Comparison of AFLP and SAMPL markers for assessment of intra-population genetic variation in Azadirachta indica A. Juss.

Abstract

Neem ( Azadirachta indica) is an important tropical tree species with a number of medicinal and biopesticidal properties. In the present work, the extent of intra-population genetic variation was evaluated in neem accessions growing in district Kanpur (UP), India, along with two exotic accessions. Two PCR-based markers namely, AFLP and SAMPL were employed to measure the genetic variation. The relative efficiencies of these marker techniques were compared with respect to their applicability in genetic diversity studies. The fingerprints corresponding to both the AFLP and SAMPL markers revealed high levels of heterozygosity, indicating that neem is predominantly an out-crossing species. The average percentage polymorphism, within Kanpur accessions, was detected as 35 and 69 on utilizing AFLP and SAMPL data, respectively. Similarly, the average genetic similarity (GS) values based on Jaccard's coefficient were 0.80 and 0.68 for AFLP and SAMPL, respectively. Hence, SAMPL markers were more efficient in resolving differences between closely related accessions as these target hyper-variable microsatellite loci in the genome. Both the SAMPL and AFLP markers were equally informative in revealing phenetic relationships and produced well-correlated principal correspondence plots. The overall levels of genetic variation present in the neem collection were finally determined by combining the AFLP and SAMPL datasets to ensure wide genome coverage. The phenogram based on unweighted pair group method of averages (UPGMA) analysis depicted that the Kanpur accessions were genetically distinct from the Thai accessions, as the two were linked at a low GS value of 0.41. The Kanpur group on the other hand clustered together at a GS value of 0.8. Principal correspondence analysis revealed that the Kanpur individuals were spread out on the plot indicating that these were genetically diverse. Based on AFLP and SAMPL analysis, it is concluded that neem maintains high levels of genetic variation at intra-population level.