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DC. (\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    ) is a crop with medicinal and food properties. Currently, the majority of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    available on the market is cultivated in extensive agricultural fields. This led to phenotypic variation in the plant and a reduction in the content of active ingredients. However, the cultivation of the understory can facilitate the phenotype of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    . This, in turn, aligns with the characteristics of \u201cexcellent shape\u201d and \u201chigh quality.\u201d Nonetheless, there is a paucity of research focusing on the phenotypic changes and molecular mechanisms underlying quality formation in understory\u2010cultivated\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    . In this study, a comprehensive analysis of DNA methylation, phytohormone network regulation, and changes in energy metabolism in\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    across different habitats was performed through the integration of transcriptomic and proteomic data, representative phytohormone assays, and methylation\u2010sensitive amplified polymorphism analysis. The results of the study revealed that the cultivation of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    in the understory was predominantly characterized by a demethylation pattern, with its total methylation rate closely approximating that of the wild type. Understory\u2010cultivated\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    maintains resource allocation equilibrium between growth and defense by upregulating genes (e.g., Lipoxygenase) and proteins associated with the jasmonic acid synthesis and signaling pathway, while downregulating genes (e.g., indole\u20103\u2010pyruvate monooxygenase) and proteins linked to the auxin synthesis and signaling pathway. This cultivation method optimizes primary and secondary metabolism, thereby enhancing the bioactive components of\n                    <jats:styled-content style=\"fixed-case\">\n                      <jats:italic>A. lancea<\/jats:italic>\n                    <\/jats:styled-content>\n                    . The findings of this study provide a molecular\u2010level theoretical framework for further advancement and implementation of the forest\u2010medicine composite planting model.\n                  <\/jats:p>","DOI":"10.1111\/ppl.70722","type":"journal-article","created":{"date-parts":[[2025,12,29]],"date-time":"2025-12-29T09:28:04Z","timestamp":1767000484000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Molecular Basis of Phenotypic Plasticity: Understory\u2010Induced\n                    <scp>DNA<\/scp>\n                    Methylation and Phytohormone Shifts Optimize\n                    <i>Atractylodes lancea<\/i>\n                    (Thunb.)\n                    <scp>DC<\/scp>\n                    Quality"],"prefix":"10.1111","volume":"178","author":[{"ORCID":"https:\/\/orcid.org\/0009-0008-9627-1548","authenticated-orcid":false,"given":"Yueyu","family":"Ye","sequence":"first","affiliation":[{"name":"School 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