataka showed comparatively higher diversity than accessions from other states. The diverse accessions identified in this study may be useful in Pongamia pinnata improvement to meet the future demands of biodiesel.