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Drought represents a major constraint on maize production worldwide. Understanding the genetic basis for natural variation in drought tolerance of maize may facilitate efforts to improve this trait in cultivated germplasm. Here, using a genome-wide association study, we show that a miniature inverted-repeat transposable element (MITE) inserted in the promoter of a  NAC  gene ( ZmNAC111 ) is significantly associated with natural variation in maize drought tolerance. The 82-bp MITE represses  ZmNAC111  expression via RNA-directed DNA methylation and H3K9 dimethylation when heterologously expressed in  Arabidopsis . Increasing  ZmNAC111  expression in transgenic maize enhances drought tolerance at the seedling stage, improves water-use efficiency and induces upregulation of drought-responsive genes under water stress. The MITE insertion in the  ZmNAC111  promoter appears to have occurred after maize domestication and spread among temperate germplasm. The identification of this MITE insertion provides insight into the genetic basis for natural variation in maize drought tolerance.

A transposable element in a NAC gene is associated with drought tolerance in maize seedlings