Genetic diversity, population structure, and clonal verification in South African avocado cultivars using single nucleotide polymorphism (SNP) markers

Since the start of avocado cultivation in South Africa, superior rootstocks and fruit cultivars have been selected based on morphological traits, which is time consuming and expensive. Technological advances, such as the development of a single nucleotide polymorphism (SNP) genotyping platform for avocado, may reduce these limitations. Therefore, the aim of this study was to implement molecular marker technologies for the validation of clonal material, verification of horticultural varieties, and determining the genetic diversity and population structure of an avocado cultivar germplasm in South Africa. An avocado cultivar breeding population, containing 375 individuals, was genotyped using 384 SNP markers. Our affinity propagation analysis (APA) indicated a 10.74% mislabelling in the germplasm. The principal component analysis (PCA) and discriminate analysis of principal components (DAPC) suggested that the germplasm was admixed in relation to the three known avocado varieties, Guatemalan, Mexican, and West Indian. Additionally, the ancestral origins were determined for 27 individuals with unknown ancestry. Furthermore, the population diversity was assessed and revealed moderate levels of differentiation in the germplasm, suggesting a high level of gene flow between the different populations. This research highlights the value of clonal verification and horticultural variety identification—for the reliable propagation of material with desired traits. The accurate propagation of material and clonal identity could aid avocado growers to link morphological characters and stress tolerance to accurate genetic backgrounds, which could improve the selection of avocados for current and future environmental stressors, especially as Africa is set to be significantly impacted by climate change.