Morphological variation in five edible Capsicum species from Ecuador

Morphological characterization provides a fundamental phenotypic basis for documenting, managing, and prioritizing plant genetic resources for subsequent breeding-oriented evaluation. This study characterized 74 edible Capsicum accessions conserved by the Ecuadorian National Institute for Agricultural Research (INIAP), representing C. annuum (n = 4), C. baccatum (n = 23), C. chinense (n = 26), C. frutescens (n = 17), and C. pubescens (n = 4). Twenty standardized IPGRI descriptors were recorded on five plants per accession under a common greenhouse environment, yielding 370 plant-level observations. Seven continuous descriptors were analyzed using descriptive statistics, hierarchical variance partitioning, repeatability of accession means, and standardized principal component analysis (PCA), whereas 13 categorical descriptors were examined through species-level profiles and multiple correspondence analysis (MCA). Plant-to-plant variation within accessions accounted for only 3.5–8.2% of total phenotypic variance across the seven continuous descriptors, resulting in high repeatability of accession means (R = 0.94–0.99). Notably, variation among accessions within species accounted for 57.1% of fruit-length variance and 61.2% of fruit-biomass variance, revealing substantial phenotypic diversity within species for breeding-relevant fruit traits. The first two PCA components explained 76.21% of standardized quantitative variance (PC1 = 47.67%; PC2 = 28.54%); fruit biomass, fruit width, and fruit wall thickness primarily defined PC1, whereas leaf width, leaf length, and pedicel length characterized PC2. Categorical descriptors provided complementary discrimination, particularly through floral, reproductive, and fruit traits. MCA revealed structured but partially overlapping species profiles, with C. frutescens showing a particularly distinctive categorical phenotype. Together, these results demonstrate that Ecuadorian Capsicum germplasm contains structured inter- and intraspecific morphological diversity and identify fruit-related and floral descriptors as useful criteria for prioritizing contrasting accessions for conservation and subsequent breeding-oriented evaluation. Because the study was conducted in a single unreplicated environment, the observed variation should be interpreted as phenotypic rather than exclusively genetic; molecular characterization and replicated multi-environment testing are required before inferring genetic divergence, trait stability, or breeding value.