Dissecting the Structural and Physiological Determinants of Edible Ratio and Juice Yield in a Large Lychee Germplasm Collection

Lychee (Litchi chinensis Sonn.) is a major subtropical fruit crop, yet the regulatory hierarchy underlying edible ratio (flesh weight/whole fruit weight, %) and juice yield (juice weight/whole fruit weight, %), the core processing-quality traits, remains unresolved. We phenotyped 301 accessions from ten origins under uniform conditions and used hierarchical regression to predict and evaluate edible ratio and juice yield based on structural and physiological fruit traits, thereby separating the contributions of structural constraints and physiological modulation. Both traits exhibited broad population variation and were significantly modulated by maturity stage, with late-maturing accessions outperforming early types. A strong positive correlation (r = 0.679, p < 0.001) supported the identification of “double-high” germplasm combining superior edible ratio and juice yield. Kernel ratio emerged as the dominant structural constraint on edible ratio (R2 = 0.6699, p < 0.001), while the combined inedible fraction served as the basal limiting factor for juice yield (R2 = 0.4262, p < 0.001). Critically, after controlling for structural variation, physiological traits contributed an independent 9.2% of explained variance (ΔR2 = 0.092, p < 0.001). pH was identified as the primary positive physiological predictor (β = 0.322, p < 0.001), whereas soluble solids content (SSC) exhibited a weak negative effect (β = −0.064, p = 0.008), indicating that high sugar content is not a priority target for processing-oriented breeding. An Integrated Ideotype Score (IIS) was constructed to objectively rank germplasm; elite accessions including ‘10_269’, ‘Yujinqiu’ and ‘Nuomici’ combined edible ratio > 75% with juice yield > 40%. These findings establish a “structural constraint-physiological modulation” two-tier regulatory hierarchy for lychee processing quality and provide a multivariate framework for germplasm evaluation and breeding selection.