Natural variation in a cortex/epidermis-specific transcription factor bZIP89 determines lateral root development and...

Lateral roots (LRs) branching is crucial for water and nutrient acquisition in plants, ultimately determining the overall plant performance and productivity. However, the transcriptional regulation of LR development in crops and its role in stress resilience remain largely unexplored. Leveraging integrated transcriptome-wide association study and single-cell RNA sequencing data, we identified a basic leucine zipper (bZIP) transcription factor ZmbZIP89 as an important regulator of LR elongation and mapped its spatial expression pattern in cortex/epidermis cell types. ZmbZIP89 can activate the expression of ZmPRX47 to regulate the production of root reactive oxygen species homeostasis, contributing to increased lateral root length (LRL) and enhanced drought resistance. Natural variations in the 3' untranslated region of ZmbZIP89 enhance gene expression by increasing mRNA stability, leading to increases in LRL and drought tolerance. These findings contribute to our understanding of the molecular mechanisms underlying LR development and provide potential gene targets for breeding stress-resilient crops.