A Five-Locus SSR Molecular-Affinity Framework Provides Redundancy Context for Previously Identified Elite-Relevant Lines in a ‘Morita II’-Derived Stevia rebaudiana Breeding Collection

The molecular management of elite-relevant lines in clonally exploited crops requires more than broad genetic structure alone. In Stevia rebaudiana, breeding materials derived from cv. ‘Morita II’ may retain useful variation while also concentrating molecularly similar lines, increasing redundancy within selection pipelines. This study assessed whether a reduced five-locus SSR dataset could provide an operational molecular-affinity framework for redundancy screening and breeding-context interpretation of previously identified elite-relevant lines in a ‘Morita II’-derived breeding collection. A curated five-locus SSR dataset comprising 85 genotypes from a tropical breeding programme was analysed using the Wang relatedness estimator, operational molecular-affinity classes, UPGMA clustering based on Wang-derived dissimilarity and permutation-based assessment of mean Wang relatedness. The collection combined a broad fraction of comparisons showing no detectable positive molecular affinity with a relevant high-affinity component, and this pattern differed between the two reference molecular strata. One subset showed a compact high-affinity profile and higher mean Wang relatedness than expected under random reassignment, whereas the other was dominated by comparisons with no detectable positive molecular affinity. Importantly, the five-locus SSR framework is interpreted here as an operational, locally validated decision-support tool rather than as genome-wide or pedigree-level relatedness inference. These findings suggest that reduced SSR-derived molecular-affinity information can complement phenotypic, physiological and clonal evaluations by providing redundancy context for line retention, clonal advancement, and parental-diversification decisions in tropical stevia breeding.