Integrating SSR Genotyping and Morphological Traits for Reliable Identification of Apple Rootstocks in Kazakhstan

Apple (Malus domestica Borkh.) rootstocks play a key role in modern intensive orchard systems, where their accurate identification is essential for breeding, nursery production, and certification of planting material. This is particularly important in Kazakhstan, a recognized center of origin of cultivated apple, where local germplasm remains insufficiently characterized at the molecular level. In this study, we integrated simple sequence repeat (SSR) genotyping and morphological trait analysis to develop a reliable approach for the identification of clonal apple rootstocks cultivated in Kazakhstan. Five widely used rootstocks (Zhetysu 5, ARM-18, B-7-35, M9, and B9) were analyzed using 17 polymorphic SSR markers and 30 vegetative traits. SSR analysis revealed moderate genetic polymorphism (PIC = 0.28–0.54; He = 0.35–0.58) and enabled clear discrimination among all studied genotypes. Cluster analysis based on genetic distances grouped rootstocks according to their genetic similarity, reflecting their origin and differentiation. Morphological evaluation demonstrated significant phenotypic variability and identified correlations among key vegetative traits related to plant vigor and leaf development. The integration of molecular and morphological data allowed the development of comprehensive genotype profiles (“molecular–morphological passports”) for each rootstock, ensuring their reliable identification. The proposed approach provides a practical framework for the certification of planting material and the management of apple genetic resources in Kazakhstan. It can be applied to improve nursery systems, support breeding programs, and ensure the production of true-to-type planting material in modern horticulture.