Morpho-Physicochemical, Bioactive, and Antioxidant Profiling of Peruvian Coffea arabica L. Germplasm Reveals Promising Accessions for Agronomic and Nutraceutical Breeding

Coffee quality arises from the interaction among genotype, environment, and postharvest management, yet few large-scale studies jointly integrate agronomic, phytochemical, and processing traits. We characterized 150 <i>Coffea arabica</i> L. accessions from six Peruvian regions, evaluated in the INIA coffee germplasm collection, quantifying agro-morphological traits, colorimetric parameters in cherries and beans, fermentation indicators, bioactive compounds, and antioxidant activity. Correlation analyses showed that total phenolics (TPCs) and total flavonoids (TFCs) were strongly associated with antioxidant activity, whereas caffeine content (CAF) varied, largely independently. Several chromatic parameters in parchment and green coffee (<i>a*</i>, <i>b*</i>, <i>C*</i>) showed positive correlations with phenolic content and antioxidant activity (ABTS, DPPH, FRAP), while final fermentation pH (FPH) was negatively associated with these compounds, supporting both color metrics and pH as operational indicators of chemical quality. Principal component analysis disentangled a morphometric gradient from a functional (phenolic-antioxidant) gradient, indicating that bean size and antioxidant potential can be improved in a semi-independent manner. Hierarchical clustering identified complementary ideotypes, and a multi-trait selection index highlighted promising accessions-PER1002197 (Cajamarca), PER1002222 (Cajamarca), PER1002288 (Pasco), and PER1002184 (Cajamarca)-that combine high phenolic/antioxidant levels, favorable chlorogenic acid (CGA)/trigonelline (TGN) profiles, contrasting (high/low) caffeine, and competitive yield (YPP)/bean size. These accessions represent promising candidates for breeding climate-smart and nutraceutical-oriented coffee.