Transcriptional Dynamics of Rice Under Individual, Combined, and Sequential Abiotic Stresses: Insights Across Stress Severity and Recovery in Contrasting Genotypes

Plants in natural environments frequently encounter multiple abiotic stresses, which may occur individually, simultaneously, or sequentially, significantly impacting crop productivity. The transcriptional response to these stresses varies across genotypes, and understanding these variations at the molecular level is critical for improving stress resilience. In a previous study, we identified two contrasting rice genotypes, Lomello (highly stress-tolerant) and C57-5043 (highly stress-sensitive), from a screen of ~400 genotypes for abiotic stress tolerance. Here, we performed time-course transcriptomic profiling to dissect the molecular basis of their differential stress responses under varying severity levels (mild, moderate, and severe) of high temperature (HT), drought (D), submergence (S), combined heat and drought stress (HTD), and post-submergence drought (PSD). Our results reveal that transcriptional responses are highly context-dependent, with distinct expression patterns emerging under individual, combined, and sequential stress conditions. Notably, while submergence induced significant transcriptomic changes within the first few days, subsequent drought exposure, particularly at higher severity levels, did not elicit a strong transcriptional response, likely due to transcriptional silencing resulting from physiological damage. Comparative analysis between genotypes showed that Lomello exhibits constitutively higher expression of genes involved in phytoalexin biosynthesis, even in the absence of stress, potentially conferring a preemptive defense advantage. Furthermore, Lomello demonstrated a robust induction of genes associated with reactive oxygen species (ROS) scavenging, abscisic acid (ABA) biosynthesis and signaling, and secondary metabolite production in response to stress, followed by a rapid reversion to near-baseline expression levels during recovery. These findings suggest that Lomello's superior stress tolerance is driven by enhanced secondary metabolite accumulation, efficient ROS detoxification, and a stronger recovery response. This study provides novel insights into genotype-specific transcriptional strategies for stress resilience, offering potential targets for breeding climate-resilient rice varieties.