Genomic Diversity of Avocado in the Morogoro Region and Southern Highlands of Tanzania

Avocado (Persea americana Mill.) is one of the most widely consumed fruit tree crops worldwide, with cultivation expanding rapidly beyond its Mesoamerican and northwest South America center of origin. In emerging secondary diversity centers such as East Africa, farmers have long propagated seedling naturalized populations that may hold valuable reservoirs of genetic diversity, yet these resources remain underexplored. To help fill this gap, this study developed the first genomic resources for avocados in Tanzania, where avocado has a long history of introduction and diversification dating to the first Arab incursions and Catholic missionary missions. Low-coverage whole-genome resequencing (lcWGS) data were obtained from 95 trees sampled in Tanzania across the low- to mid-altitude Morogoro region (n = 25) and the Southern Highlands—i.e., the Iringa (n = 20), Mbeya (n = 30) and Ruvuma (n = 20) regions. In order to guide racial assignation, sequences were merged with NCBI-available lcWGS data from 205 avocado trees, including 42 commercial varieties, with reported ancestry. Population stratification as inferred via maximum likelihood phylogenetic inference, genetic principal component analysis, and ADMIXTURE unsupervised clustering suggested that the sampled Tanzanian avocado trees were genetically closer to the West Indian race and more distant from the northwest South American Caribbean and Andean groups. Additionally, while the trees from the low- to mid-altitude region of Morogoro were almost exclusively West Indian type, some trees from the Southern Highlands aligned more closely with West Indian × Guatemalan and West Indian × Mexican hybrids. These trends were equally supported by a subset of 10,460 high-coverage (10×) SNP markers. Together these findings clarify the dynamics of avocado diversification in a secondary center in East Africa, spanning recent introductions from a single Mesoamerican race, adaptation to a wide range of locally geographic conditions, and farmer-driven selection matching local tribal preferences. Characterizing these locally adapted resources is key for identifying underrepresented yet promising provenances, developing resilient and sustainable horticultural production systems, and safeguarding the species’ global genetic heritage.