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However, the regulatory mechanisms by which this genomic integration confers increased environmental adaptability in allohexaploid remains largely unexplored. Here, we investigated the change of transcriptome, chromatin interactome and metabolome in three independent polyploidization events. Our findings reveal that polyploidization triggers the activation of defense\u2010related genes through a comprehensive reorganization of the epigenome and 3D chromatin architecture. Furthermore, polyploidization significantly enriches secondary metabolites\u2014specifically alkaloids and flavonoids\u2014which are pivotal for environmental adaptation. We further found that B\u2010subgenome genes\n                    <jats:italic>TaRLK\u20101B<\/jats:italic>\n                    and\n                    <jats:italic>TaRLK\u20103B<\/jats:italic>\n                    are activated via\n                    <jats:italic>de novo<\/jats:italic>\n                    chromatin interactions to enhance alkali stress tolerance, whereas\n                    <jats:italic>TaGT\u20102D<\/jats:italic>\n                    boosts UV\u2010B resistance through the accumulation of glycosylated flavonoids. These results shed light on the mechanistic basis of enhanced adaptability in hexaploid wheat, especially to salt, alkali, and UV\u2010B stress, and highlight the indispensable contribution of the D\u2010genome to the evolutionary success of the allohexaploid lineage.\n                  <\/jats:p>","DOI":"10.1002\/advs.77894","type":"journal-article","created":{"date-parts":[[2026,9,27]],"date-time":"2026-09-27T18:00:31Z","timestamp":1790532031000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Integration of the D\u2010Genome Reshapes Gene Transcription, Chromatin Architecture, and Metabolome of Allohexaploid Wheat, Leading to Enhanced Environmental Adaptability"],"prefix":"10.1002","author":[{"given":"Yanyan","family":"Liu","sequence":"first","affiliation":[{"name":"National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory Huazhong Agricultural University  Wuhan 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