Genetic diversity and population structure of Azadirachta indica using simple sequence repeat (SSR) markers for genetic resource conservation and utilization

Azadirachta indica (neem) is a multipurpose tree species that is distributed in Asian and African countries. It is used in food, medicine and agriculture. Our study used 20 neem-specific polymorphic simple sequence repeat (SSR) markers to investigate the genetic diversity among 170 neem germplasm from three distinct populations [North Central (NC), West Central, and South Eastern (SE)]. The study revealed moderate levels of genetic diversity. The SE population exhibited the highest genetic variation, as indicated by the observed heterozygosity (Ho = 0.63) and expected heterozygosity (He = 0.64) values, while the NC population showed the lowest genetic diversity. Furthermore, evidence of inbreeding was exhibited by the overall positive value of the fixation index (F = 0.13). The polymorphic Information content value 0.583 indicates a moderate level of marker diversity within the populations. The significant genetic differentiation coefficient (Fst) was 0.25. Analysis of molecular variance revealed that 12% of the total genetic variation was observed among the populations, whereas 88% was found within populations. Principal component analysis, clustering, and structure analysis were in correspondence with each other and identified three populations of A. indica with slight admixtures. The results of this study provide a genetic diversity of the A. indica germplasm for harnessing its genetic potential and conservation.