Melia azedarach (Chinaberry), a deciduous tree of Meliaceae family is an ecologically significant forest tree. Given the attributes like co-dominance, high polymorphism and reproducibility, microsatellite markers make an important tool to get insight about the genetic variability present within a species. In this study, we developed 43 genomic microsatellite markers from (AG)n enriched genomic library and subsequently employed 23 of them for characterization among 14 populations encompassing 95 genotypes from Indian Thar Desert. A total of 1912 recombinant clones from enriched library were sequenced on ABI 3730 xl DNA Analyzer. 573 (30%) of total sequenced clones were identified positive in secondary enrichment, of which 339 (59%) possessed SSRs with a range of 10-100bps. We found a moderate level of diversity (Na = 3.211, Ho = 0.558, He = 0.549, P = 94.41%) in the studied population. Gene diversity (h) among population pairs varied from 0.566 to 0.714 with very low overall genetic differentiation (F = 0.021). The highest value of ΔK estimated using STRUCTURE indicated 2 subpopulations (K=2) and admixed cluster occupied maximum area (75.79%) under Bar plot. Genetic distance based UPGMA dendrogram also identified 2 major clusters among 14 Melia azedarach populations. This study helps in interpreting genetic diversity and management of M. azedarach.
