Avocado (Persea americana Mill.) Genomic Divergence Across the Victoria, Tanganyika and Rukwa Lake Basins of Tanzania
- 1Department of Plant Breeding, Swedish University of Agricultural Sciences, 23436 Lomma, Sweden
- 2Department of Molecular Biology and Biotechnology, University of Dar es Salaam, Dar es Salaam P.O. Box 35179, Tanzania
- 3Department of Food Science and Technology, University of Dar es Salaam, Dar es Salaam P.O. Box 35134, Tanzania
Abstract
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.
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BibTeX
@article{cortes2026avocado,
title = {{Avocado (Persea americana Mill.) Genomic Divergence Across the Victoria, Tanganyika and Rukwa Lake Basins of Tanzania}},
author = {Andrés J. Cortés and Juma M. Hussein and Ibrahim Juma},
journal = {International Journal of Molecular Sciences},
year = {2026},
month = oct,
doi = {10.3390/ijms27219699},
url = {https://www.mdpi.com/1422-0067/27/21/9699},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Avocado (Persea americana Mill.) Genomic Divergence Across the Victoria, Tanganyika and Rukwa Lake Basins of Tanzania
AU - Andrés J. Cortés
AU - Juma M. Hussein
AU - Ibrahim Juma
PY - 2026
DA - 2026/10/29
JO - International Journal of Molecular Sciences
DO - 10.3390/ijms27219699
UR - https://www.mdpi.com/1422-0067/27/21/9699
AB - 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.
SN - 1422-0067
ER -