A pangenome of maize provides genetic insights into drought resistance

Drought poses a severe threat to the stability of crop yields. It is crucial to identify genetic resources and decipher the molecular mechanisms underlying drought resistance in crops. Here we generated high-quality genome assemblies of 25 maize germplasms exhibiting substantial variation in drought resistance. Combined with 31 additional maize genome sequences, a comprehensive pangenome analysis was performed. Rare allelic variations and extensive regulatory diversity were revealed in abscisic acid-related or drought-related genes, which may contribute to the diversity in drought resistance among germplasms. Furthermore, we identified three genes, ZmUGE2, ZmSIL2 and ZmASI3, that enhance maize drought resistance by strengthening mechanical support of the cell wall, regulating stress-responsive gene expression and coordinating male and female inflorescence development, respectively. Thus, this study provides valuable insight into the genetic control of drought resistance in maize at different growing stages. The expanded maize pangenome information serves as a valuable resource for maize genomic research.