Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.6
4.1
Journals
Plants
Special Issues
Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd...
share announcement

Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Molecular Biology".

Deadline for manuscript submissions: 31 October 2026 | Viewed by 3214

Special Issue Editors

Dr. Yi He

E-Mail Website
Guest Editor
College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: photosynthesis; signal transduction; gene regulation; flower development
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Dali Zeng

E-Mail Website
Guest Editor
College of Advanced Agricultural Sciences, Zhejiang Agriculture and Forestry University, Hangzhou 311300, China
Interests: molecular breeding; gene regulation; plant genetics and genomics
Special Issues, Collections and Topics in MDPI journals
Dr. Lichao Huang

E-Mail Website
Guest Editor
College of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou, China
Interests: research on the molecular mechanism of wood formation and genetic engineering breeding of trees

Special Issue Information

Dear Colleagues,

Transcriptome sequencing has become more and more important for understanding biological phenomena, and provides vital insight for understanding gene regulatory mechanisms in the process of plant growth development. Therefore, it is a hot topic for many plant biologists, showing how to efficiently explore the information underlying transcriptome sequencing to understand the gene regulatory mechanisms of the phenomenon. In addition, an integrated multi-omics framework based on transcriptome analysis has provided insight into the gene regulatory mechanisms of plant growth development, especially in some non-model plants. The importance of new mathematical and statistical methods for transcriptome analysis will also help us to better understand the hidden secrets of plant growth and development. This Special Issue of Plants will highlight the new tools, methods, strategies, and perspectives of transcriptome analysis, and their role in explaining gene regulatory networks.

Dr. Yi He
Prof. Dr. Dali Zeng
Dr. Lichao Huang
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 250 words) can be sent to the Editorial Office for assessment.

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

  • plant growth
  • plant development
  • transcriptome/genome analysis
  • genetics
  • gene expression
  • transcriptome
  • signal transduction
  • plant genome
  • transcriptome
  • proteome
  • gene expression
  • epigenetic regulations

Benefits of Publishing in a Special Issue

  • Ease of navigation: Grouping papers by topic helps scholars navigate broad scope journals more efficiently.
  • Greater discoverability: Special Issues support the reach and impact of scientific research. Articles in Special Issues are more discoverable and cited more frequently.
  • Expansion of research network: Special Issues facilitate connections among authors, fostering scientific collaborations.
  • External promotion: Articles in Special Issues are often promoted through the journal's social media, increasing their visibility.
  • Reprint: MDPI Books provides the opportunity to republish successful Special Issues in book format, both online and in print.

Further information on MDPI's Special Issue policies can be found here.

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

Jump to: Review

29 pages, 10115 KB  
Article
ABA-Induced Transcriptomic Dynamics in Arabidopsis thaliana Anthers: Insights into Pollen Development and Fertility
by Lu Liu, Huiting Huang, Dexi Shi, Shuo Wang, Ziyi Lin, Fengming Huang, Li Huang and Sue Lin
Plants 2026, 15(6), 894; https://doi.org/10.3390/plants15060894 - 13 Mar 2026
Viewed by 482
Abstract
Pollen development is a complex process that is highly sensitive to environmental stresses. Abscisic acid (ABA), a key hormone mediating plant growth and stress responses, has been implicated in the regulation of sexual reproduction, especially pollen development, yet its precise regulatory role remains [...] Read more.
Pollen development is a complex process that is highly sensitive to environmental stresses. Abscisic acid (ABA), a key hormone mediating plant growth and stress responses, has been implicated in the regulation of sexual reproduction, especially pollen development, yet its precise regulatory role remains unclear. This study investigated the effects of exogenous ABA on Arabidopsis thaliana pollen development and function through integrated phenotypic, cytological, and transcriptomic approaches. ABA treatment specifically impaired pollen function by reducing germination rates and inhibiting pollen tube elongation, which resulted in shortened siliques and decreased seed set, without affecting pollen morphology or viability. Transcriptome analysis of mature anthers revealed a transient and time-dependent transcriptional response, with the number of differentially expressed genes (DEGs) peaking at 8 h post-ABA treatment and markedly declining by 22 h. These DEGs were enriched in stress-response pathways (e.g., salt, cold, and dehydration), hormone signaling, and carbohydrate metabolism. Moreover, we identified 25 differentially expressed transcription factors and 16 pollen development and function-related genes, highlighting their key roles in ABA-mediated regulation. In parallel, 146 differentially expressed lncRNAs (DELs) were identified, which formed 144 cis-regulatory pairs with genes involved in ABA response and pollen tube growth, with their predicted targets enriched in pathways such as hormone and MAPK signaling, carbohydrate metabolism and stress response. Trans-regulatory analysis further revealed that these DELs co-expressed with DEGs in modules enriched for stress response, pollen development, and tube growth pathways. Notably, key pollen function genes showed strong co-expression with DELs, indicating that lncRNAs participate in ABA-induced transcriptional reprogramming that shifts metabolic resources from growth to defense, thereby suppressing pollen germination and tube elongation. Together, these findings elucidate a coordinated regulatory network involving mRNAs, lncRNAs and transcription factors roles in modulating ABA responses during pollen/anther development. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition)
►▼ Show Figures

Figure 1

15 pages, 979 KB  
Article
Transcriptomic Regulation of Aquaporins During Seed Germination in the Marine Seagrass Cymodocea nodosa
by Pilar Garcia-Jimenez, David Osca, Diana del Rosario-Santana and Rafael R. Robaina
Plants 2026, 15(5), 732; https://doi.org/10.3390/plants15050732 - 28 Feb 2026
Viewed by 276
Abstract
Seed germination is a key phase that transitions the seed from dormancy to active growth, where imbibition emerges as the initial event, followed by aquaporin-mediated regulation of cellular water that supports metabolic reactivation under favourable conditions. Aquaporins are small integral membrane proteins that [...] Read more.
Seed germination is a key phase that transitions the seed from dormancy to active growth, where imbibition emerges as the initial event, followed by aquaporin-mediated regulation of cellular water that supports metabolic reactivation under favourable conditions. Aquaporins are small integral membrane proteins that facilitate the passive transport of water and small solutes across membranes and play key roles in plant development and physiology. In terrestrial plants, aquaporins are classified into five main types—PIPs, TIPs, NIPs, SIPs, and XIPs—with PIPs and TIPs being the most abundant and widely expressed. Whilst knowledge of seagrass aquaporins and their physiological roles remains limited, their functional involvement in seed germination is largely unknown. In this study of the marine seagrass Cymodocea nodosa, transcriptome assembly and analysis enabled the identification of aquaporin-encoding sequences, which were subsequently used for gene expression analysis during germination. Three well-defined seed stages of C. nodosa were analysed to assess expressions patterns of PIPs, TIPs, NIPs, and SIPs. Results showed that transcript levels of PIP, TIP, and SIP aquaporins exhibit differential expression patterns, and the changes are mainly associated with activation responses related to seed germination progress. Overall, this study provides one of the first foundations for investigating aquaporin function during seed germination in marine seagrasses, defining expression patterns across imbibition and early germination, and positioning C. nodosa as a valuable in vitro model for exploring the regulation of aquaporin activity by environmental and physiological factors. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition)
►▼ Show Figures

Figure 1

19 pages, 6107 KB  
Article
Identification, Transcriptome, and Proteome Analysis of Expansin-like Subfamilies in the Storage Root Across I. trifida (2x), Wild (4x, 6x) and Cultivated Sweet Potatoes
by Jingjing Li, Zhiyu Zhang, Qiuzhuo Li, Chunli Geng, Haoxi Huang, Xiaojian Qin, Yongshu Liang, Wenbin Nan, Hanma Zhang, Yufan Fu and Ming Li
Plants 2026, 15(2), 305; https://doi.org/10.3390/plants15020305 - 20 Jan 2026
Viewed by 405
Abstract
The expansin-like subfamilies (EXLA and EXLB) are vital for plant cell wall dynamics, but it remains uncharacterized in wild tetraploid and hexaploid Ipomoea batatas, and its role in the storage root (SR) development is poorly understood. In this work, we identified 4, [...] Read more.
The expansin-like subfamilies (EXLA and EXLB) are vital for plant cell wall dynamics, but it remains uncharacterized in wild tetraploid and hexaploid Ipomoea batatas, and its role in the storage root (SR) development is poorly understood. In this work, we identified 4, 3, 3, and 3 EXLAs, alongside 11, 9, 13, and 8 EXLBs, in diploid I. trifida strain Y22, wild tetraploid I. batatas strain Y428B, and hexaploid I. batatas strain Y601, and cultivated sweet potato ‘Nancy Hall’, respectively. A comprehensive bioinformatic analysis of the expansin-like genes and proteins was performed to reveal their potential roles in SR development. Gene expression profiling showed that EXLA members were expressed during SR development, while approximately half of the EXLB members were expressed in Y22, Y428B (pencil root), Y601, and NH, respectively. Proteomic analysis (4D-DIA) detected 2, 1, 1, and 1 EXLAs, and 3, 3, 3, and 3 EXLBs in the mature SRs of the respective species. Integrated transcriptomic and proteomic analyses suggested that downregulating Iba6xEXLB2 and Iba6xEXLB1 may be associated with SR swelling in sweet potato. Furthermore, subcellular localization assays confirmed that Iba6xEXLB2 and Iba6xEXLB8 are localized to the cell wall/membrane. This study enhances the understanding of the expansin-like gene subfamily in sweet potato and its wild relatives and lays the groundwork for future functional studies on the role of expansin-like genes in SR development. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition)
►▼ Show Figures

Figure 1

16 pages, 1406 KB  
Article
Transcriptional Regulation of the Phenylalanine Ammonia-Lyase (PAL) Gene Family in Mulberry Under Chitosan-Induced Stress
by Apidet Rakpenthai, Mutsumi Watanabe, Arunee Wongkaew and Sutkhet Nakasathien
Plants 2025, 14(17), 2783; https://doi.org/10.3390/plants14172783 - 5 Sep 2025
Viewed by 1145
Abstract
Regulation of the phenylpropanoid pathway is critical for plant development and defense. This research investigates the transcriptional control of six Phenylalanine Ammonia-Lyase (PAL) gene homologs identified in the mulberry genome. A comprehensive in silico pipeline was employed to analyze the promoter [...] Read more.
Regulation of the phenylpropanoid pathway is critical for plant development and defense. This research investigates the transcriptional control of six Phenylalanine Ammonia-Lyase (PAL) gene homologs identified in the mulberry genome. A comprehensive in silico pipeline was employed to analyze the promoter architecture of these genes. Using the MEME suite, we identified three statistically significant conserved motifs within the 2000 bp upstream region. Subsequent TF binding prediction with FootprintDB for these motifs implicated the TCP, NAC, AP2/ERF, B3, and BBR-BPC families as potential regulators. A parallel analysis with PlantRegMap highlighted a high density of binding sites for the BBR-BPC and AP2/ERF families in the core promoter regions. A comparative analysis showed a weak correlation between the databases, underscoring the necessity of a multi-faceted predictive approach. Transcriptomic profiling under chitosan-induced conditions validated our in silico framework, suggesting the involvement of these TF families. Specifically, the data support NAC083 as a putative transcriptional activator and suggest a repressive function for members of the AP2/ERF and BBR-BPC families, providing a robust, experimentally supported model of PAL regulation. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition)
►▼ Show Figures

Figure 1

Review

Jump to: Research

28 pages, 8538 KB  
Review
Advances in the Function Roles of Hydroxycinnamoyl-CoA Shikimate/Quinate Hydroxycinnamoyl Transferases: A Key Enzyme Linking Phenylpropanoid Metabolism to Plant Terrestrial Adaptation
by Jingyi Chen, Chuting Liang, Xian He, Jiayi Huang, Wanying Huang, Anqi Huang, Ying Yang, Gaojie Hong, Yue Chen, Dali Zeng, Jiangfan Guo and Yi He
Plants 2026, 15(8), 1162; https://doi.org/10.3390/plants15081162 - 9 Apr 2026
Viewed by 338
Abstract
Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, a key acyltransferase in the phenylpropanoid pathway and a canonical member of the BAHD acyltransferase family (BAHD), catalyzes the formation of pivotal intermediates in the biosynthesis of secondary metabolites such as lignin, chlorogenic acid, and flavonoids. These compounds serve [...] Read more.
Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, a key acyltransferase in the phenylpropanoid pathway and a canonical member of the BAHD acyltransferase family (BAHD), catalyzes the formation of pivotal intermediates in the biosynthesis of secondary metabolites such as lignin, chlorogenic acid, and flavonoids. These compounds serve indispensable protective functions in terrestrial plants, underpinning their adaptive responses to abiotic stresses such as drought, ultraviolet (UV) radiation, and oxidative damage. Although the role of HCT/HQT in the core phenylpropanoid pathway has been extensively characterized, its precise functional contributions to the flavonoid biosynthetic branch—particularly with respect to substrate selectivity, kinetic regulation, and metabolic channeling—remain incompletely understood. This review systematically analyzes the structural features, spatial conformation, catalytic mechanism, and substrate promiscuity of HCT/HQT to clarify its molecular determinants of activity and specificity. Furthermore, it highlights regulatory factors influencing HCT/HQT gene expression, such as transcription factors (MYB, bHLH, WRKY), phytohormones (GA3, Eth, MeJA, 6-BA, MT), and abiotic/biotic stressors (temperature, blue light, nitric oxide, nano-selenium). Collectively, these insights illuminate how plants dynamically fine-tune phenylpropanoid metabolism in coordination with developmental programs and environmental challenges. This work provides a foundation for further research on HCT/HQT and supports efforts to develop improved crop varieties through targeted regulation of this central metabolic node. Full article
(This article belongs to the Special Issue Transcriptome Analysis and Gene Regulation in Plant Growth Development, 3rd Edition)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop