TgLCYB1 regulated by TgWRKY22 enhances the tolerance of Torreya grandis to waterlogging stress

β-Carotene functions in plant growth and development and plays an important role in resisting abiotic stress, such as drought and salt stress. The specific function and mechanism by which β-carotene responds to waterlogging stress, however, remain elusive. In this study, we found that β-carotene content and lycopene cyclase (TgLCYB1) expression, both in leaves and roots of Torreya grandis, were increased under waterlogging treatment. Subcellular localization assays indicated that TgLCYB1 was localized in the chloroplasts. Phenotypic, physiological, and metabolome analysis showed that overexpression of TgLCYB1 enhanced the tolerance of tomato plants to waterlogging stress. Furthermore, application of a LCYB enzyme inhibitor, 2-(4-chlorophenylthio)-triethylamine hydrochloride, markedly enhanced the sensitivity of T. grandis to waterlogging stress. In addition, yeast one-hybrid assay, the dual luciferase assay system, and real-time quantitative PCR indicated that waterlogging stress induced TgWRKY22 to increase TgLCYB1 expression by binding to the TgLCYB1 promoter. Collectively, our results indicated that TgWRKY22 positively regulated TgLCYB1 expression to improve the activities of antioxidant enzyme and increase the levels of some key metabolites, thereby relieving waterlogging-induced oxidative damage, and consequently modulating the waterlogging stress response. This study contributes to a more comprehensive understanding of carotenoid functions and the role LCYB genes play in plant stress response.