Trade-off between yield and quality driven by artificial domestication in Gleditsia sinensis: Phenotypic and functional component variation in a common garden and variety selection.

Gleditsia sinensis is an ecological and economic native tree species, yet previous origin-based studies suffer from genotype-by-environment (G×E) interactions, lacking systematic comparisons of morphology-metabolism associations between cultivated and wild types without environmental bias. To address this, pod/seed morphology and key quality traits of 15 G. sinensis germplasms (one wild control, 14 cultivars) were evaluated in a common garden, integrating analysis of variance (ANOVA), random forest, correlation, principal component analysis (PCA), and cluster analyses. Cultivars significantly outperformed the wild type in pod dry weight, 1000-seed weight, and total saponins, whereas the wild type accumulated significantly higher total polyphenols and flavonoids. Phenotypic variation was greater in pods than in seeds, and morphological variation of both pods and seeds exceeded that of nutritional quality, indicating that the latter exhibits higher genetic stability. Random forest identified seeds per pod, 1000-seed weight, seed dry weight, and pod dry weight as the top predictors for nutritional quality. Notably, larger and heavier structures correlated negatively with total polyphenols, flavonoids, total sugar, and crude fiber, but positively with pectin, ash, soluble protein, and total soluble sugar, suggesting a potential growth-defense trade-off. Multidimensional evaluation categorized the germplasms into four distinct clusters (Cluster I: YJ5, YJ4, YJ6; Cluster II: JD2, JD3, JD9, JD10, YJ3; Cluster III: CK, JD1; Cluster IV: JD7, YJ10, YJ2, JD11, YL1). Within these, JD9, YJ2, and YJ10 demonstrated balanced agronomic and nutritional performance, making them promising comprehensive cultivars. Meanwhile, the wild type (CK) and JD1 are highlighted as crucial donor parents for nutritional improvement, whereas YJ5 and YJ6 are ideal materials for enhancing morphological traits. Ultimately, this study elucidates the potential growth-defense trade-off during woody plant domestication, providing a scientific basis for the differentiated directional breeding and the utilization of wild genes in G. sinensis.