Avocado (Persea americana Mill.) Genomic Divergence Across the Victoria, Tanganyika and Rukwa Lake Basins of Tanzania

Avocado (Persea americana Mill.) is a crucial horticultural tree crop for food security and rural income in Tanzania. Despite its importance, the genomic divergence of avocado populations in the country’s Lake Zone, Western Zone, and the Southern Highlands region of Rukwa has not previously been investigated. While the Southern Highlands are recognized as a major production hub, a significant knowledge gap exists regarding the genomic diversity, population stratification and racial ancestry of landraces in the Western Rift and Lake Victoria Basin, areas characterized by unique microclimates and historical transboundary trade routes with neighboring Great Lakes nations. Therefore, this study aimed to characterize the genomic diversity of avocado germplasm through low-coverage whole-genome resequencing (lcWGS) of 105 trees from five key regions: Mara, Mwanza and Kagera in the Lake Zone and Lake Victoria Basin; Kigoma in the Western Zone and Lake Tanganyika Basin of the Western Rift; and Rukwa in the Southern Highlands’ Lake Rukwa Basin adjacent to the Lake Tanganyika Basin and Western Rift. The study sought to identify patterns of local differentiation and gene flow. We hypothesized that the avocado populations in these regions are not panmictic but are structured by geographic and ecological barriers, where (i) regions bordering the Albertine Rift (i.e., Kigoma and Kagera) exhibit distinct West Indian types likely shaped by transboundary exchange and climate heterogeneity and (ii) the Lake Victoria Eastern Basin regions of Mwanza and Mara harbor unique intermediate genotypes resulting from inter-racial hybridization with lowland genotypes. The lcWGS screening generated more than 63,577,355 SNPs across a total of 405 studied trees, after compilation with published lcWGS reads from 300 avocado trees from Tanzanian Morogoro and the Southern Highlands of Iringa, Mbeya and Ruvuma (95) and racial control groups in the Americas (205). Phylogenetic, unsupervised principal component and ADMIXTURE analyses found that germplasm from Rukwa clustered with Southern Highlands germplasm from Iringa, Mbeya, and Ruvuma. In contrast, accessions from Kigoma and Kagera formed a distinct Western Rift lineage enriched for West Indian ancestry, and populations in Mara and Mwanza occupied intermediate positions, suggesting extensive inter-racial admixture in the eastern Lake Victoria Basin. These genetic clusters may guide the utilization of East African avocado landraces.