{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T05:17:00Z","timestamp":1787894220918,"version":"build-2784847793"},"reference-count":128,"publisher":"MDPI AG","issue":"17","license":[{"start":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T00:00:00Z","timestamp":1787702400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100002855","name":"Ministry of Science and Technology of the People's Republic of China","doi-asserted-by":"publisher","award":["2021YFD2200103"],"award-info":[{"award-number":["2021YFD2200103"]}],"id":[{"id":"10.13039\/501100002855","id-type":"DOI","asserted-by":"publisher"}]},{"award":["2021YFD2200103"],"award-info":[{"award-number":["2021YFD2200103"]}],"id":[{"id":"https:\/\/ror.org\/027s68j25","id-type":"ROR","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["U21A20213"],"award-info":[{"award-number":["U21A20213"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["U21A20213"],"award-info":[{"award-number":["U21A20213"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Plants"],"abstract":"<jats:p>Metabolic changes are often described as drivers of plant development even when the evidence establishes only association or a permissive requirement. This review separates biological role from causal status and evaluates claims across seven dimensions: association, necessity, localization, transport, rescue and mediation, sufficiency, and quantitative-threshold testing. We apply a when\u2013where\u2013how framework to four cases. Perturbations of T6P, SnRK1, and TOR support T6P-dependent kinase regulation as a mediator of lateral-root development and are consistent with a context-dependent candidate gate, but its window and threshold remain unresolved. Circadian regulation of AHA3 and SUC2 by CCA1 provides the most complete chain, combining cell-specific perturbation, transport, and rescue. The OsARF18\u2013OsARF2\u2013OsSUT1 pathway supports sucrose transport as a mediator of rice fertility, although receiving-cell necessity and quantitative restoration remain unresolved. H+-ATPase perturbations identify apoplastic pH as a proximal mediator of Arabidopsis hypocotyl and cotton-fiber elongation, with context-dependent optima rather than a shared threshold. Nutrient and redox regulation, specialized metabolism, stress, and senescence provide boundary comparisons. Causal confidence depends on claim-matched evidence for responding cells and developmental windows and, where relevant, transport routes, mechanisms, and whole-plant trade-offs. The framework can guide AI-assisted breeding by prioritizing genotype-, stage-, and tissue-specific interventions for prospective perturbation and rescue.<\/jats:p>","DOI":"10.3390\/plants15172604","type":"journal-article","created":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T15:04:32Z","timestamp":1787756672000},"page":"2604","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Evaluating Causal Claims in Plant Developmental Metabolism: A When\u2013Where\u2013How Framework"],"prefix":"10.3390","volume":"15","author":[{"given":"Xiangfei","family":"Cheng","sequence":"first","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"},{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanan","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"},{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0001-7548-210X","authenticated-orcid":false,"given":"Leidi","family":"Liu","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"},{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yaning","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruohang","family":"Zhao","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhiyao","family":"Yang","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinci","family":"Hao","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6346-1582","authenticated-orcid":false,"given":"Zhongling","family":"Yang","sequence":"additional","affiliation":[{"name":"International Joint Research Laboratory for Global Change Ecology, Laboratory of Biodiversity Conservation and Ecological Restoration, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chengde","family":"Yu","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1352-8301","authenticated-orcid":false,"given":"Chengming","family":"Fan","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhifang","family":"Li","sequence":"additional","affiliation":[{"name":"Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China"},{"name":"State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, Kaifeng 475004, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,26]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1016\/j.pbi.2009.12.002","article-title":"Sugar signals and molecular networks controlling plant growth","volume":"13","author":"Smeekens","year":"2010","journal-title":"Curr. 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