Autonomous recovery of wheat spikelet development following cold stress arrest mediated by modulation of sucrose degradation and IAA/ABA homeostasis

Abstract Wheat rapidly induces complex metabolic reactions in response to cold stress, yet the physiological mechanisms governing its natural recovery process remain poorly understood. In a 2 year pot experiment, we examined recovery dynamics of the wheat cultivar Zhengmai 366 during the booting stage under control (CK, 10/10 °C), chilling (CS, 10/2 °C), and freezing (FS, 10/−2 °C) treatments. Following stress relief, we performed comprehensive analyses on spikelet morphology, physiology, transcriptome, and metabolome. Spikelet development was consistently delayed in both post-cold recovery scenarios, with irreversible damage due to cellular breakdown during FS recovery. Physiological investigations demonstrated that antioxidant enzyme activities and sucrose, hexose, and proline concentration were restored to normal levels after CS recovery but remained suppressed after FS recovery. Furthermore, a progressive increase in indole-3-acetic acid (IAA) levels and a progressive decline in abscisic acid (ABA) levels coincided during the CS recovery, which may facilitate the resumption of spikelet development. Machine learning highlighted sucrose content and the IAA/ABA ratio as primary predictors of grain number. Multi-omics integration further confirmed that the recovery is determined by the sucrose–hexose conversion efficiency and hormonal balance. Collectively, this study revealed that wheat recovery from cold is mediated by coordinated carbon metabolism and hormonal homeostasis. This provided valuable insights toward improving cold tolerance in wheat production.