Integrating Morphological, Sensory, and Chloroplast Genetic Diversity Reveals Regional Structuring and Domestication Potential of Mimusops zeyheri Sond. in South Africa

Mimusops zeyheri Sond. is an underutilized indigenous fruit tree with significant nutritional, ecological, and socio-economic value in southern Africa. However, its domestication potential remains constrained by a limited understanding of intraspecific variation across geographically distinct populations. This study integrated morphological, sensory, and chloroplast genetic analyses to assess the diversity and population structuring of M. zeyheri in two regions of South Africa (Limpopo and Mpumalanga). A total of 40 trees (20 per region) were evaluated for fruit, nut, and leaf traits, while sensory attributes were assessed by 100 participants using a 9-point hedonic scale. Genetic diversity was examined using the chloroplast markers matK and trnH–psbA. Significant regional differences were observed in reproductive morphology, with Mpumalanga populations producing larger fruits (29.41 ± 0.61 mm) and nuts (2.11 ± 0.36 cm) than those from Limpopo. In contrast, sensory evaluation revealed consistently higher preference scores for Limpopo fruits across all attributes, particularly taste, aroma, and overall acceptability (mean scores 7.7–8.0 vs. 5.0–5.4). Genetic analyses identified two major chloroplast lineages corresponding broadly to geographic origin, alongside rare haplotypes indicating localized divergence. Leaf morphology remained largely conserved across regions. The combined evidence demonstrates strong regional structuring driven by both environmental gradients and historical genetic divergence. Importantly, the decoupling of fruit size and sensory preference highlights the need to prioritize quality traits in domestication strategies. These findings point to a promising domestication direction, through crossbreeding superior-tasting Limpopo genotypes with larger-fruited Mpumalanga genotypes to combine consumer-preferred sensory quality with an improved fruit size. These findings provide a foundation for conservation planning and the selection of superior genotypes for the development of M. zeyheri as a high-value indigenous fruit crop.