Phenotypic Diversity and Ideotype Structuring in a Segregating Population of Stevia rebaudiana Derived from Cv. ‘Morita II’

Intraspecific phenotypic diversity in clonally propagated crops is frequently constrained by narrow domestication histories and the widespread use of a limited number of elite cultivars. In Stevia rebaudiana, commercial production has largely centred on cv. ‘Morita II’, raising concerns about reduced diversity and adaptive potential. This study characterised and structured phenotypic diversity within a segregating population derived from ‘Morita II’ under tropical field conditions. Eighty-six progeny-derived genotypes (clonally propagated) plus the commercial control (87 genotypes total) were evaluated using 25 agromorphological descriptors (qualitative and quantitative). Quantitative traits showed broad variation, including plant height (28.26–119.50 cm) and dry yield rate (0.94–28.55 g plant−1). Multivariate analyses of mixed descriptors (PCA and hierarchical clustering based on Gower distance) identified plant architecture, vegetative growth, and phenology as the main sources of differentiation. The first two principal components explained 19.65% and 12.58% of total phenotypic variance, respectively (32.23% cumulative). Hierarchical clustering (UPGMA; dissimilarity cut-off = 0.25) resolved four phenotypic groups (GI–GIV) with sizes n = 3, 1, 66, and 17, respectively, enabling the definition of contrasting ideotype candidates based on recurrent trait combinations. These results provide a quantitative baseline for phenotypic structuring, prioritization of materials for further evaluation, and management of clonal stevia collections in tropical production systems. These ideotype candidates should be considered preliminary until validated across environments and linked to chemical quality traits.