Abiotic stress tolerance has been significantly weakened in modern crops during the domestication process. Regaining tolerance has become a critical task in light of current climate trends and their impact on global food security. Abiotic stress tolerance is an extremely complex trait and is conferred at various levels of plant functional organization and developmental stages, with regulatory mechanisms operating across multiple scales, from individual cells to tissues and the entire plant. The emergence of advanced molecular tools such as single-cell RNA sequencing and spatial omics technologies has revolutionized the field, advancing our understanding of plant responses to hostile environments. However, the implementation of this knowledge in crop breeding programmes is handicapped by the lack of appropriate phenotyping platforms. Here, we argue that current phenotyping methods may be excellent tools for functional validation of previously discovered traits but have limited predictive value in stress biology. We also propose that bridging the mismatch between omics technologies and phenotyping is the only way to account for cell-specific operation of key genes conferring stress tolerance and implementing them in breeding programmes. Some practical examples using cell-based phenotyping tools such as fluorescence dyes or electrophysiological methods are given, and current limitations and prospects of cell-based phenotyping are discussed.
Sergey Shabala, Ping Yun, Zhong-Hua Chen et al.· New Phytologist· 0 citations
Hypoxic conditions caused by submergence or soil waterlogging constrain plant growth and productivity. To survive, plants coordinately reprogram both sugar metabolism and phytohormone signaling to trigger adaptive responses; yet, the integrative regulatory frameworks governing this interaction remain unresolved. Here, we synthesize current knowledge on how sugars, acting as both metabolites and signals, intersect with phytohormone networks to regulate growth and survival under low-oxygen stress. Under hypoxia, ethylene and auxin reshape root architecture, while cytokinin mediates sugar-dependent regulation of shoot branching to optimize resource allocation. The dynamic interplay between abscisic acid and sugars is central to maintaining energy balance under cyclic day-night hypoxia. This interaction modulates the stomatal aperture, facilitates controlled starch degradation, and coordinates sucrose transport to sustain metabolism. Furthermore, crosstalk between primary sugars, gibberellin, and brassinosteroid fine-tunes critical developmental transitions, including seed germination and internode elongation. Although individual signaling pathways under hypoxia have been well studied, their integration via sugar-hormone crosstalk remains elusive. To address these issues, we propose integrating synthetic low-oxygen sensors that initially detect hypoxic stress with engineered sugar-hormone balancing circuits that subsequently fine-tune metabolic and hormonal responses, thereby creating closed-loop feedback systems for adaptive stress resilience. Such systems could enable "Sensing, Metabolism, Adaptation, and Regulation Technology" (SMART) crops to autonomously sense and adapt to hypoxia stress. By synthesizing current knowledge and existing gaps, our work proposes future directions to advance the development of hypoxia-resilient crops through optimizing growth and yield stability under stress.
Muhammad Ateeq, Muhammad Atiq Ashraf, Muhammad Asim et al.· Journal of Integrative Plant...· 1 citation