Transcriptome Profiling of Resistance Gene Analogs in Soybean's Cross‐Tolerance to Water Limitation and Rust Stress

Asian soybean rust (ASR), caused by Phakopsora pachyrhizi , is the most destructive foliar disease of soybean, with yield losses up to 90%. With climate change intensifying drought and expanding disease incidence, it is critical to understand how combined abiotic and biotic stresses influence plant defense. We investigated the transcriptomic response of a susceptible soybean cultivar to ASR infection under normal and water‐limited conditions at four infection stages (12, 24, 72, and 192 h after inoculation). We observed a biphasic expression of defense‐related genes, particularly resistance gene analogs (RGAs), with an early peak at 12 h and a late resurgence at 192 h. Combined stress induced a greater number of differentially expressed genes (DEGs) than rust alone, especially at early infection. Among the differentially expressed RGAs (RGADEs), over 64% belonged to the TM‐LRR class, and NBS‐LRR genes were the most enriched at known ASR resistance loci, particularly Rpp2. Water limitation strongly modulated gene expression at late stages, revealing stress‐specific transcriptional reprogramming. These findings were consistent with the activation of potential cross‐tolerance mechanisms in soybean, highlighted the temporal dynamics of RGADEs under dual stress, and provided potential targets for developing cultivars with improved resilience to both rust and water scarcity.