Molecular Mechanisms Underlying Plant Responses to Environmental Cues: From Signal Perception and Integration to Stress Memory and Crop Improvement

Plants must tolerate fluctuating and increasingly concurrent abiotic and biotic stresses while maintaining growth and reproduction. Understanding how plants integrate these environmental cues is therefore central to developing climate-resilient crops. Plant stress tolerance is not governed by isolated pathways but by a multilayered signaling network in which stress perception is translated into calcium (Ca2+), reactive oxygen species (ROS) and reactive nitrogen species (RNS) signals, integrated through phytohormone networks and mitogen-activated protein kinase (MAPK) cascades, and decoded by transcription factors, post-translational modifications and chromatin-based mechanisms. In this Review, we synthesize recent advances from stress perception and early signaling through hormone crosstalk, transcriptional and post-translational regulation, epigenetic control and stress memory, with particular emphasis on the integration of abiotic and biotic stress responses. We highlight how shared signaling components generate both convergence and stimulus-specific outputs, and why responses to combined stresses cannot be reliably predicted from single-stress experiments. We further examine how mechanistic knowledge is being translated into crop improvement through genome editing, synthetic biology, microbiome-based strategies, priming and data-driven breeding. Finally, we identify critical gaps in signal specificity, network integration, stress memory, genotype-by-environment interactions and field validation. We propose that future crop improvement should prioritize conditional, tissue-specific and quantitatively tuned interventions evaluated under realistic multifactorial stress environments. This integrative framework links molecular stress perception and signaling with memory and crop engineering, providing a mechanistic basis for developing crops that maintain productivity under increasingly complex environmental conditions.