A cis-regulatory variant in ZmABI45 modulates drought tolerance and adaptation by escaping ZmbHLH80 repression in maize

Drought stress during flowering severely threatens maize productivity by disrupting the synchrony of male and female flowering, while its genetic basis remains poorly understood. Through a genome-wide association study (GWAS) and quantitative trait locus (QTL) analysis, we identify an ABI3 transcription factor gene ZmABI45 as a key regulator of drought-induced anthesis-silking interval (ASI). We characterize a 12-bp insertion or deletion (indel) in the promoter of ZmABI45, demonstrating that its deletion allele enhances drought tolerance by escaping transcriptional repression by ZmbHLH80. Overexpression of ZmABI45 significantly shortens ASI and improves grain yield under drought. ZmABI45 activates stress-responsive genes under drought and suppresses growth-related processes under normal conditions. Evolutionary and ecological analyses further indicate that the drought-tolerance haplotype has been selected during modern maize breeding and shows a geographic distribution correlated with low-precipitation areas. Our work highlights how cis-regulatory variation fine-tunes stress adaptation and provides a valuable gene resource for breeding drought-resilient maize.