Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.6
4.0
Journals
Plants
Special Issues
Gene Regulatory Mechanisms of Flower and Fruit Development in Plants...
share announcement

Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition)

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: 30 June 2025 | Viewed by 4245

Special Issue Editor

Prof. Dr. Stefan de Folter

E-Mail Website
Guest Editor
UGA-LANGEBIO, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), 36670 Irapuato, Mexico
Interests: plant molecular biology; transcription factors; flower and fruit development; gene regulatory networks; cytokinin signaling; protein–protein interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Flower and fruit development are processes tightly regulated by genes and phytohormones. In recent decades, an enormous wealth of information and knowledge has been obtained on the developmental processes underlying the formation and development of flowers and fruits in model plants, non-model plants, and crops. The generation, integration, and translation of gene regulatory networks driving development are important goals of many colleagues around the world. Many challenges and opportunities lie ahead of the generation of a deep understanding of regulatory networks guiding plant reproductive development. This Special Issue of Plants will highlight the function of genes, phytohormones, and gene regulatory networks in flower and fruit development.

Prof. Dr. Stefan de Folter
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 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

  • gene regulation
  • transcription factors
  • flower
  • gynoecium
  • fruit
  • plant development
  • regulatory networks
  • plant reproduction

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.

Related Special Issue

Published Papers (7 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

20 pages, 4211 KiB  
Article
Interactions Between the Transcription Factor BOL/DRNL/ESR2 and the Jasmonate Pathway
by Beatriz E. Ruiz-Cortés, Yolanda Durán-Medina, C. Cecilia Ramos-Tamayo, Herenia Guerrero-Largo, Ma. Isabel Cristina Elizarraraz-Anaya, Omar Fabián Hernández-Zepeda, Enrique Ramírez-Chávez, Michiel Lammers, Ruud A. de Maagd, Jorge Molina-Torres, Stefan de Folter and Nayelli Marsch-Martínez
Plants 2025, 14(12), 1757; https://doi.org/10.3390/plants14121757 - 8 Jun 2025
Abstract
BOL/DRNL/ESR2, an AP2/ERF transcription factor, regulates early organ development in Arabidopsis (Arabidopsis thaliana). Its loss of function causes flower organ defects, while its overexpression induces green callus formation in roots without the addition of hormones. Jasmonates, plant hormones known as major [...] Read more.
BOL/DRNL/ESR2, an AP2/ERF transcription factor, regulates early organ development in Arabidopsis (Arabidopsis thaliana). Its loss of function causes flower organ defects, while its overexpression induces green callus formation in roots without the addition of hormones. Jasmonates, plant hormones known as major players in stress responses, also regulate some aspects of organ development (e.g., stamen development and plant and organ growth). Here, we studied the interaction between BOL and the JA pathway. We found that exogenous application of methyl jasmonate (MeJA) partially rescued the stamen phenotypes in bol-cr mutants, linking BOL and JA-mediated stamen development. Moreover, MeJA treatments in wild-type plants partially mimicked some bol-D mutant phenotypes like reduced rosette and root size, while JA inhibition restored wild-type leaf curvature, suggesting an alteration in JA homeostasis in the gain-of-function mutant. BOL overexpression caused increased JA levels, whereas bol loss-of-function plants had reduced levels. Furthermore, inducible BOL activity led to downregulation of a JA-responsive marker. Finally, JA biosynthesis inhibition affected BOL-induced root callus formation and led to an expansion of the BOL expression domain in roots. Our findings indicate that BOL modulates parts of the JA pathway and that feedback from the JA pathway appears to affect expression of the transcription factor. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition))
►▼ Show Figures

Figure 1

20 pages, 5967 KiB  
Article
Site-Directed Mutagenesis Mediated by Molecular Modeling and Docking and Its Effect on the Protein–Protein Interactions of the bHLH Transcription Factors SPATULA, HECATE1, and INDEHISCENT
by Pablo López-Gómez, Daniela De La Mora-Franco, Humberto Herrera-Ubaldo, Corina Díaz-Quezada, Luis G. Brieba and Stefan de Folter
Plants 2025, 14(12), 1756; https://doi.org/10.3390/plants14121756 - 8 Jun 2025
Abstract
The aim of this study was to investigate the biological relevance of predicted sites involved in protein–protein interaction formation by bHLH transcription factors associated with gynoecium development in Arabidopsis (Arabidopsis thaliana). We used AlphaFold2 to generate three-dimensional protein structures of the [...] Read more.
The aim of this study was to investigate the biological relevance of predicted sites involved in protein–protein interaction formation by bHLH transcription factors associated with gynoecium development in Arabidopsis (Arabidopsis thaliana). We used AlphaFold2 to generate three-dimensional protein structures of the bHLH proteins SPATULA (SPT), HECATE1 (HEC1), and INDEHISCENT (IND). These structures were subjected to molecular docking using the HawkDock server, enabling the identification of potential interaction sites. PCR-based site-directed mutagenesis was used to modify the predicted interaction sites, followed by testing for protein–protein interaction formation using Bimolecular Fluorescence Complementation (BiFC) assays. Furthermore, these modified versions were overexpressed in Arabidopsis to observe whether gynoecium and fruit development would be affected. BiFC assays with the modified versions revealed a complete loss of the SPT-HEC1 interaction and a strong reduction in the SPT-IND interaction. The overexpression experiments in Arabidopsis showed that the 35S::SPT-4A line exhibited strong phenotypes in the development of the medial tissues of the gynoecium, resulting in reduced seed number and shorter fruits. In the 35S::HEC1-2A line, a reduced seed number and shorter fruits were also observed, but no other obvious defects were observed. Finally, the 35S::IND-3A line was less affected than the 35S::IND line. In the latter, medial tissue development was strongly affected, while in the 35S::IND-3A line, it was only slightly affected; however, a reduced seed number and shorter fruits were observed. In summary, the predicted interaction sites are relevant and, when modified, affect gynoecium development in Arabidopsis. The findings demonstrate that predictive computational tools represent a viable strategy for a deeper understanding of protein–protein interactions. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition))
►▼ Show Figures

Figure 1

25 pages, 4697 KiB  
Article
Assessing Functional Conservation Amongst FT- and TFL1-like Genes in Globe Artichoke
by Rick Berentsen, María José Domenech, Peter Visser, Francisco Madueño, Vicente Balanzà and Reyes Benlloch
Plants 2025, 14(9), 1364; https://doi.org/10.3390/plants14091364 - 30 Apr 2025
Viewed by 294
Abstract
Globe artichoke [Cynara cardunculus var. scolymus (L.)] is a perennial composite cultivated for its immature inflorescences. Over time, the market for growers has steadily shifted away from vegetatively propagated varieties and towards seed-propagated hybrids. Since the latter tend to produce relatively late [...] Read more.
Globe artichoke [Cynara cardunculus var. scolymus (L.)] is a perennial composite cultivated for its immature inflorescences. Over time, the market for growers has steadily shifted away from vegetatively propagated varieties and towards seed-propagated hybrids. Since the latter tend to produce relatively late in the season, advancing the moment of flowering remains a major objective for breeders, who can benefit from insight gained into the genetic architecture of this trait. In plants, the timing of flowering is strongly regulated at the genetic level to ensure reproductive success. Genetic studies in model and non-model species have identified gene families playing crucial roles in flowering time control. One of these is the phosphatidylethanolamine-binding protein (PEBP) family, a conserved group of genes that, in plants, not only regulate the vegetative-to-reproductive phase transition, but also the development of inflorescences. In this work, we identified seven PEBP family members in the globe artichoke genome, belonging to three major clades: MOTHER OF FT AND TFL1 (MFT)-like, TERMINAL FLOWER 1 (TFL1)-like, and FLOWERING LOCUS T (FT)-like. Our results further show that CcFT expression is upregulated after the floral transition and partially complements the ft-10 mutant, whilst CcTFL1 is expressed in the shoot apex and developing inflorescences and complements the tfl1-1 mutant. These results suggest that the flowering-suppressing function of CcTFL1 is conserved in globe artichoke whereas conservation of the floral promoting function of CcFT remains uncertain. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition))
►▼ Show Figures

Graphical abstract

18 pages, 5169 KiB  
Article
Transcriptomic Analysis of Gibberellin-Mediated Flower Opening Process in Tree Peony (Paeonia suffruticosa)
by Bole Li, Qianqian Wang, Zefeng Qiu, Zeyun Lu, Junli Zhang, Qionghua He, Jiajun Yang, Hangyan Zhang, Xiangtao Zhu and Xia Chen
Plants 2025, 14(7), 1002; https://doi.org/10.3390/plants14071002 - 23 Mar 2025
Viewed by 453
Abstract
Gibberellin (GA3) plays a crucial role in regulating the flowering time of tree peony (Paeonia suffruticosa Andr.). However, its function on flower opening after dormancy release remains unclear, and its molecular mechanism need further study. We investigated the effects of [...] Read more.
Gibberellin (GA3) plays a crucial role in regulating the flowering time of tree peony (Paeonia suffruticosa Andr.). However, its function on flower opening after dormancy release remains unclear, and its molecular mechanism need further study. We investigated the effects of exogenous GA3 treatments at 800 mg/L, 900 mg/L, and 1000 mg/L on the flowering process of five-year-old peony plants (‘Luhehong’) under greenhouse conditions. Our results showed that exogenous GA3 significantly accelerated the flower opening process. Specifically, flower buds treated with 800 mg/L and 900 mg/L GA3 bloomed after 42 and 45 days, respectively. In contrast, all flower buds treated with 1000 mg/L GA3 aborted, while only one flower bud in the control group bloomed after 56 days. Furthermore, analysis of endogenous hormone levels revealed that GA3 treatment rapidly increased endogenous GA3 levels, decreased ABA levels, and gradually increased IAA levels. Transcriptomic analysis of flower buds released from dormancy following GA3 treatment identified multiple key genes involved in the flower opening process of peony. Notably, members of the C2H2, C3H, ERF, bHLH, MYB, bZIP, NAC, and WRKY families showed significant differential expression. Moreover, several key genes involved in GA3, ABA, and IAA hormone signaling pathways were also differentially expressed. Our findings suggested that an appropriate concentration of exogenous GA3 treatment could accelerate the flower opening process in tree peony through multiple pathways, which would provide valuable insights into the molecular mechanisms underlying the gibberellin-mediated flower opening process in tree peony. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition))
►▼ Show Figures

Figure 1

20 pages, 8153 KiB  
Article
Genome-Wide Identification and Functional Analysis of AP2/ERF Gene Family in Passiflora edulis Sims
by Lanjun Luo, Liping Zhang, Ronghao Gu, Shihao Ni, Jingyao Yu, Yachao Gao and Chuanying Fang
Plants 2025, 14(5), 645; https://doi.org/10.3390/plants14050645 - 20 Feb 2025
Viewed by 582
Abstract
The Apetala2/Ethylene Responsive Factor (AP2/ERF) family represents a critical group of transcription factors in plants, recognized for their roles in growth, development, fruit ripening, and postharvest processes. This study aimed to identify and characterize the AP2/ERF gene family in passion fruit (Passiflora [...] Read more.
The Apetala2/Ethylene Responsive Factor (AP2/ERF) family represents a critical group of transcription factors in plants, recognized for their roles in growth, development, fruit ripening, and postharvest processes. This study aimed to identify and characterize the AP2/ERF gene family in passion fruit (Passiflora edulis Sims) and investigate their potential roles in flavor enhancement. A total of 91 PeAP2/ERF genes were identified and classified into five subfamilies. Chromosome localization and collinearity analysis demonstrated their distribution across all nine chromosomes of passion fruit, with tandem duplication events identified as a key driver of family expansion. Exon–intron configurations and motif compositions were highly conserved among PeAP2/ERF genes. Promoter cis-acting element analysis indicated potential regulation by environmental signals, including abiotic and biotic stresses, as well as hormonal cues. Postharvest storage induced the expression of 59 PeAP2/ERF genes over time. Notably, PeAP2-10 was found to enhance the expression of PeSTP6, a gene associated with sugar transport, suggesting its potential influence on the flavor profile of passion fruit. These findings provide valuable insights into the functional roles of PeAP2/ERF genes in passion fruit, highlighting their significance in postharvest management and flavor quality enhancement strategies. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition))
►▼ Show Figures

Figure 1

13 pages, 4067 KiB  
Article
Machine Learning Inference of Gene Regulatory Networks in Developing Mimulus Seeds
by Albert Tucci, Miguel A. Flores-Vergara and Robert G. Franks
Plants 2024, 13(23), 3297; https://doi.org/10.3390/plants13233297 - 23 Nov 2024
Viewed by 793
Abstract
The angiosperm seed represents a critical evolutionary breakthrough that has been shown to propel the reproductive success and radiation of flowering plants. Seeds promote the rapid diversification of angiosperms by establishing postzygotic reproductive barriers, such as hybrid seed inviability. While prezygotic barriers to [...] Read more.
The angiosperm seed represents a critical evolutionary breakthrough that has been shown to propel the reproductive success and radiation of flowering plants. Seeds promote the rapid diversification of angiosperms by establishing postzygotic reproductive barriers, such as hybrid seed inviability. While prezygotic barriers to reproduction tend to be transient, postzygotic barriers are often permanent and therefore can play a pivotal role in facilitating speciation. This property of the angiosperm seed is exemplified in the Mimulus genus. In order to further the understanding of the gene regulatory mechanisms important in the Mimulus seed, we performed gene regulatory network (GRN) inference analysis by using time-series RNA-seq data from developing hybrid seeds from a viable cross between Mimulus guttatus and Mimulus pardalis. GRN inference has the capacity to identify active regulatory mechanisms in a sample and highlight genes of potential biological importance. In our case, GRN inference also provided the opportunity to uncover active regulatory relationships and generate a reference set of putative gene regulations. We deployed two GRN inference algorithms—RTP-STAR and KBoost—on three different subsets of our transcriptomic dataset. While the two algorithms yielded GRNs with different regulations and topologies when working with the same data subset, there was still significant overlap in the specific gene regulations they inferred, and they both identified potential novel regulatory mechanisms that warrant further investigation. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second Edition))
►▼ Show Figures

Figure 1

19 pages, 3116 KiB  
Article
A Model for the Gene Regulatory Network Along the Arabidopsis Fruit Medio-Lateral Axis: Rewiring the Pod Shatter Process
by José Moya-Cuevas, Elizabeth Ortiz-Gutiérrez, Patricio López-Sánchez, Miguel Simón-Moya, Patricia Ballester, Elena R. Álvarez-Buylla and Cristina Ferrándiz
Plants 2024, 13(20), 2927; https://doi.org/10.3390/plants13202927 - 18 Oct 2024
Viewed by 1265
Abstract
Different convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at maturity through openings (dehiscence zones, DZs) [...] Read more.
Different convergent evolutionary strategies adopted by angiosperm fruits lead to diverse functional seed dispersal units. Dry dehiscent fruits are a common type of fruit, characterized by their lack of fleshy pericarp and the release of seeds at maturity through openings (dehiscence zones, DZs) in their structure. In previous decades, a set of core players in DZ formation have been intensively characterized in Arabidopsis and integrated in a gene regulatory network (GRN) that explains the morphogenesis of these tissues. In this work, we compile all the experimental data available to date to build a discrete Boolean model as a mechanistic approach to validate the network and, if needed, to identify missing components of the GRN and/or propose new hypothetical regulatory interactions, but also to provide a new formal framework to feed further work in Brassicaceae fruit development and the evolution of seed dispersal mechanisms. Hence, by means of exhaustive in-silico validations and experimental evidence, we are able to incorporate both the NO TRANSMITTING TRACT (NTT) transcription factor as a new additional node, and a new set of regulatory hypothetical rules to uncover the dynamics of Arabidopsis DZ specification. Full article
(This article belongs to the Special Issue Gene Regulatory Mechanisms of Flower and Fruit Development in Plants (Second 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 1-7
Back to TopTop