The ability of plants to respond to abiotic stress is strongly shaped by time of day, with the circadian clock gating transcriptional, metabolic, and physiological responses to optimize fitness in fluctuating environments. However, translating these insights into crops remains challenging, particularly in polyploid species where genome duplication and fractionation generate extensive paralog diversity, complicating the identification of conserved regulatory targets. To address this, we performed dense time-course transcriptomic profiling of cold acclimation across diverse Brassica rapa morphotypes, capturing diel gene expression dynamics under stress. Cold exposure induces widespread transcriptional reprogramming accompanied by genotype-specific shifts in circadian period, indicating that stress alters clock pace in a manner that varies across accessions. We observe extensive divergence in time-of-day–specific expression among paralogs, alongside limited conservation of inferred regulatory interactions at the paralog level. In contrast, conservation emerges at the ortholog level, suggesting that shared functional responses are maintained despite regulatory diversification following genome triplication. To identify the regulatory basis of this divergence, we integrate comparative genomics with temporal transcriptomic data to uncover conserved noncoding sequences (CNS) associated with time-of-day–specific expression patterns. These CNS represent candidate regulatory elements that may encode conserved temporal control across accessions and species. Building on these findings, we are establishing a scalable experimental framework to systematically evaluate candidate CNS for their ability to drive time-of-day–specific expression. This approach links large- scale temporal datasets to functional validation, enabling prioritization of regulatory elements that control the timing of stress-responsive gene expression. Together, this work provides a path toward identifying and testing conserved regulatory elements underlying temporal stress responses in polyploid crops, advancing efforts to engineer crops with improved resilience through precise control of gene expression timing.