Abstract

White-flowered alfalfa (Medicago sativaL.) persisting in Qinghai–Tibet Plateau’s saline–alkali habitats provides a unique model to explore floral color polymorphism-linked ecological adaptation. We systematically compared phenotypic, physiological, transcriptomic, and metabolomic profiles of white-flowered (WF) and purple-flowered (PF) alfalfa under high-altitude cold/saline–alkali field conditions (three biological replicates; Student’st-test). WF showed a significant growth-defense trade-off: flower size and chlorophyll a content decreased by 18.9% and 46.0%, with reduced gibberellin levels, while jasmonic acid (36.3%), proline (51.5%), antioxidant enzyme activities, total flavonoids (17.7%), and condensed tannins (18.2%) were significantly increased (p< 0.001). Multi-omics analysis revealed phenylpropanoid pathway reprogramming (suppressed anthocyanin biosynthesis, precursor accumulation) and coordinated hormone signaling (jasmonic acid activation, salicylic acid inhibition). Our findings confirm the white-flower trait is not an isolated mutation. It is a key component of a coordinated adaptive syndrome, mediated by metabolic reprogramming and hormonal crosstalk. These results provide theoretical and technical support for breeding stress-resistant alfalfa varieties suitable for marginal land cultivation.