Shuhui Wang, Dongqing Liu, Yingying Li, Qinglin Sun, Xingyu Liu, Minghao Li, Wei Li, Ziyue Wang, Ju Zhang, Qiang He, Yu Wang, Qingbin Sun, Xiaoying Hu, Jia Liu, Yuanyuan Peng, Zhizhong Gong, Huilong Du
Drought threatens global crop yields, and common oat, a vital nutritional source for food and feed, is particularly constrained in the semi‑arid regions where it is widely cultivated. Here, we report two high-quality genome assemblies for drought-resilient (Borris37) and drought-sensitive (XymC06) oat accessions with distinct seedling survival rates and genome sizes of 10.92 Gb and 10.96 Gb, and construct comprehensive landscapes of insertion‑deletions (InDels) and structural variants (SVs). Integrating population-level genomic, transcriptomic and phenotypic (seedling survival rate), we demonstrate that InDels and SVs underpin divergent drought resilience and identify 52 candidate genes associated with drought resistance whose expression is significantly modulated by these variants. Borris37 accumulates 36 favorable alleles of these genes. An InDel in the AsNF-YB3 promoter enhances binding to AsARF1, upregulating AsNF‑YB3 under drought, and overexpression of AsNF‑YB3 reduces ROS accumulation. Our findings provide resources and targets for drought‑resistance breeding in oat, thereby supporting global food security.