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Functional Genomics and Molecular Mechanisms of Plant Stress Responses

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 30 June 2026 | Viewed by 3421

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Dr. Zupeng Wang

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Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430074, China
Interests: kiwifruit; bacterial canker disease; molecular breeding; gene editing

Special Issue Information

Dear Colleagues,

Plants encounter various biotic and abiotic stresses that significantly limit their growth, yields, and global distribution. Understanding how plants respond to and cope with these stresses at the genetic and molecular levels is crucial for improving crop resilience and productivity. This Special Issue focuses on recent advances in elucidating the functional genomics and molecular mechanisms underlying plant responses to diverse stress conditions, including pathogens, pests, drought, salinity, extreme temperatures, nutrient deficiency, and oxidative stress. We invite researchers to contribute original research articles, reviews, and methodological papers highlighting novel discoveries in gene identification, signaling pathways, transcriptional regulation, epigenetic modifications, and stress-responsive proteins. We particularly encourage the submission of studies utilizing cutting-edge approaches, such as genome editing, transcriptomics, proteomics, metabolomics, and integrative bioinformatics analyses. This Special Issue aims to provide insights into the complex regulatory networks involved in plant stress tolerance and facilitate the development of innovative strategies for crop improvement under challenging environmental conditions.

Dr. Zupeng Wang
Guest Editor

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Keywords

plant stress responses
abiotic stress
biotic stress
molecular mechanisms
functional genomics

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Published Papers (4 papers)

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Research

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23 pages, 10643 KB

Open AccessArticle

Genome-Wide Identification Analysis of the MAPKKK Gene Family in Cotton and Its Role in Development and Stress Response

by Yahui Deng, Nan Zhao, Shuo Ning, Yifan Wang, Weiran Wang, Meng Wang, Zixin Zhou, Yaohua Li, Caixia Li, Lingfang Ran, Jiahui Zhu, Zhiqing Liu, Jing Yang, Alifu Aierxi, Jie Kong, Aixing Gu and Jianping Li

Int. J. Mol. Sci. 2026, 27(2), 1124; https://doi.org/10.3390/ijms27021124 - 22 Jan 2026

Viewed by 603

Abstract

Mitogen-activated protein kinase kinase kinases (MAPKKKs) are pivotal upstream regulators of MAPK cascades, integrating signals that coordinate plant development and stress responses. However, the specific functions of MAPKKKs, particularly within the MEKK subfamily, in mediating cotton resistance to Verticillium wilt and Fusarium wilt remain poorly characterized. To address this, we conducted a systematic, cross-species analysis of the MAPKKK family in four key cotton species: Gossypium arboreum, Gossypium barbadense, Gossypium hirsutum, and Gossypium raimondii. Genome-wide identification and phylogenetic analysis revealed 660 MAPKKK genes, classifying them into the MEKK, Raf, and ZIK subfamilies. Evolutionary analysis indicated that Whole-Genome Duplication (WGD) events were the primary driver of family expansion. Promoter cis-element and Gene Ontology (GO) enrichment analyses implicated these genes in hormone signaling and stress adaptation. Expression profiling demonstrated functional modularity, with distinct members responding specifically to cold stress or cooperatively to drought and salt stresses. Upon pathogen infection, members diverged into regulatory modules associated with immune homeostasis, tissue-specific defense, and core signaling potentially governing systemic acquired resistance (SAR). The temporal expression patterns of core candidate genes were validated by qRT-PCR. This study provides, for the first time, a comprehensive evolutionary and functional framework for the MEKK subfamily within the cotton MAPKKK family. It reveals the conserved and divergent roles of this subfamily in stress adaptation and identifies key candidate genes for breeding disease-resistant cotton varieties. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Mechanisms of Plant Stress Responses)

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25 pages, 12246 KB

Open AccessArticle

Evolutionary History, Transcriptome Expression Profiles, and Abiotic Stress Responses of the SBP Family Genes in the Three Endangered Medicinal Notopterygium Species

by Dan-Ting Zhang, Yan-Jun Cheng, Rui Yang, Hui-Ling Wang, Xiao-Jing He, Cai-Yun Luo, Zhong-Hu Li and Mi-Li Liu

Int. J. Mol. Sci. 2026, 27(2), 979; https://doi.org/10.3390/ijms27020979 - 19 Jan 2026

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Abstract

Squamosa promoter binding protein (SBP) plays a vital role in plant growth, development, and responses to abiotic stresses. The genus Notopterygium is an endangered perennial herbaceous plant mainly distributed in the high-altitude Qinghai–Tibet Plateau and adjacent areas, which possibly occurred the adaptive evolution to the extreme environmental conditions. In this study, we firstly determined the genome-wide structural characteristics, evolutionary history, and expression profiles of the SBP family genes in Notopterygium species by using genome, transcriptome, and DNA resequencing data. We have also investigated the response patterns of SBPs of N. franchetii to the drought and high-temperature stresses. The 21, 18, and 18 SBP family genes of three Notopterygium species, N. incisum, N. franchetii, and N. forrestii, were, respectively, identified and classified into eight subfamilies, with four subfamily members regulated by miR156. The structure analysis showed that the members of the same SBP subfamily had similar structures and conserved motif composition. Cis-element analysis suggested that those SBP genes may have been essential to the growth and environmental adaptation of Notopterygium. The expansion of the SBP gene family was mainly caused by the whole genome duplication/segmental duplication and transposable element duplication. Evolutionary analysis showed the SBP gene family experienced severe contraction events and most of the gene copies underwent purification selection. Population genetics analysis based on SBPs variations suggested that the genus Notopterygium species have obvious genetic structure and interspecific differentiation. RNA-seq and qRT-PCR experiments demonstrated that the expressions of SBPs genes in Notopterygium were not species-specific, but tissue-specific. NinSBP08 and NinSBP10/12 may have played the key roles in heat tolerance and drought resistance, respectively. These results provided novel insights into the evolutionary history of the SBP gene family in the endangered herb Notopterygium species in the high-altitude Qinghai–Tibet Plateau and adjacent areas. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Mechanisms of Plant Stress Responses)

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20 pages, 1478 KB

Open AccessArticle

Physiological and Proteomic Responses of Sugarcane to Water Deficit Stress: Insights from a Self-Fertilized Clone

by João de Andrade Dutra Filho, Adauto Gomes Barbosa Neto, Cinthya Mirella Pacheco Ladislau, Marcelle Almeida da Silva, Geisenilma Maria Gonçalves da Rocha, Rômulo Gil de Luna, Anielson dos Santos Souza, Lauter Silva Souto, Ancélio Ricardo de Oliveira Gondim, Andréa Chaves Fiuza Porto, Fabiana Aparecida Cavalcante Silva, Josimar Mendes de Vasconcelos, Guilherme Rocha Moreira, Diogo Gonçalves Neder, Francisco Cássio Gomes Alvino, Leonardo de Sousa Alves, Lucas Carvalho de Freitas, Djalma Euzébio Simões Neto, Marcelo Menossi and Tercilio Calsa Junior

Int. J. Mol. Sci. 2025, 26(23), 11571; https://doi.org/10.3390/ijms262311571 - 28 Nov 2025

Viewed by 672

Abstract

Abiotic stresses, particularly water deficit, are major constraints to global agricultural productivity. This study aimed to evaluate physiological and proteomic responses in two sugarcane genotypes, a cross-commercial cultivar and a self-fertilization clone, subjected to water deficit stress in the field. The experiment was conducted under rain-fed conditions. Organic solutes, photosynthetic pigments, gas exchange, and the quantum efficiency of photosystem II were evaluated. Total protein was extracted using the phenol method, and the peptides were analyzed using mass spectrometry. Elevated proline levels in clone RB061047 suggest a potentially enhanced adaptive response to water-deficit stress. There were no marked differences in the photosynthetic pigments between clone RB061047 and the commercial cultivar, RB867515. Self-fertilization did not negatively affect the physiological performance of RB061047 under water-deficit conditions because the higher photosynthetic rate and the consequent more efficient use of water suggest a marked gain in biomass and productivity. The ATP synthase alpha subunit YABB2 protein, fructose-bisphosphate aldolase, and nucleoside diphosphate kinase 1 emerged as potential candidates for the development of functional molecular markers for the selection and development of new sugarcane cultivars that are more tolerant to water-deficit stress. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Mechanisms of Plant Stress Responses)

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Review

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22 pages, 1605 KB

Open AccessReview

Network-Driven Insights into Plant Immunity: Integrating Transcriptomic and Proteomic Approaches in Plant–Pathogen Interactions

by Yujie Lv and Guoqiang Fan

Int. J. Mol. Sci. 2026, 27(3), 1242; https://doi.org/10.3390/ijms27031242 - 26 Jan 2026

Cited by 2 | Viewed by 980

Abstract

Plant immunity research is being reshaped by integrative multi-omics approaches that connect transcriptomic, proteomic, and interactomic data to build systems-level views of plant–pathogen interactions. This review outlines the scope and methodological landscape of these approaches, with particular emphasis on how transcriptomic and proteomic insights converge through network-based analyses to elucidate defense regulation. Transcriptomics captures infection-induced transcriptional reprogramming, while proteomics reveals protein abundance changes, post-translational modifications, and signaling dynamics essential for immune activation. Network-driven computational frameworks including iOmicsPASS, WGCNA, and DIABLO enable the identification of regulatory modules, hub genes, and concordant or discordant molecular patterns that structure plant defense responses. Interactomic techniques such as yeast two-hybrid screening and affinity purification–mass spectrometry further map host–pathogen protein–protein interactions, highlighting key immune nodes such as receptor-like kinases, R proteins, and effector-targeted complexes. Recent advances in machine learning and gene regulatory network modeling enhance the predictive interpretation of transcription–translation relationships, especially under combined or fluctuating stress conditions. By synthesizing these developments, this review clarifies how integrative multi-omics and network-based frameworks deepen understanding of the architecture and coordination of plant immune networks and support the identification of molecular targets for engineering durable pathogen resistance. Full article

(This article belongs to the Special Issue Functional Genomics and Molecular Mechanisms of Plant Stress Responses)

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