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The Trade-Offs Between Growth and Development and Stress in Plants—2nd...
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The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Physiology and Metabolism".

Deadline for manuscript submissions: 30 November 2025 | Viewed by 2542

Special Issue Editors

Dr. Dayong Zhang

E-Mail Website
Guest Editor
National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cotton Germplasm Innovation and Application Engineering Center, The Ministry of Education, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
Interests: drought and salt stress; molecular mechanism of abiotic stress; m6a modification
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Zhiyong Ni

E-Mail Website
Guest Editor
College of Life Sciences, Xinjiang Agricultural University, Urumqi 830052, China
Interests: gene function; cotton fiber development; plant stress responses
Special Issues, Collections and Topics in MDPI journals
Dr. Wenfeng Nie

E-Mail Website
Guest Editor
College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271002, China
Interests: DNA demethylation; abiotic stress; fruit ripening; fruit quality
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Due to their sessile nature, plants are often subjected to various stresses. These stresses affect the normal growth of plants to varying degrees. For example, drought often causes plants to grow short, strong winds cause plant stems to break, floods cause plants to log and wilt, and so on. Environmental changes are complicated processes caused by both internal and external factors in which changes to plant-growing environments largely affect the growth and development of plants and even reduce or destroy the yield of crops in agricultural production. Moreover, trade-offs between growth, development, and stress in plants and their interactions with intensive agricultural management constrain human food security at the global scale. However, how plants balance growth and development and stress is still relatively not well understood. Therefore, to gain deeper insight into the stress response mechanisms of plants, it is necessary to explore the perception and transmission links of plants in response to stress stimulations.

This Special Issue aims to highlight the recent advances in our understanding of the trade-offs between growth, development, and stress in plants, with a main focus on physiological, cellular, and biochemical effects, as well as on underlying genetic determinations and molecular control (e.g., stress signaling, pathway activation, and tolerance/resistance mechanisms). Meanwhile, studies on the mechanisms and functions of epigenetic modifications, gene editing techniques, and accumulation-enhanced adaptation to balance growth and abiotic stress tolerance are also warmly welcomed.

Dr. Dayong Zhang
Prof. Dr. Zhiyong Ni
Dr. Wenfeng Nie
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Plants is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • biotic and abiotic stresses
  • epigenetic modifications
  • stress tolerance
  • growth and development
  • stress signaling
  • molecular mechanism

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Related Special Issue

Published Papers (4 papers)

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Research

16 pages, 7336 KiB  
Article
Identification of Quality-Related Genomic Regions and Candidate Genes in Silage Maize by Combining GWAS and Meta-Analysis
by Yantian Lu, Yongfu Ding, Can Xu, Shubin Chen, Chunlan Xia, Li Zhang, Zhiqing Sang and Zhanqin Zhang
Plants 2025, 14(15), 2250; https://doi.org/10.3390/plants14152250 - 22 Jul 2025
Viewed by 341
Abstract
Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage [...] Read more.
Enhancing quality traits is a primary objective in silage maize breeding programs. The use of genome-wide association studies (GWAS) for quality traits, in combination with the integration of genetic resources, presents an opportunity to identify crucial genomic regions and candidate genes influencing silage maize quality. In this study, a GWAS was conducted on 580 inbred lines of silage maize, and a meta-analysis was performed on 477 quantitative trait loci (QTLs) from 34 studies. The analysis identified 27 significant single nucleotide polymorphisms (SNPs) and 87 consensus QTLs (cQTLs), with 7 cQTLs associated with multiple quality traits. By integrating the SNPs identified through association mapping, one SNP was found to overlap with the cQTL interval related to crude protein, neutral detergent fiber, and starch content. Furthermore, enrichment analysis predicted 300 and 5669 candidate genes through GWAS and meta-analysis, respectively, highlighting pathways such as cellular metabolism, the biosynthesis of secondary metabolites, ribosome function, carbon metabolism, protein processing in the endoplasmic reticulum, and amino acid biosynthesis. The examination of 13 candidate genes from three co-located regions revealed Zm00001d050977 as a cytochrome P450 family gene, while the other 2 genes primarily encode proteins involved in stress responses and other biological pathways. In conclusion, this research presents a methodology combining GWAS and meta-analysis to identify genomic regions and potential genes influencing quality traits in silage maize. These findings serve as a foundation for the identification of significant QTLs and candidate genes crucial for improving silage maize quality. Full article
(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)
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11 pages, 1440 KiB  
Communication
GAG Protein of Arabidopsis thaliana LTR Retrotransposon Forms Retrosome-like Cytoplasmic Granules and Activates Stress Response Genes
by Alexander Polkhovskiy, Roman Komakhin and Ilya Kirov
Plants 2025, 14(13), 1894; https://doi.org/10.3390/plants14131894 - 20 Jun 2025
Viewed by 571
Abstract
LTR retrotransposons are widespread genomic elements that significantly impact genome structure and function. In Arabidopsis thaliana, the EVD LTR retrotransposon encodes a GAG protein essential for retrotransposon particle assembly. Here, we present a comprehensive analysis of the structural features, intracellular localization, and [...] Read more.
LTR retrotransposons are widespread genomic elements that significantly impact genome structure and function. In Arabidopsis thaliana, the EVD LTR retrotransposon encodes a GAG protein essential for retrotransposon particle assembly. Here, we present a comprehensive analysis of the structural features, intracellular localization, and transcriptomic effects of the EVD GAG (evdGAG) protein. Using AlphaFold3, we identified canonical capsid (CA-NTD and CA-CTD) and nucleocapsid (NC) domains, with predicted disordered regions likely facilitating oligomerization. Transient expression of GFP-tagged evdGAG in protoplasts of A. thaliana and distant plant species (Nicotiana benthamiana and Helianthus annuus) revealed the formation of multiple large cytoplasmic aggregates resembling retrosomes, often localized near the nucleus. Stable overexpression of evdGAG in wild-type and ddm1 mutant backgrounds induced significant transcriptomic changes, including up-regulation of stress response and defense-related genes and downregulation of photosynthesis and chloroplast-associated pathways. Importantly, genes linked to stress granule formation were also up-regulated, suggesting a role for evdGAG in modulating cellular stress responses. Our findings provide novel insights into the cellular and molecular properties of plant retrotransposon GAG proteins and their influence on host gene expression. Full article
(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)
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14 pages, 1708 KiB  
Article
Comprehensive Evaluation of 202 Cotton Varieties (Lines) and Their Physiological Drought Resistance Response During Seedling Stage
by Jiazila Baha, Wenhong Liu, Xiaoman Ma, Yage Li, Xiaohong Zhao, Xue Zhai, Xinchuan Cao and Weifeng Guo
Plants 2025, 14(12), 1770; https://doi.org/10.3390/plants14121770 - 10 Jun 2025
Cited by 1 | Viewed by 391
Abstract
To identify seedling traits closely associated with drought resistance and to screen for drought-tolerant germplasm, 202 cotton varieties (lines) were evaluated under controlled indoor conditions using a nutrient soil cultivation method. Seedling-stage traits measured included plant height, cotyledon node diameter, true leaf number, [...] Read more.
To identify seedling traits closely associated with drought resistance and to screen for drought-tolerant germplasm, 202 cotton varieties (lines) were evaluated under controlled indoor conditions using a nutrient soil cultivation method. Seedling-stage traits measured included plant height, cotyledon node diameter, true leaf number, chlorophyll content, and fresh and dry biomass of both shoots and roots. Drought resistance was assessed using drought resistance coefficients for each trait, followed by descriptive statistics, principal component analysis (PCA), partial correlation analysis, and comprehensive evaluation via the entropy weight method. PCA and partial correlation analysis revealed that plant height, cotyledon node diameter, aboveground fresh weight, and underground fresh weight were strongly associated with drought resistance at the seedling stage. The comprehensive drought resistance index (D-value) classified the 202 cotton lines into four categories: highly drought-resistant, moderately drought-resistant, drought-sensitive, and highly drought-sensitive. Physiological assays indicated that malondialdehyde (MDA) content in drought-resistant lines first increased and then declined with prolonged drought stress, while it continued to increase in sensitive lines. In contrast, proline (Pro) content and superoxide dismutase (SOD) activity increased steadily in drought-resistant lines but showed negligible changes in sensitive lines. These four morphological traits and three physiological indicators represent reliable criteria for evaluating drought resistance in cotton seedlings. Four highly drought-resistant and thirteen moderately drought-resistant lines were identified, providing valuable germplasm for genetic improvement of drought tolerance in cotton. Full article
(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)
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19 pages, 5427 KiB  
Article
Screening and Identification of Drought-Tolerant Genes in Tomato (Solanum lycopersicum L.) Based on RNA-Seq Analysis
by Yue Ma, Yushan Li, Fan Wang, Quan Qing, Chengzhu Deng, Hao Wang and Yu Song
Plants 2025, 14(10), 1471; https://doi.org/10.3390/plants14101471 - 14 May 2025
Viewed by 816
Abstract
Drought is one of the major abiotic stresses that inhibits plant growth and development. Therefore, it is critical to explore drought resistance genes in crops to obtain high-quality breeding materials. In this study, the drought-sensitive tomato line “FQ118” and the resistant line “FQ119” [...] Read more.
Drought is one of the major abiotic stresses that inhibits plant growth and development. Therefore, it is critical to explore drought resistance genes in crops to obtain high-quality breeding materials. In this study, the drought-sensitive tomato line “FQ118” and the resistant line “FQ119” were treated with PEG-6000 and, at 0 h (CK), 6 h, 24 h, 36 h and 48 h, the plants were evaluated for growth and physiological indicators, and leaf tissues were collected for RNA-seq. The growth indicators (growth trend, dry and fresh weights above- and below-ground, etc.) and the antioxidant enzyme system reflect that “FQ119” has stronger drought tolerance. Through RNA-seq analysis, a total of 68,316 transcripts (37,908 genes) were obtained. The largest number of significant differentially expressed genes (DEGs) in the comparison of “FQ118” and “FQ119” was observed at 6 h and 48 h. KEGG analysis demonstrated the significant enrichment of certain pathways associated with drought stress, such as glycerolipid metabolism and galactose metabolism. Co-expression analysis revealed that 7 hub DEGs, including genes encoding a photosystem reaction center subunit protein, chlorophyll a-b binding protein, glyceraldehyde-3-phosphate dehydrogenase A (GAPDH), and others, were coenriched in both comparisons. In addition, three hub genes specific to the comparison during the 6-h processing stage, encoding oxygen-evolving enhancer protein 1, receptor-like serine/threonine-protein kinase and calcium-transporting ATPase, were identified. The above hub genes were related to plant resistance to drought stress, and RT‒qPCR verified that the overall magnitudes of the differences in expression between the two lines gradually increased over time. Virus-induced gene silencing (VIGS) experiments have demonstrated that GAPDH plays a relevant role in the drought resistance pathway. In addition, the differences in expression of 7 DEGs encoding transcription factors, including Dofs, WRKYs, MYBs, and MYCs, also tended to increase with increasing duration of drought treatment, as determined via qPCR. In summary, this study identified several valuable genes related to plant drought resistance by screening genes with differential transcription under drought stress. This in-depth gene mining may provide valuable references and resources for future breeding for drought resistance in tomato. Full article
(This article belongs to the Special Issue The Trade-Offs Between Growth and Development and Stress in Plants—2nd Edition)
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