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Gene Regulatory Mechanisms of Flower and Fruit Development in Plants...
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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 3366

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

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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

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Related Special Issue

Published Papers (4 papers)

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Research

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 319
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))
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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 479
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))
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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 723
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))
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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 1189
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))
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