Cell‐based crop phenotyping for future climates

Abiotic stress tolerance has been significantly weakened in moderncrops during the domestication process. Regaining tolerance hasbecome a critical task in light of current climate trends and theirimpact on global food security. Abiotic stress tolerance is anextremely complex trait and is conferred at various levels of plantfunctional organization and developmental stages, with regulatorymechanisms operating across multiple scales, from individual cells totissues and the entire plant. The emergence of advanced moleculartools such as single-cell RNA sequencing and spatial omicstechnologies has revolutionized the field, advancing our under-standing of plant responses to hostile environments. However, theimplementation of this knowledge in crop breeding programmes ishandicapped by the lack of appropriate phenotyping platforms.Here, we argue that current phenotyping methods may be excellenttools for functional validation of previously discovered traits buthave limited predictive value in stress biology. We also propose thatbridging the mismatch between omics technologies and phenotyp-ing is the only way to account for cell-specific operation of key genesconferring stress tolerance and implementing them in breedingprogrammes. Some practical examples using cell-based phenotyp-ing tools such as fluorescence dyes or electrophysiological methodsare given, and current limitations and prospects of cell-basedphenotyping are discussed.