Large-scale non-destructive crown-level assessment of Ginkgo pigments via hyperspectral and machine learning techniques.

The photosynthetic pigments - chlorophyll a (Chl a), chlorophyll b (Chl b), and carotenoids (Car) - in juvenile ginkgo leaves are crucial for growth monitoring as they reflect physiological status and directly influence the biosynthesis of bioactive compounds such as flavonoids and terpene lactones. Traditional pigment measurement methods (acetone/ethanol extraction, SPAD, etc.) are inadequate for large-scale dynamic monitoring and high-throughput phenotyping analysis. To address this, this study developed a non-destructive prediction model for Chl a, Chl b, and Car contents in ginkgo seedlings using hyperspectral imaging combined with machine learning algorithms, which is applicable to seedlings with different genetic backgrounds and at various color development phases. A total of 3,460 seedlings from 590 families, sourced from ancient trees across 19 provinces in China, were analyzed using hyperspectral imaging and biochemical pigment quantification. A phased optimization strategy was implemented, including preprocessing method screening, model comparison, and feature wavelength selection. Among the four tested preprocessing methods (raw reflectance, normalization, first derivative, and second derivative), normalization significantly improved model accuracy. The Adaptive Boosting (AdaBoost) algorithm outperformed partial least squares regression (PLSR) and random forest (RF), achieving coefficients of determination (R²) above 0.83 and the ratio of performance to deviation (RPD) values exceeding 2.4 across all pigments. Compared with competitive adaptive reweighted sampling (CARS), the successive projections algorithm (SPA) demonstrated more effective spectral dimensionality reduction while preserving predictive power. This framework enables efficient, accurate, and scalable pigment phenotyping in Ginkgo biloba, offering technical support for large-scale germplasm screening and precision breeding.