A natural variation within duplicated <i>AsWRKY49‐D2</i> drives the subgenomic functional divergence of homeologs in salt response of allohexaploid oats

Salt stress is a major abiotic constraint limiting global crop production. Oat (Avena sativa L.), an allohexaploid cereal renowned for robust stress tolerance, remains poorly understood in terms of the molecular mechanisms underlying its response to salt stress. Here, we perform transcriptome profiling across multiple developmental stages and tissues of oat under salt stress, and construct the co-expression regulatory network to identify salt tolerance-associated gene modules. Notably, 10 salt-responsive transcription factor (SRTF) families with dynamic expression patterns are identified as core regulators, showing extensive subgenomic functional divergence, characterized by subgenome-dominant expression, as well as subgenome-specific duplication or loss events. Further integration with a genome-wide association study (GWAS) of the germination rate under salt stress in 225 oat accessions identified a 3-bp InDel variation within the duplicated gene AsWRKY49-D2, which specifically modulates its expression by facilitating binding of the TF AsZAT18, with AsWRKY49-D2 further mediating oat salt tolerance through targeted regulation of AsSOS2 and AsSOS3. Intriguingly, the salt-tolerant allele of AsWRKY49 is scarcely distributed in Chinese oat accessions, highlighting its considerable potential for breeding application. These results shed light on the regulatory mechanisms underlying oat salt tolerance, providing valuable information for exploring salt tolerance genes and breeding new salt-tolerant oat varieties.