From Stress to Recovery: Divergent Chilling Responses in Contrasting <scp> <i>Miscanthus sinensis</i> </scp> Genotypes

ABSTRACT Chilling temperatures are a major constraint on the early‐season performance of C 4 bioenergy crops in temperate regions. To dissect the temporal architecture of chilling resilience, we conducted an integrative, time‐resolved analysis of two Miscanthus sinensis genotypes contrasting in chilling tolerance, Ms12 (LCT) and Ms16 (HCT). Through stepwise chilling and recovery treatments, we profiled genotype‐specific changes in shoot physiology, hormone accumulation, gene expression, and importantly cell wall composition, a key yet understudied determinant of chilling resilience in perennial grasses. The high chilling‐tolerant genotype (HCT) maintained its shoot growth, photosynthetic performance, and membrane stability by activating a delayed but sustained program involving secondary wall reinforcement, ABA–JA hormonal crosstalk, and raffinose family oligosaccharide (RFO) accumulation in response to the extreme conditions. While, low chilling‐tolerant genotype (LCT) initiated a rapid transcriptional and hormonal response, which lacked persistence and failed to support structural recovery or metabolic buffering. In‐depth transcriptomic profiling revealed divergent dynamics between studied genotypes. The LCT genotype mounted an early transcriptional burst, while the HCT genotype showed prolonged induction of the cell wall biosynthesis, energy metabolism, and stress‐response genes. FTIR (Fourier‐transform infrared spectroscopy) and sugar quantification confirmed genotype‐specific remodeling of cell wall polymers. Moreover, hormone profiling showed that only the HCT genotype sustained ABA and JA signaling through the recovery process. RFOs accumulation, tightly linked to transcriptional activation of GolS (galactinol synthase) and RS (raffinose synthase) genes, was also more pronounced in the HCT genotype. Our findings demonstrate that chilling resilience in M. sinensis depends not on early response magnitude, but on the integration and temporal coordination of stress mitigation and recovery pathways. This work establishes a multiscale framework for identifying traits and regulatory modules underpinning chilling tolerance in perennial grasses, with direct relevance to climate‐resilient biomass plant breeding.