cc_byLi, RonglanLi, DongdongGuo, YuhangWang, YueliZhang, YufengLi, LeYang, XiaosongChen, ShaojiangWürschum, TobiasLiu, WenxinHan, De-Guo2025-07-232025-07-232025https://doi.org/10.3390/ijms26136285https://hohpublica.uni-hohenheim.de/handle/123456789/17943Drought severely limits crop yield every year, making it critical to clarify the genetic basis of drought tolerance for breeding of improved varieties. As drought tolerance is a complex quantitative trait, we analyzed three phenotypic groups: (1) agronomic traits under well-watered (WW) and water-deficit (WD) conditions, (2) stress tolerance indices of these traits, and (3) phenotypic plasticity, using a multi-parent doubled haploid (DH) population assessed in multi-environment trials. Genome-wide association studies (GWAS) identified 130, 171, and 71 quantitative trait loci (QTL) for the three groups of phenotypes, respectively. Only one QTL was shared among all trait groups, 25 between stress indices and agronomic traits, while the majority of QTL were specific to their group. Functional annotation of candidate genes revealed distinct pathways of the three phenotypic groups. Candidate genes under WD conditions were enriched for stress response and epigenetic regulation, while under WW conditions for protein synthesis and transport, RNA metabolism, and developmental regulation. Stress tolerance indices were enriched for transport of amino/organic acids, epigenetic regulation, and stress response, whereas plasticity showed enrichment for environmental adaptability. Transcriptome analysis of 26 potential candidate genes showed tissue-specific drought responses in leaves, ears, and tassels. Collectively, these results indicated both shared and independent genetic mechanisms underlying drought tolerance, providing novel insights into the complex phenotypes related to drought tolerance and guiding further strategies for molecular breeding in maize.engMaizeDrought toleranceGenome-wide association studyAgronomic traitsStress tolerance indicesPhenotypic plasticity630Article2025-07-18