Genetic Diversity and Population Structure of Khaya senegalensis (Meliaceae) in the Savanna Zone of Nigeria Using Microsatellite Markers

Khaya senegalensis (African mahogany) is a highly valued timber tree of the Nigerian savanna that is threatened by overexploitation, and understanding its genetic diversity and population structure across its Nigerian range is essential for developing evidence-based conservation and restoration strategies. This study assessed the genetic diversity and population structure of Khaya senegalensis using 12 microsatellite (SSR) markers across 9 populations distributed from Kogi State in the south to Sokoto State in the north of the savanna zone. Leaf material from 15 individuals per population was sampled, DNA extracted, and SSR loci amplified by polymerase chain reaction and genotyped on an ABI 3730 capillary sequencer. Standard population genetic parameters including allelic richness, observed and expected heterozygosity, inbreeding coefficient, and pairwise FST were calculated. Bayesian clustering (STRUCTURE software) and principal coordinate analysis were used to assess population structure. Results revealed moderate to high genetic diversity overall (mean expected heterozygosity: 0.64, mean allelic richness: 5.8 alleles/locus). Significant genetic differentiation was detected among populations (global FST = 0.19, p < 0.001). STRUCTURE analysis identified three genetic clusters corresponding approximately to northern (Sokoto, Kebbi), central (Niger, Kwara), and southern (Kogi, Benue) populations. Evidence of past bottlenecks was detected in two northern populations, consistent with overexploitation history. The study concludes that Khaya senegalensis populations in Nigeria show meaningful genetic structuring that must inform seed sourcing decisions in restoration plantings, and recommends provenance-matched restoration guidelines for each genetic cluster. Keywords: Khaya senegalensis, genetic diversity, microsatellites, population structure, savanna restoration