Submit to Plants Review for Plants Propose a Special Issue

Journal Menu

Journal Browser

► Journal Browser

Advances in Plant Molecular Biology and Gene Function

Special Issue Editors
Special Issue Information
Keywords
Benefits of Publishing in a Special Issue
Published Papers

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

Deadline for manuscript submissions: closed (10 February 2026) | Viewed by 6295

Share This Special Issue

Special Issue Editor

Prof. Dr. Ying Chang

E-Mail Website
Guest Editor

College of Life Sciences, Northeast Agricultural University, Harbin 150030, China
Interests: plant molecular biology; gene function; transcription factors; Dryopteris fragrans; fern

Special Issue Information

Dear Colleagues,

Research on plant molecular biology and gene function represents a cutting-edge frontier in modern life sciences, with its central aim being to unravel the fundamental principles of plant life processes through elucidating the molecular mechanisms of genes. The rapid advancement of high-throughput sequencing, gene editing, and multi-omics technologies has propelled this field from single-gene functional characterization to a new era of systematically investigating gene regulatory networks. Gene function studies not only provide crucial theoretical foundations for understanding fundamental biological processes such as plant growth and development, environmental adaptation, and secondary metabolism, but also pioneer novel approaches for crop genetic improvement, medicinal plant development, and synthetic biology applications.

Contemporary plant gene function research has evolved into a multidimensional, interdisciplinary technological framework. Genomic methodologies, including genome-wide association studies (GWASs) and quantitative trait locus (QTL) mapping, serve as powerful tools for identifying genes associated with important traits, while proteomics and metabolomics technologies reveal the molecular basis of gene function across different biological layers. Nevertheless, the field continues to face significant challenges that necessitate the development of more precise gene-editing tools, the establishment of more efficient functional validation systems, and the in-depth exploration of the dynamic characteristics of gene regulatory networks.

This Special Issue aims to compile the most recent advances in plant molecular biology and gene function research, with particular emphasis on the following: (1) the development of novel gene function analysis technologies, (2) the investigation of key gene regulatory mechanisms, and (3) applications in molecular breeding. We particularly encourage submissions employing innovative approaches such as integrated multi-omics analysis and AI-assisted prediction, as well as functional characterization of genes governing important agronomic traits and secondary metabolic regulation. By serving as an important platform for theoretical innovation and technological breakthroughs in plant gene function research, this Special Issue will contribute significantly to sustainable agricultural development and the efficient utilization of plant resources.

Prof. Dr. Ying Chang
Guest Editor

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 molecular biology
gene function
gene editing
multi-omics technologies
gene regulation
molecular breeding
agronomic traits
secondary metabolism

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 (8 papers)

Download All Papers

Order results

Result details

Show export options Show export options

Select all

Export citation of selected articles as:

Research

Jump to: Review

23 pages, 4973 KB

Open AccessArticle

Genome-Wide Identification of the PLATZ Transcription Factor Family in Populus euphratica Oliv. and Functional Characterisation of PePLATZ8 in Drought Tolerance

by Tiantian Ran, Jianhao Sun, Chen Qiu, Xiaoli Han, Lijun Gao and Zhijun Li

Plants 2026, 15(7), 1065; https://doi.org/10.3390/plants15071065 - 31 Mar 2026

Viewed by 559

Abstract

Plant AT-rich sequence and zinc-binding (PLATZ) proteins are a class of plant-specific transcription factors that have been identified and functionally characterised in multiple species. However, the PLATZ gene family has not yet been systematically characterised in Populus euphratica. In this study, 19 PePLATZ genes were identified and classified into five subgroups. The analyses of gene structure, conserved motifs and protein domains indicated that the PLATZ family is highly conserved during evolution. Meanwhile, promoter cis-acting element profiling suggested their potential roles in stress-responsive transcriptional regulation. Transcriptomic and qRT-PCR analyses showed that PePLATZ1, PePLATZ6, PePLATZ8, PePLATZ14 and PePLATZ19 were highly expressed in the roots, stems and leaves of P. euphratica and were strongly induced by drought stress. PePLATZ8 localised to the nucleus and lacked transactivation activity but acted as a transcriptional repressor in planta. Transgenic poplar lines overexpressing PePLATZ8 exhibited significantly enhanced drought tolerance. Furthermore, after drought treatment, PePLATZ8-overexpressing plants accumulated high levels of H₂O₂ and exhibited significantly increased total superoxide dismutase activity, which likely contributed to improved drought tolerance. Together, the above findings deepen our understanding of the structure–function relationships of PePLATZ proteins and identify PePLATZ8 as a promising candidate gene for the molecular breeding of drought-resistant poplar germplasm. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

16 pages, 2772 KB

Open AccessArticle

AtAUGs Suppress the Expression of PP2C Genes to Redundantly Regulate ABA Responses in Arabidopsis

by Xutong Wang, Kaijie Zheng, Ruqian Su, Wei Wang, Xiaoxiao Jing, Yating Wang, Yaowen Wu, Nini Cheng, Siyu Chen and Shucai Wang

Plants 2026, 15(7), 1028; https://doi.org/10.3390/plants15071028 - 26 Mar 2026

Viewed by 439

Abstract

The modulation of plant responses to abscisic acid (ABA) and/or abiotic stresses can be manipulated by the expression of ABA-responsive genes, which is affected by phytohormone ABA. While some ABA-responsive genes have been shown to regulate plant responses to ABA and/or abiotic stresses, the functions of numerous ABA-responsive genes remain unknown. Therefore, characterizing these unstudied genes would provide a practical way to identify novel regulators of plant adaptations to ABA and/or abiotic stresses. Here, we characterized four closely related unstudied ABA-responsive genes in Arabidopsis thaliana, named Arabidopsis thaliana ABA-up regulated genes (AtAUGs). We found that ABA treatment induces AtAUGs expression level, and our results in transfected protoplasts show that AtAUGs exhibit nucleus localization and downregulate the co-transfected reporter expression level. The results of ABA sensitivity assays, including seed germination, cotyledon greening, and root extension assay show that transgenic plants overexpressing AtAUGs had increased sensitivity, but ataugs mutants generated by isolating T-DNA insertion lines or through CRISPR/Cas9 gene-editing of AtAUGs had decreased sensitivity; in addition, the greatest decrease in ABA sensitivity was observed in the ataug1 ataug2 ataug3 ataug4 (ataug1234) quadruple mutants. The qRT-PCR results show that the expression levels of several Type 2C Protein Phosphatase (PP2C) genes, the key negative regulator genes of ABA signaling including PP2CA, Hypersensitive to ABA 1 (HAB1), HAB2, Highly ABA-Induced PP2C protein 3 (HAI3), ABA-Hypersensitive Germination 1 (AHG1), and ABA Insensitive 2 (ABI2) decreased in 35S:AtAUGs transgenic plants, but increased in the ataug1234 quadruple mutants. Taken together, these results suggest that AtAUGs are ABA-responsive genes, and AtAUGs positively regulate ABA responses in a redundant manner, by downregulating the expression of crucial negative regulator genes in ABA signaling. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

20 pages, 11869 KB

Open AccessFeature PaperArticle

Genome-Wide Analysis of Heat Shock Transcription Factors (HSFs) in Kelp (Saccharina japonica) and Analysis of Their Expression in Response to Abiotic Stresses

by Wentai Mao, Wenbo Zhu, Ruixue Li, Jianjun Lu, Yijuan Han, Weiqi Tang, Hongmei Lin, Wenshan Wang, Xiaoting Chen, Songbiao Chen, Wenwei Lin and Zhongyuan Lin

Plants 2026, 15(3), 429; https://doi.org/10.3390/plants15030429 - 30 Jan 2026

Viewed by 661

Abstract

Heat shock transcription factors (HSFs) play a crucial role in mediating responses to abiotic stresses. However, characterization of HSFs in macroalgae remains largely unexplored. In this study, a comprehensive analysis of HSFs was carried out in Saccharina japonica. A total of sixteen SjHSFs were identified. Phylogenetic analysis revealed that HSFs from brown algae form a distinct clade, separate from those from red algae, green algae, moss, and Arabidopsis thaliana. The DNA-binding domain was found to be highly conserved among SjHSFs. Analysis of cis-acting elements in SjHSF promoters suggested their potential roles in regulating growth, development, and stress responses. Tissue-specific expression profiles revealed differential expression of SjHSFs across various tissues of S. japonica. Under abiotic stresses, certain SjHSFs exhibited dynamic expression patterns, with particularly pronounced changes observed under high-temperature stress. We further employed a transcription factor-centered yeast one-hybrid (TF-Centered Y1H) to determine the motifs recognized by SjHSF-03. Seven conserved motifs were identified, and the distributions of these motifs were screened in the promoter regions of S. japonica genes involved in diverse biological processes and pathways. Notably, 23 heat shock protein (HSP) genes were among these motif-containing genes, and 21 out of these 23 SjHSPs were up-regulated under heat stress. Our results provide a solid foundation for future research on the specific functions of HSFs under different stress conditions and the regulatory mechanisms of HSF-mediated stress responses in S. japonica and other brown algae. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

19 pages, 2842 KB

Open AccessArticle

Signaling Pathway Analysis and Downstream Genes Associated with Disease Resistance Mediated by GmSRC7

by Aoga Li, Chongyang Yao, Ting Yan, Xiaomin Hao, Dongying Geng, Qi Zhang, Hui Li, Wenquan Bao and Yue Bai

Plants 2026, 15(2), 318; https://doi.org/10.3390/plants15020318 - 21 Jan 2026

Viewed by 683

Abstract

GmSRC7 is a broad-spectrum antiviral R gene from soybean, but its downstream and functionally related genes remain unclear. Virus-induced gene silencing (VIGS) assays in Nicotiana benthamiana (Nb) showed that suppression of several gene families—WRKY transcription factors, chaperones, ethylene pathway components, MAPK cascade elements, salicylic acid (SA) signaling genes, calcium-dependent protein kinases, nuclear migration proteins, RNA replication-related genes, and immune regulators—consistently weakened GmSRC7-mediated resistance to Soybean Mosaic Virus (SMV) and Tobacco Mosaic Virus (TMV). Targeted silencing of four regulatory genes—NbEDS1, NbARF1, NbSGT1, and NbCOI1—markedly enhanced GmSRC7-mediated resistance to SMV and TMV in our experiments. Silencing the serine/threonine kinase gene NbPBS1 increased GmSRC7-conferred resistance to SMV but did not significantly alter its resistance to TMV. Transient expression assays showed that NbARF1, NbSGT1, and NbCOI1 antagonize GmSRC7-mediated defense against SMV and TMV, whereas NbPBS1 specifically suppresses anti-SMV activity without affecting TMV resistance. Transient overexpression of SA-degrading enzymes (AtS3H, AtS5H, and NahG) significantly reduced GmSRC7-conferred resistance to SMV, indicating that SA is essential for this R protein-mediated defense. Genes were also grouped by immune pathways and function: co-expression of chaperone family genes inhibited GmSRC7 activity against SMV and TMV, while co-expression of WRKY family genes enhanced anti-SMV activity of GmSRC7. Finally, transient silencing of soybean genes GmEDS1, GmSGT1-1, GmSGT1-2, GmJAR1, and GmSGS3 compromised GmSRC7-mediated resistance to SMV. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

16 pages, 6867 KB

Open AccessArticle

A Polycistronic tRNA-amiRNA System Reveals the Antiviral Roles of NbAGO1a/1b/2 Against Soybean mosaic virus Infection

by Wenhua Bao, Danyang Sun, Yan Qiu, Xiaoke Zhao and Hada Wuriyanghan

Plants 2025, 14(24), 3724; https://doi.org/10.3390/plants14243724 - 6 Dec 2025

Viewed by 796

Abstract

RNA interference (RNAi) is a crucial antiviral defense mechanism in plants, where Argonaute (AGO) proteins play a central role. However, the function of AGO proteins in the interaction between Soybean mosaic virus (SMV) and Nicotiana benthamiana remains unclear. In this study, SMV pathogenicity was confirmed using an SMV-GFP infectious clone, with typical symptoms and systemic GFP fluorescence observed 14 days post-inoculation. Real-time quantitative reverse transcription polymerase chain reaction analysis revealed dynamic regulation of multiple NbAGO genes upon infection. Notably, NbAGO1a, NbAGO1b, and NbAGO2 were significantly upregulated and positively correlated with viral accumulation, suggesting their critical roles in antiviral defense. Based on these findings, these three genes were selected as targets for artificial microRNA (amiRNA) silencing. Three amiRNAs were designed for each gene using the Arabidopsis miR1596 backbone, with the most effective sequences exhibiting silencing efficiencies ranging from 75.2% to 98.1%. A polycistronic tRNA-amiRNA (PTA) cassette was constructed using Golden Gate cloning technology to simultaneously target all three genes. Co-infection assays indicated that the PTA cassette enhanced SMV accumulation more effectively than single amiRNAs, as evidenced by increased GFP fluorescence (49.1–60.5%) and pronounced leaf necrosis. The PTA system downregulated the expression of NbAGO1a, NbAGO1b, and NbAGO2 by 18.4–26.7%. Furthermore, silencing NbAGO2 alone resulted in severe necrosis, underscoring its essential role in this antiviral defense mechanism. This study elucidates the importance of NbAGO1a, NbAGO1b, and NbAGO2 in antiviral immunity and demonstrates the utility of the PTA system for efficient multi-gene silencing, offering valuable insights for developing RNAi-based antiviral strategies. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

16 pages, 3548 KB

Open AccessArticle

Identification and Functional Analysis of Two UGT84 Glycosyltransferases in Flavonoid Biosynthesis of Carthamus tinctorius

by Chaoxiang Ren, Jinxin Guo, Siyu Liu, Bin Xian, Yuhang Li, Changyan Yang, Cheng Peng, Jin Pei and Jiang Chen

Plants 2025, 14(19), 3112; https://doi.org/10.3390/plants14193112 - 9 Oct 2025

Cited by 1 | Viewed by 1132

Abstract

Safflower (Carthamus tinctorius L.) is a multipurpose economic crop. Flavonoid glycosides are its key bioactive constituents, and several glycosyltransferases involved in their biosynthesis have been identified. The glycosyltransferase 84 subfamily represents a specialized branch with diverse functions, involved not only in catalyzing flavonoid glycosylation but also in the biosynthesis of auxins, tannins, and other compounds. However, this subfamily remains poorly characterized in safflower. In this study, two UGT84 subfamily genes, UGT84A28 and UGT84B3, were screened based on expression patterns and phylogenetic evolution analysis. Recombinant proteins were induced and purified using prokaryotic expression systems. Functional characterization was subsequently conducted through enzymatic assays in vitro and transient expression in tobacco leaves. Molecular docking was employed to investigate the binding modes of UGTs with UDP-glucose. The results indicated that both UGTs demonstrated glycosylation activity at the flavonoid 7-OH position. Notably, when luteolin was employed as the aglycone, both enzymes also exhibited 3′-O-glycosylation activity. Combined with amino acid sequence alignment, we propose that residues A351/T343 and G263/F254, which affect spatial conformation and hydrogen bonding ability, may be one of the reasons for the functional differences between these two enzymes. These findings provide new insights into the catalytic diversity of glycosyltransferases. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

25 pages, 5845 KB

Open AccessArticle

Functional Identification and Transcriptional Activity Analysis of Dryopteris fragrans HMGR Gene

by Meng Sun, Qian Ma, Xueqi Wang, Jialiang Guo, Jiaxuan Wang, Dongrui Zhang, Kirill Tkachenko, Wenzhong Wang and Ying Chang

Plants 2025, 14(14), 2190; https://doi.org/10.3390/plants14142190 - 15 Jul 2025

Viewed by 1048

Abstract

Dryopteris fragrans (L.) Schott synthesizes volatile sesquiterpenes through the mevalonate pathway (MVA), in which 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) serves as the key rate-limiting enzyme. Although HMGR plays a crucial role in terpenoid biosynthesis, its functional characteristics in D. fragrans and its involvement in stress responses remain unclear. This study identified three HMGR genes (DfHMGR1/2/3) from the transcriptome data of D. fragrans. Bioinformatics analysis revealed that the encoded proteins are localized to the endoplasmic reticulum and share high sequence similarity with fern homologs. Under abiotic stress conditions, DfHMGRs exhibited differential expression patterns, with marked upregulation under salt and drought stress. To validate the functions of these genes, we generated transgenic Nicotiana tabacum L. plants overexpressing DfHMGRs. Compared with wild-type controls, the transgenic lines showed enhanced tolerance to drought and heat stress. Promoter analysis identified functional regulatory regions controlling DfHMGR expression, and co-expression network analysis predicted 21 potential transcriptional regulators. This study validates the function of D. fragrans HMGRs in a heterologous system and provides candidate genes for improving stress resistance in plants. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Figure 1

Review

Jump to: Research

22 pages, 2135 KB

Open AccessReview

RNA Tailing by Nucleotidyltransferases in Plants: Mechanisms, Functions, and Biological Significance

by Xintong Xu, Xinwen Qing, Xiaoli Peng, Xiangze Chen, Tengbo Huang, Beixin Mo and Yongbing Ren

Plants 2026, 15(6), 925; https://doi.org/10.3390/plants15060925 - 17 Mar 2026

Viewed by 560

Abstract

RNA tailing, the non-templated addition of nucleotides to RNA 3′ ends, is a conserved post-transcriptional modification that plays a critical role in regulating RNA metabolism. In plants, this process is primarily mediated by nucleotidyltransferase proteins (NTPs). In this review, we analyze current knowledge of plant NTPs by integrating evidence from genetic, biochemical, and phylogenetic analyses of the gene-family across model plants and crops. We summarize the composition and evolutionary diversification of the plant NTP gene family, with emphasis on lineage-specific expansion and conservation patterns. Using Arabidopsis thaliana as a reference framework, we then describe the molecular roles of NTPs in the tailing of distinct RNA classes, emphasizing how tail type and length confer context-dependent regulatory outcomes including stabilization versus degradation and processing/maturation versus clearance. We further examine the determinants of substrate choice, focusing on RNA type, terminal structure, and subcellular localization. Finally, we discuss the biological functions of NTP-mediated RNA tailing in plants, linking RNA tailing to development, stress responses, antiviral immunity, and agronomic traits in crops. We conclude by outlining key mechanistic and physiological challenges that define future directions for understanding and harnessing NTP-mediated RNA regulation. Collectively, this review provides an integrated framework for understanding how RNA tailing by NTPs shapes plant RNA metabolism and biological fitness. Full article

(This article belongs to the Special Issue Advances in Plant Molecular Biology and Gene Function)

► Show Figures

Journal Menu

Journal Browser

Advances in Plant Molecular Biology and Gene Function

Share This Special Issue

Special Issue Editor

Special Issue Information

Keywords

Benefits of Publishing in a Special Issue

Published Papers (8 papers)

Research

Review

Further Information

Guidelines

MDPI Initiatives

Follow MDPI