Integrated metabolomics and transcriptomics reveal sugar metabolism associated with cold tolerance in chrysanthemum

BACKGROUND: The ground-grown chrysanthemum (Chrysanthemum morifolium) is an important ornamental species valued for its stress resilience, particularly in cold regions. However, low temperature stress remains a major constraint on its growth and landscape utility. Understanding the molecular mechanism of its cold tolerance is crucial for breeding cold-resistant cultivars. RESULTS: We performed metabolomic and transcriptomic analyses on the three chrysanthemum cultivars before and after exposure to the low temperature. Among the 1,371 detected metabolites, a subset of 21 sugar-related differential accumulation metabolites (DAMs) greatly responded to the low temperature. Under the low temperature, the chrysanthemum cultivars ZR and FSD activated metabolic defense mechanisms via the significant accumulation of key osmoprotectants, such as sucrose, trehalose, and raffinose, etc. Weighted gene co-expression network analysis (WGCNA) revealed two key modules, red and tan, which were significantly correlated with sugar-related metabolic changes. KEGG enrichment analysis established starch and sucrose metabolism as a central pathway in the cold response. Further transcriptional analysis suggested that transcription factors CmWRKY65 and CmLBD18 potentially integrated cold signaling with this pathway by directly regulating key biosynthesis genes. Additionally, we identified three putative SWEET genes, CHR00080209, CHR00064977, and CHR00048779, which may be involved in sucrose transport into vacuoles and could potentially contribute to mitigating cold-induced damage. CONCLUSIONS: These findings delineate the role of sugar metabolism in the low‑temperature adaptation of Chrysanthemum morifolium and identify pivotal genetic resources for breeding cultivars with enhanced cold resilience. The results provide a mechanistic basis for prolonging the autumnal floral display period, thereby supporting the sustainable application of ground‑cover chrysanthemum in the late‑season landscapes of Northeast China.