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Volume 15
Issue 17
10.3390/plants15172604
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This is an early access version, the complete PDF, HTML, and XML versions will be available soon.
Review

Evaluating Causal Claims in Plant Developmental Metabolism: A When–Where–How Framework

by
Xiangfei Cheng
1,2,†,
Yanan Zhao
1,2,†,
Leidi Liu
1,2,
Yaning Li
1,
Ruohang Zhao
1,
Zhiyao Yang
1,
Xinci Hao
1,
Zhongling Yang
3,
Chengde Yu
1,
Chengming Fan
4,* and
Zhifang Li
1,2,*
1
Center for Molecular Interactions and Translational Applications, School of Life Sciences, Henan University, Kaifeng 475004, China
2
State Key Laboratory of Cotton Bio-Breeding and Integrated Utilization, School of Life Sciences, Henan University, Kaifeng 475004, China
3
International Joint Research Laboratory for Global Change Ecology, Laboratory of Biodiversity Conservation and Ecological Restoration, School of Life Sciences, Henan University, Kaifeng 475004, China
4
State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
*
Authors to whom correspondence should be addressed.
†
These authors contributed equally to this work.
Plants 2026, 15(17), 2604; https://doi.org/10.3390/plants15172604
Submission received: 22 July 2026 / Revised: 18 August 2026 / Accepted: 25 August 2026 / Published: 26 August 2026
(This article belongs to the Special Issue Insights and Regulation of Plant Growth and Metabolism)
Versions Notes

Abstract

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–where–how 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–OsARF2–OsSUT1 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.
Keywords: developmental competence; causal inference; metabolic state; source–sink allocation; spatial metabolism; trehalose 6-phosphate; SnRK1–TOR signaling; phloem transport; specialized metabolism; AI-assisted breeding developmental competence; causal inference; metabolic state; source–sink allocation; spatial metabolism; trehalose 6-phosphate; SnRK1–TOR signaling; phloem transport; specialized metabolism; AI-assisted breeding

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MDPI and ACS Style

Cheng, X.; Zhao, Y.; Liu, L.; Li, Y.; Zhao, R.; Yang, Z.; Hao, X.; Yang, Z.; Yu, C.; Fan, C.; et al. Evaluating Causal Claims in Plant Developmental Metabolism: A When–Where–How Framework. Plants 2026, 15, 2604. https://doi.org/10.3390/plants15172604

AMA Style

Cheng X, Zhao Y, Liu L, Li Y, Zhao R, Yang Z, Hao X, Yang Z, Yu C, Fan C, et al. Evaluating Causal Claims in Plant Developmental Metabolism: A When–Where–How Framework. Plants. 2026; 15(17):2604. https://doi.org/10.3390/plants15172604

Chicago/Turabian Style

Cheng, Xiangfei, Yanan Zhao, Leidi Liu, Yaning Li, Ruohang Zhao, Zhiyao Yang, Xinci Hao, Zhongling Yang, Chengde Yu, Chengming Fan, and et al. 2026. "Evaluating Causal Claims in Plant Developmental Metabolism: A When–Where–How Framework" Plants 15, no. 17: 2604. https://doi.org/10.3390/plants15172604

APA Style

Cheng, X., Zhao, Y., Liu, L., Li, Y., Zhao, R., Yang, Z., Hao, X., Yang, Z., Yu, C., Fan, C., & Li, Z. (2026). Evaluating Causal Claims in Plant Developmental Metabolism: A When–Where–How Framework. Plants, 15(17), 2604. https://doi.org/10.3390/plants15172604

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