Molecular mechanisms and adaptive strategies for hypoxia tolerance in horticultural crops: beyond model systems

Abstract Waterlogging-induced hypoxia threatens horticultural crop production by disrupting metabolic processes, nutrient uptake, and plant health. Despite significant progress in model plants, such as Arabidopsis and rice, the unique hypoxia responses and regulatory mechanisms in vegetable and fruit crops remain underexplored. This review bridges critical knowledge gaps by synthesizing recent advances and highlighting species-specific adaptations aimed at enhancing hypoxia tolerance in horticultural crops. Although the central roles of Ethylene response factor group VII (ERF-VIIs), metabolic reprogramming, and redox signaling in oxygen homeostasis have been elucidated in model species, recent studies on horticultural crops have demonstrated the conservation of this core regulatory module and the emergence of unique species-specific adaptations that optimize hypoxia tolerance. Horticultural crops employ diverse morphological, physiological, and molecular strategies to maintain energy homeostasis under hypoxic conditions. In this review, we summarize the key mechanisms, including antioxidant defense activation, dynamic reprogramming of carbon and nitrogen metabolism, and integrated hormonal crosstalk and signaling networks. Plants adapt to hypoxia through a complex molecular network that orchestrates multifaceted responses involving dynamic epigenetic reprogramming, the induction of hypoxia-responsive genes, and translational control to fine-tune protein function and stability. Recent advances in genetics, molecular breeding, and grafting have accelerated the development of hypoxia-tolerant horticultural crops. By integrating adaptive traits from wild relatives through genome editing and multi-omics approaches and optimizing rootstock performance, sustainable productivity can be enhanced under oxygen-limiting conditions. Elucidating these mechanisms provides fundamental insights into plant resilience, and directly informs innovative breeding and biotechnological strategies for climate-smart horticulture.