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J. Mol. Sci.","IJMS"],"abstract":"<jats:p>Water deficit severely limits rice productivity. The elite Dian (D1)-type hybrid japonica rice \u2018Dianheyou 615 (ZH1)\u2019 exhibits exceptional drought adaptation in high-altitude rainfed uplands of the Yungui Plateau, yet the underlying molecular mechanisms remain unknown. We compared phenotypic and transcriptomic responses of ZH1 and six other japonica cultivars under well-watered and water-deficit conditions. Water-deficit stress significantly impaired agronomic traits across all cultivars; however, ZH1 uniquely maintained relatively stable flag leaf morphology and seed-setting rate, and displayed distinctive stomatal traits, in stark contrast to its parental lines and other cultivars. Transcriptomic profiling at the jointing-to-booting stage defined a core drought response module of 174 conserved genes across all cultivars. Critically, by intersecting 1097 ZH1-specific genes with drought-responsive elements, we pinpointed 15 core, cultivar-specific regulatory genes. These candidates are enriched in functions related to cuticle formation, carbohydrate metabolism, and stress signaling; among them, a DREB transcription factor (LOC4347618) is a prime candidate. qRT-PCR validated their expression. Using CRISPR\/Cas9-mediated gene editing, we generated homozygous knockout mutants for LOC4333842, LOC4347618, and LOC4328441. Under 20% PEG-6000-simulated drought stress, all three mutant lines showed significantly increased drought susceptibility relative to wild-type controls, confirming the positive regulatory roles of these genes in drought stress tolerance in japonica rice. These results establish these three genes as promising targets for molecular breeding aimed at enhancing drought resistance in rice.<\/jats:p>","DOI":"10.3390\/ijms27167469","type":"journal-article","created":{"date-parts":[[2026,8,20]],"date-time":"2026-08-20T16:05:19Z","timestamp":1787241919000},"page":"7469","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Comparative Transcriptomic Analysis of Water-Deficit Responses in Japonica Hybrid Rice \u2018Dianheyou 615\u2019"],"prefix":"10.3390","volume":"27","author":[{"given":"Xiaoli","family":"Zhou","sequence":"first","affiliation":[{"name":"Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China"},{"name":"College of Agricultural Science, Xichang University, Xichang 615013, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junjie","family":"Li","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xianyu","family":"Wang","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-0385-832X","authenticated-orcid":false,"given":"Chunli","family":"Wang","sequence":"additional","affiliation":[{"name":"School of Life Sciences, Yunnan University, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0006-1858-7948","authenticated-orcid":false,"given":"Fan","family":"Luo","sequence":"additional","affiliation":[{"name":"College of Agricultural Science, Xichang University, Xichang 615013, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-6745-2363","authenticated-orcid":false,"given":"Wenfeng","family":"Zhang","sequence":"additional","affiliation":[{"name":"College of Agricultural Science, Xichang University, Xichang 615013, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Changhe","family":"Wei","sequence":"additional","affiliation":[{"name":"College of Agricultural Science, Xichang University, Xichang 615013, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Zhu","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China"},{"name":"The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lijuan","family":"Chen","sequence":"additional","affiliation":[{"name":"Rice Research Institute, Yunnan Agricultural University, Kunming 650201, China"},{"name":"The Key Laboratory for Crop Production and Smart Agriculture of Yunnan Province, Yunnan Agricultural University, Kunming 650201, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,20]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","unstructured":"Wang, X., Liu, X., Su, Y., and Shen, H. 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