Ndalo, Jantor2026-03-162026-03-162025-11https://ir-library.ku.ac.ke/handle/123456789/32755A Thesis Submitted in Partial Fulfilment of the Requirements for the Award of the Degree of Master of Science (Biotechnology) in the School of Pure and Applied Sciences of Kenyatta University, November 2025. Supervisors Prof. Steven Runo Dr. Alice MuchugiMoringa oleifera is a versatile tree native to the foothills of the Himalayas and now naturalized in the tropics. Moringa is nutritionally significant owing to its high nutrient and antioxidant content. Despite its increasing use as a fodder crop, wood fuel, medicine, an anticoagulant and a potential source of biodiesel, the genetic diversity of Moringa across the tropics remains a subject of intense investigation. Previous studies have used hybridization-based methods such as microsatellites which have not fully resolved its genetic diversity. In this study, genetic diversity and structure of 95 accessions of Moringa from tropical regions were analyzed using single nucleotide polymorphisms. Genomic DNA was extracted from 19 provenances collected from Africa, Caribbean and Southeast Asia. 3968 SNP markers were identified using DArTSEQ technology, which combines complexity reduction methods with next-generation sequencing. These were culled to a final set of 1913 informative markers that were then used for population structure and genetic diversity analysis. Unweighted neighbour joining phylogeny and principal coordinate analysis revealed four distinct clusters related to the geographic origin: Caribbean (Haiti/Jamaica) and East African (Kenya/Tanzania) were identified to be a subset of the West African (Mali/Ghana) population while the Southern African (Malawi) segregated distinctly. Philippines samples clustered separately and farthest as expected. Analysis of molecular variance revealed high gene flow within populations (77 %) compared to among populations (23 %). Bayesian modelling in structure with best k being two still distinctly segregated the Southern African (Malawi) population from the other African regions suggesting a distinct introduction. The significant admixture of individuals noted in structure is typical of unnatural introductions possibly through anthropogenic events. This study highlights the power of SNP markers from DArTSEQ technology in elucidating the genetic structure and molecular diversity of Moringa oleifera. Malawi and Philippines being the most diverse should be considered as candidates for conservation improvement and utilization since they have higher ecosystem functioning. The discovered SNPs enable genome-wide association studies to accelerate marker-assisted breeding. These results too have implications for germplasm collection, improvement, conservation, utilization strategies and policies. Further research utilizing advanced genomic tools will enhance our knowledge of Moringa oleifera and support its sustainable utilization for various applications.enThesis