Phenological, Pomological, and Molecular Characterization of Capuli (Prunus serotina Ehrh.) Accessions from the INIAP-Ecuador National Germplasm Bank for Breeding Purposes

Abstract Prunu s sero tina Ehrh., commonly known as capuli, represents a valuable genetic resource for breeding programs aimed at improving fruit quality. This study presents the in situ morpho-agronomic and molecular characterization of sixty capuli accessions that were collected in situ and are currently conserved in the INIAP-Ecuador National Germplasm Bank. Thirty quantitative and qualitative traits were evaluated, supported by principal component analysis (PCA) and hierarchical clustering to explore phenotypic structure. ANOVA revealed significant regional differentiation in key fruit traits, including fruit weight ( p = 0.000015), equatorial and polar fruit diameter ( p = 0.0036 and p = 0.0015), epidermis weight ( p = 0.0065), and seed diameter ( p = 0.011), as well as floral traits such as flower diameter ( p = 0.0002) and sepal width ( p = 0.0018). Tukey’s post hoc comparisons indicated that the strongest contrasts occurred between Cotopaxi–Tungurahua and Chimborazo–Tungurahua. Molecular analysis using five SSR primer pairs (AB, PceGA34, PS12A02, Pchpgms3, and Pchgms2) revealed high genetic variability, with an average polymorphism information content (PIC) of 0.792. Population structure analysis (STRUCTURE and PCoA) identified three major genetic groups. The results demonstrate considerable phenotypic and genetic diversity, providing essential insights for breeding strategies aimed at developing superior capuli cultivars in Ecuador.