Multi-omics analysis reveals the transcription factor AtuMYB306 improves drought tolerance by regulating flavonoid metabolism in Chinese chive (Allium tuberosum Rottler)

• Flavonoids were substantially altered under drought stress in chive leaves. • AtuMYB306, as a hub gene regulating flavonoid synthesis was identified by integrating transcriptomics, metabolomics, and proteomics analyses. • AtuMYB306 directly binds to the promoters of three flavonoid biosynthetic genes ( Atu4CL, AtuF3H , and AtuF3’H ) and activates their expression in response to drought stress. Drought is one of the most detrimental stresses that severely constrains plant growth and productivity. Although Chinese chive ( Allium tuberosum Rottler) is a vegetable species that is cultivated and consumed worldwide, few studies have investigated how this species responds to drought. In this study, we conducted transcriptomics, metabolomics, and proteomics analyses on chive seedlings exposed to different water availability conditions (mild drought, moderate drought, severe drought, and re-watering) and found that the accumulation of flavonoids in chive leaves was substantially altered under drought stress. Gene co-expression regulatory network analysis, conducted by integrating transcriptome and metabolome data, revealed a chive R2R3-MYB transcription factor, AtuMYB306, as a central regulator of flavonoid synthesis. Overexpression of AtuMYB306 significantly improved osmotic stress tolerance and enhanced flavonoid content in Arabidopsi s. We further demonstrated that AtuMYB306 directly binds to the promoters of three flavonoid biosynthetic genes ( Atu4CL, AtuF3H , and AtuF3’H ) and activates their expression. These results suggest that AtuMYB306 improves drought tolerance in Chinese chive by enhancing flavonoid biosynthesis to scavenge reactive oxygen species (ROS) generated under water-deficit conditions. Thus, our findings provide evidence that AtuMYB306 playing a pivotal role in improving drought resistance in Chinese chive.