Low temperature is a major threat to plant growth, causing yield losses in agricultural and horticultural crops worldwide. Cold stress triggers a cascade of cellular damage: ion imbalance, hypertonicity, and a burst of reactive oxygen species (ROS) that attacks nucleic acids, proteins, and membranes. Plants defend themselves with a two-layered antioxidant system — enzymatic and non-enzymatic — and flavonoids serve as a crucial part of this shield. However, most commercial lilies have a narrow thermal comfort zone, thriving only between 5°C and 30°C. Their complex genetic makeup and large genomes (33–36 Gb) have made molecular breeding particularly challenging. Based on these challenges, there is an urgent need for in-depth research into the natural cold-resistance strategies of wild lily species.
Now, a collaborative team from Central South University of Forestry and Technology, the Hunan Academy of Agricultural Sciences, and Beijing Forestry University has cracked part of that code. Publishing (DOI: 10.1093/hr/uhag065) on February 27, 2026, in Horticulture Research — a leading open-access journal in plant science — the researchers reveal how a transcription factor called LlR3MYB acts as a master regulator that redirects flavonoid metabolism to protect tiger lilies (Lilium lancifolium) against freezing stress. The study was supported by the Yuelushan Laboratory Breeding Project, the China National Natural Science Foundation, and other funding sources.
The team discovered that LlR3MYB belongs to the CPC-type R3-MYB family — transcription factors traditionally known for suppressing anthocyanin pigmentation. But in tiger lilies, this protein plays a double game. Under cold conditions, it shuts down late-stage anthocyanin genes such as LlDFR and LlANS, slashing production of energy-costly red and purple pigments. At the same time, it flips on early flavonoid genes like LlCHS and LlFLS, ramping up the synthesis of non-anthocyanin flavonoids — quercetin, kaempferol, flavones, and chalcones — that are far more effective at scavenging the reactive oxygen species generated by cold stress. When the researchers overexpressed LlR3MYB in tobacco and tiger lilies, total flavonoids surged while anthocyanins dropped — and the plants showed significantly stronger cold tolerance, with elevated antioxidant enzyme activity and less cellular damage. Silencing the gene produced the opposite effect: more anthocyanins, fewer protective flavonoids, and compromised cold resistance. The team also traced the upstream signal: another transcription factor, LlDREB, binds to the LlR3MYB promoter in a cold-dependent manner, activating the entire cascade. Remarkably, structural mutations in LlR3MYB‘s C-terminal repressor motifs appear to have transformed this protein from a conventional suppressor into a dual-function activator — the first R3-MYB ever shown to directly turn on a flavonoid biosynthetic gene.
“We were surprised to find that a classical anthocyanin repressor actually promotes cold tolerance by boosting other types of flavonoids,” the authors said. “It's like the plant makes a strategic trade-off — sacrificing colorful pigments for protective compounds that better combat oxidative stress. This is the first time an R3-MYB has been shown to directly activate flavonoid biosynthesis, and the structural changes in its C-terminal motifs seem to be the key. Understanding how a single protein can both repress and activate different branches of the same pathway gives us a powerful tool for engineering stress-tolerant crops.”
The findings have immediate implications for lily breeding and beyond. Tiger lily is already valued as a cross-breeding resource for Asiatic hybrid cultivars, and this work provides a clear molecular target for enhancing cold tolerance without compromising ornamental quality. Beyond horticulture, the regulatory module — LlDREB–LlR3MYB–LlCHS2 — offers a blueprint for engineering flavonoid profiles in other crops. By selectively boosting non-anthocyanin flavonoids, breeders could improve stress resilience in temperature-sensitive species ranging from fruits to vegetables. As climate change makes cold snaps more unpredictable, this strategy of “metabolic reprogramming” could become an essential tool for safeguarding food production — all by understanding how one wild flower learned to survive the freeze.
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References
DOI
10.1093/hr/uhag065
Original Source URL
https://doi.org/10.1093/hr/uhag065
Funding information
Yuelushan Laboratory Breeding Project (YLS-2025-ZY02051), China National Natural Science Foundation (32102417), Hunan Provincial Natural Science Foundation of China (2024JJ6711), Natural Science Foundation of Guangxi (2025GXNSFBA069050), Key Discipline of the State Forestry Administration ([2016] 21), “Double First-Class” Cultivation Discipline of Hunan Province ([2018] 469), and National Long-term Scientific Research Base of Qingxiushan Landscape Architecture in Nanning, Guangxi.
About Horticulture Research
Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.