Morphological and Genetic Variation in Strychnos madgascariensis Poir (Loganiaceae) at Bonamanzi Game Reserve, KwaZulu-Natal, South Africa

Abstract

Background: Strychnos madagascariensis Poir (Loganiaceae) is a drought-tolerant indigenous fruit tree of East and southern Africa, valued for its food, medicinal, and socio-economic contributions to rural communities. Despite its importance as a candidate food crop, intraspecific morphological and genetic diversity had not previously been characterized, and no simple sequence repeat (SSR) markers had been developed for this species, leaving breeders and conservation planners without the basic diversity baseline needed to prioritize material for domestication. Methods: This study assessed vegetative and reproductive trait variation, variance components, and broad-sense heritability, and SSR-based genetic diversity among 27 morphologically defined S. madagascariensis morphotypes at Bonamanzi Game Reserve, KwaZulu-Natal, South Africa. Three trees were measured per morphotype (81 trees total), over two growing seasons. Genetic diversity was characterized in one representative tree per morphotype using seventeen newly developed SSR loci, the first such markers reported for this species, and analyzed with population structure (STRUCTURE version 2.3.4), PCA, and Nei’s genetic distance. Results: Twenty-seven morphotypes were identified based on leaf colour, shape, hairiness and size, dominated by grey (41%), elongated (59%), less hairy (48%), and medium-sized (>50–90 mm) leaves. Fruit diameter and mass showed the highest inter-morphotype variation (r = 0.949) and also the highest broad-sense heritability (H2 = 55.3% and 47.8%, respectively), indicating strong genetic control of these traits and their suitability as targets for selective breeding. Environmental variance exceeded genotypic variance for most traits. A total of 144 alleles were identified across 17 SSR loci (mean 4.24 alleles/locus; mean PIC = 0.31). Population structure gave a preliminary, tentative signal of two genetic clusters (K = 2) with substantial admixture, which we interpret cautiously, given the limited sampling depth. Conclusions: This is the first study to characterize intraspecific morphological variation in S. madagascariensis and the first to develop SSR markers for the species. The results provide a preliminary, single-site framework for conservation genetics and crop improvement that should be validated with larger, multi-site samples. Grey morphotypes GyEvH1, GyEvH2, GyEvH3, GyRlH1 and GyEH2 combined consistent fruiting performance with favourable fruit-trait values and are proposed as priority candidates for further evaluation in domestication and breeding programmes.