Efficacy of two dominant marker systems, ISSR and TE-AFLP for assessment of genetic diversity in biodiesel species Pongamia pinnata

The extent of genetic diversity was assessed in 12 Pongamia accessions from different regions of Delhi and surrounding areas using two dominant markers,namely ISSR and three endonuclease AFLP (TEAFLP).Five ISSR primers and two TE-AFLP primer combinations generated a total of 12 and 48 polymorphic bands respectively. The Jaccard's dissimilarity coefficient ranged from 0 to 0.90 for ISSR and from 0 to 0.67 for TE-AFLP markers. The polymorphic information content of both markers was equal. However, TE-AFLP had much higher values of marker index and resolving power compared to those obtained for ISSR markers. This study demonstrates the usefulness of dominant markers like ISSR and TE-AFLP for assessment of genetic diversity in Pongamia for which microsatellites markers are still not available.However, high multiplex ratio, easy scorability and other high band attributes of TE-AFLP markers make them more suitable compared to ISSR for genetic diversity analysis.