Genetic diversity, population structure and association study using TE-AFLP markers in Pongamia pinnata (L.) Pierre germplasm

Genetic diversity of Pongamia pinnata , a plant species emerging as biodiesel source, was assessed using three endonuclease (TE)-amplified fragment length polymorphism (AFLP) markers. A total of 275 accessions from different Indian geographical regions were collected. High level of polymorphism (62.6%) was observed in 334 loci amplified using six primer combinations. The Jaccard’s dissimilarity coefficient ranged from 0.17 to 0.80. Based on the neighbour joining method of clustering, accessions were grouped into six major clusters congruent with their respective geographical locations. The mean values of effective multiplex ratio, polymorphic information content, marker index and resolving power were 34.83, 0.286, 9.700 and 14.29 respectively. In addition, a core collection consisting of 20 accessions was identified. Population STRUCTURE analysis produced the highest log likelihood score when the number of populations (K) was set at 2, which was not consistent with clustering analysis based on genetic diversity. Two TE-AFLP markers, E_ac x P_a04 and E_ac x P_a39, were significantly associated with oil content (at P = 0.005). The extent of genetic diversity detected and core germplasm of CPT identified in this study could be selected and used for tree breeding, germplasm conservation and suitable feed stock for biofuel.