Omics-Driven Insights into Plant Stress Responses and Metabolic Reprogramming

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Response to Abiotic Stress and Climate Change".

Deadline for manuscript submissions: 31 December 2026 | Viewed by 395

Editors

Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and the Orchid Conservation & Research Center of Shenzhen, Shenzhen 518114, China
Interests: plant hormone; signal transduction; stress biology; tolerance mechanisms; metabolism

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Guest Editor
Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China
Interests: plant physiology; plant nutrition; stress tolerance; plant breeding

Special Issue Information

Dear Colleagues,

Plants, including crops, are under constant attack. Between unpredictable droughts, soils turning saltier by the year, sudden temperature fluctuations, and nutrient-depleted fields, plants are pushed to their absolute limits. These are not just abstract environmental issues; they directly impact plant growth, slash yields, and threaten the very foundation of our food supply.

How do plants actually cope with such stresses? To truly understand the survival strategies, we need to stop looking at just one piece of the puzzle. Instead, we should paint a full picture of the situation by incorporating techniques such as transcriptomics to see what genes are turning on, proteomics to track the functional machinery, metabolomics to capture the chemical shifts, and—just as importantly—spatial metabolomics to pinpoint exactly where and when those metabolic changes happen inside tissues. Only by combining these elements can we see how a plant reorganizes its metabolism in real time to withstand harsh conditions.

Hence, it is time to take a systems-level approach. By integrating these multi-omics datasets, we can uncover the key regulatory hubs that drive stress tolerance. And with such knowledge, we will be better equipped to develop resilient, next-generation crops, ensuring that our agricultural systems remain robust in the face of an increasingly inhospitable environment.

We encourage researchers across disciplines to present their recent discoveries, promoting new insights and enhancing our comprehension of plant stress response through metabolic reprogramming.

Dr. Zhiyong Li
Prof. Dr. Erhui Xiong
Guest Editors

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Keywords

  • drought stress
  • salt stress
  • temperature stress
  • oxidative stress
  • nutrient deficiency
  • phytohormone
  • tolerance mechanisms
  • metabolism
  • omics

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Published Papers (1 paper)

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Research

25 pages, 16643 KB  
Article
Comparative Multi-Omics Analysis of Rhizome Shooting in Fargesia rufa Under Altitudinal Temperature Variation
by Xin Zhao, Man Tang, Yanwen Zhao, Mengqiu Chen, Xiaojun Wang, Qi Lin, Zhijian Long and Shanglian Hu
Plants 2026, 15(15), 2302; https://doi.org/10.3390/plants15152302 - 27 Jul 2026
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Abstract
Bamboo shoots, as the most nutritionally valuable food source for giant pandas during key reproductive seasons, are critical for conservation because their availability and timing directly influence panda foraging and habitat use. However, the molecular mechanisms through which altitudinal temperature variation governs rhizome [...] Read more.
Bamboo shoots, as the most nutritionally valuable food source for giant pandas during key reproductive seasons, are critical for conservation because their availability and timing directly influence panda foraging and habitat use. However, the molecular mechanisms through which altitudinal temperature variation governs rhizome shooting in staple food bamboos remain largely unknown. Here, we performed integrated metabolomic and transcriptomic analyses of Fargesia rufa rhizomes collected along an elevational gradient (1000 m, 1500 m, and 2000 m), with a critical paired comparison at 2000 m between a non-shooting cold gully-edge site (16.4 °C) and a shooting warm gully-center site (21.1 °C), where soil temperature is elevated by approximately 4 °C due to prolonged solar exposure. Our results demonstrate that soil temperature, rather than elevation per se, acts as the primary driver of rhizome shooting, with an apparent threshold near 20 °C. A core shooting metabolome (CSM) comprising 843 metabolites was consistently accumulated across all shooting conditions, which featured gibberellin/auxin precursors, TCA cycle intermediates, and phenylpropanoid compounds. Correspondingly, a core shooting transcriptome (Rh_shooting) of 10,970 genes was identified, which resolved into three functionally distinct temporal clusters: “shooting-on” (activated upon threshold crossing, enriched in hormone signaling and cell wall metabolism), “temperature-dose” (progressively upregulated with rising temperature, enriched in energy metabolism and defense), and “microenvironment-enhanced” (specifically upregulated in the high-elevation warm gully, enriched in photosynthesis and antioxidant pathways). Integrative network analysis further revealed zeatin riboside and multiple hub genes as central coordinators linking hormone signaling, energy metabolism, and cell wall remodeling. Collectively, these findings establish a molecular framework linking altitudinal temperature variation to bamboo rhizome regeneration—a process that directly determines the spatiotemporal availability of bamboo shoots for giant pandas. This work provides mechanistic insights into giant panda foraging ecology and has direct implications for predicting habitat quality under climate change and informing evidence-based conservation strategies for this flagship species and its critical food resource. Full article
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