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Transcriptional Regulation in Plant Development: 2nd Edition

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: 31 May 2025 | Viewed by 4880

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Dr. Konstantinos E. Vlachonasios

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Department of Botany, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
Interests: histone acetylation; plant development; plant molecular genetics; epigenetics
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Special Issue Information

Dear Colleagues,

Many developmental processes in plants are tightly regulated at the transcription level. Expression changes in various functional and regulatory proteins result in alterations in areas ranging from embryonic structures to mature plant morphologies. A number of genetic or epigenetic players involved in plant development have been identified in model plant species like Arabidopsis and rice, and their transcriptional networks have been explored extensively at the molecular level. However, it is poorly understood, especially in non-model plant species, how these regulators integrate the internal and external signals and modify the developmental programs that involve thousands of genes. Given the complexity of the regulatory network, it remains a challenge to decipher the molecular mechanisms driving plant development from the perspective of transcriptional regulation. This Special Issue will explore the genetic, epigenetic, and metabolomic bases of plant development, focusing on horticultural plants. We particularly encourage submissions focusing on the molecular mechanisms through which environmental cues (or agronomic management) affect development-related traits, such as crop architecture, fruit shape, pigmentation, and nutritional composition. This Special Issue will cover a wide range of research topics, including, but not limited to, aspects of transcriptional regulation related to plant development, such as the following:

Molecular mechanisms related to development in horticultural plants and other economically important species;
Evo-devo genetic analysis of agronomic traits during crop domestication and improvement;
Genetic basis of agronomic management and environmental factors affecting the nutritional compositions of horticultural crops;
Characterization of transcriptional factors or other genetic/epigenetic regulators in plants;
Genomic or transcriptomic analysis of development-related events in plants.

Dr. Konstantinos E. Vlachonasios
Guest Editor

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Keywords

environmental stresses
plant development
vegetative development
plant physiology and biochemistry
transcriptional regulation
plant–environment interactions

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Published Papers (7 papers)

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Research

18 pages, 10098 KiB

Open AccessArticle

Integrated Genetic Diversity and Multi-Omics Analysis of Colour Formation in Safflower

by Yonghua Qin, Kangjun Fan, Aidiya Yimamu, Peng Zhan, Lu Lv, Gang Li, Jiao Liu, Zunhong Hu, Xingchu Yan, Xueli Hu, Hong Liu and Rui Qin

Int. J. Mol. Sci. 2025, 26(2), 647; https://doi.org/10.3390/ijms26020647 (registering DOI) - 14 Jan 2025

Abstract

Safflower (Carthamus tinctorius L.) is a medicinal and edible cash crop that is widely cultivated worldwide. However, the genetic diversity of safflower germplasm resources and the reasons for the variations in safflower flower colour remain unclear. In this study, we used a combination of agronomic traits and Indel markers to assess the genetic diversity of 614 safflower germplasm resources. The results showed that most of the evaluated agronomic traits had high variability. The mean values of the Shannon’s information index (I) and polymorphism information content (PIC) in 50 pairs of Indel markers were 0.551 and 0.296, respectively. The population structure, neighbour-joining phylogeny, and principal coordinate analyses classified all genotypes into four subgroups, and 214 safflower core germplasms were constructed. Multiple analyses of genetic diversity parameters, range conformity, and the percentage of variance difference showed that the core germplasm did not differ significantly and could represent the original germplasm better. Transcriptome and metabolome analyses revealed that flavonoid synthesis-related genes, including CHS, F3H, ANS, and BZ1, were differentially expressed in different coloured safflowers. Most significantly, different genes and metabolite compounds in white safflowers were enriched upstream from the phenylpropanoid metabolic pathway to the production of naringenin, whereas those in red safflowers were concentrated in the downstream pathway from eriodictyol. Meanwhile, the preliminary quantification of anthocyanins and carotenoids extracted from red, orange, and white types of safflower showed that the level of both anthocyanins and carotenoids were highest in red types. This work provides new insights into the formation of different safflower flower colours and in the conservation and management of safflower germplasm. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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26 pages, 7287 KiB

Open AccessArticle

Mitochondrial Genome Insights into Evolution and Gene Regulation in Phragmites australis

by Jipeng Cui, Qianhui Yang, Jiyue Zhang, Chuanli Ju and Suxia Cui

Int. J. Mol. Sci. 2025, 26(2), 546; https://doi.org/10.3390/ijms26020546 - 10 Jan 2025

Viewed by 263

Abstract

As a globally distributed perennial Gramineae, Phragmites australis can adapt to harsh ecological environments and has significant economic and environmental values. Here, we performed a complete assembly and annotation of the mitogenome of P. australis using genomic data from the PacBio and BGI platforms. The P. australis mitogenome is a multibranched structure of 501,134 bp, divided into two circular chromosomes of 325,493 bp and 175,641 bp, respectively. A sequence-simplified succinate dehydrogenase 4 gene was identified in this mitogenome, which is often translocated to the nuclear genome in the mitogenomes of gramineous species. We also identified tissue-specific mitochondrial differentially expressed genes using RNAseq data, providing new insights into understanding energy allocation and gene regulatory strategies in the long-term adaptive evolution of P. australis mitochondria. In addition, we studied the mitogenome features of P. australis in more detail, including repetitive sequences, gene Ka/Ks analyses, codon preferences, intracellular gene transfer, RNA editing, and multispecies phylogenetic analyses. Our results provide an essential molecular resource for understanding the genetic characterisation of the mitogenome of P. australis and provide a research basis for population genetics and species evolution in Arundiaceae. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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17 pages, 5618 KiB

Open AccessArticle

Comprehensive Identification of AREB Gene Family in Populus euphratica Oliv. and Functional Analysis of PeAREB04 in Drought Tolerance

by Binglei Liu, Jianhao Sun, Chen Qiu, Xiaoli Han and Zhijun Li

Int. J. Mol. Sci. 2025, 26(2), 518; https://doi.org/10.3390/ijms26020518 - 9 Jan 2025

Viewed by 242

Abstract

The transcription factors in the ABA Response Element Binding (AREB) protein family were differentially regulated under multiple stress conditions; however, functional analyses of AREB in Populus euphratica Oliv. had not been conducted previously. In the present study, the comprehensive identification of the P. euphratica AREB gene family and the function of PeAREB04 in response to drought stress in P. euphratica were elucidated. A comprehensive analysis of the PeAREB family was first performed, followed by the determination of their expression patterns under drought stress. Bioinformatics analysis revealed that thirteen AREB genes were identified across the P. euphratica genome, with these genes distributed across eight chromosomes in a seemingly random pattern. Phylogenetic analysis indicated that the PeAREB genes could be categorized into four distinct branches. Cis-acting element analysis revealed that most PeAREB genes contained multiple hormone- and stress-responsive elements. Transcriptomic sequencing of P. euphratica seedlings under drought stress showed that most PeAREB genes responded rapidly to drought stress in either the leaves or roots. One gene, PeAREB04, was selected for further functional validation due to its significant upregulation in both leaves and roots under drought stress. Overexpression of PeAREB04 in Arabidopsis thaliana resulted in a high survival rate, reduced water loss in isolated leaves, and a significant reduction in stomatal aperture under natural drought conditions. Drought stress simulations using mannitol further demonstrated that overexpression of PeAREB04 significantly enhanced root elongation. These findings indicate that the identification of the PeAREB gene family and the characterization of PeAREB04’s role in drought stress have been largely accomplished. Furthermore, the PeAREB04 gene demonstrates considerable potential as a key target for future genetic engineering strategies aimed at enhancing plant drought resistance. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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16 pages, 9890 KiB

Open AccessArticle

Genome-Wide Identification and Expression Analysis of HSP70 Gene Family Under High-Temperature Stress in Lettuce (Lactuca sativa L.)

by Qian Wang, Wenjing Sun, Yipei Duan, Yikun Xu, Huiyu Wang, Jinghong Hao, Yingyan Han and Chaojie Liu

Int. J. Mol. Sci. 2025, 26(1), 102; https://doi.org/10.3390/ijms26010102 - 26 Dec 2024

Viewed by 448

Abstract

The heat shock protein 70 (HSP70) family plays an important role in the growth and development of lettuce and in the defense response to high-temperature stress; however, its bioinformatics analysis in lettuce has been extremely limited. Genome-wide bioinformatics analysis methods such as chromosome location, phylogenetic relationships, gene structure, collinearity analysis, and promoter analysis were performed in the LsHSP70 gene family, and the expression patterns in response to high-temperature stress were analyzed. The mechanism of LsHSP70-19 in heat resistance in lettuce was studied by virus-induced gene silencing (VIGS) and transient overexpression techniques. The results showed that a total of 37 LsHSP70 genes were identified by the Hidden Markov Model (HMM) and Protein Family Database (Pfam). These 37 LsHSP70 genes were classified into groups A, B, C, and D by phylogenetic relationships. They were mainly localized on seven chromosomes except for chromosome 3; gene structure analysis showed that LsHSP70 contained 1–9 exons, and the protein structure domains of genes in the same group were highly conserved. The covariance analysis showed that nine pairs of LsHSP70 genes existed between LsHSP70 members, and lettuce LsHSP70 and sunflower HaHSP70 had been more conserved in the evolutionary process. The promoter analysis showed that there were a large number of cis-acting elements related to phytohormones, growth, development, stress, and light response in LsHSP70. In addition, the results of the expression pattern analysis for all LsHSP70 genes under high-temperature stress showed that 28 out of 37 LsHSP70 genes were able to respond to heat stress, and only LsHSP70-8, LsHSP70-14, LsHSP70-19, LsHSP70-23, and LsHSP70-24 were able to respond rapidly to heat stress (2 h). The expression of LsHSP70-19 was higher at different periods under high-temperature stress; the overexpression of LsHSP70-19, the plant fresh weight, and the root weight were better than the control (CK); and the heat resistance was better. These results suggest that LsHSP70-19 may play an important role under high-temperature stress in lettuce. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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24 pages, 14115 KiB

Open AccessArticle

Regulatory Mechanism of Exogenous ABA on Gibberellin Signaling and Antioxidant Responses in Rhododendron chrysanthum Pall. Under UV-B Stress

by Wang Yu, Kun Cao, Hongwei Xu and Xiaofu Zhou

Int. J. Mol. Sci. 2024, 25(24), 13651; https://doi.org/10.3390/ijms252413651 - 20 Dec 2024

Viewed by 389

Abstract

In the present work, we examined the effects of exogenous abscisic acid (ABA) under ultraviolet B (UV-B) exposure on gibberellin (GA) production, signaling, and antioxidant-related genes in Rhododendron chrysanthum Pall (R. chrysanthum). Using transcriptomics, acetylated proteomics, and widely targeted metabolomics, the effects of UV-B stress on R. chrysanthum and the regulatory effects of exogenous ABA on it were revealed from multiple perspectives. The findings revealed that R. chrysanthum’s antioxidant enzyme genes were differentially expressed by UV-B radiation and were substantially enriched in the glutathione metabolic pathway. Exogenous ABA supplementation boosted plant resistance to UV-B damage and further enhanced the expression of antioxidant enzyme genes. Furthermore, under UV-B stress, glutathione reductase, glutathione peroxidase, and L-ascorbate peroxidase were found to be the primary antioxidant enzymes controlled by exogenous ABA. In addition, gibberellin content was altered due to UV-B and exogenous ABA treatments, with greater effects on GA3 and GA53. The acetylation proteomics study’s outcomes disclosed that the three main oxidative enzymes’ acetylation modifications were dramatically changed during UV-B exposure, which may have an impact on the antioxidant enzymes’ functions and activities. The protective impact of exogenous ABA and gibberellin on R. chrysanthum’s photosynthetic system was further established by measuring the parameters of chlorophyll fluorescence. This research offers a theoretical foundation for the development of breeding highly resistant plant varieties as well as fresh insights into how hormone levels and antioxidant systems are regulated by plants in response to UV-B damage. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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15 pages, 8738 KiB

Open AccessArticle

Unraveling the Molecular Mechanisms by Which the miR171b-SCL6 Module Regulates Maturation in Lilium

by Qing Li, Meiqi Song, Yachen Wang, Ping Lu, Wei Ge and Kezhong Zhang

Int. J. Mol. Sci. 2024, 25(17), 9156; https://doi.org/10.3390/ijms25179156 - 23 Aug 2024

Cited by 1 | Viewed by 778

Abstract

Lilium is one of the most widely cultivated ornamental bulbous plants in the world. Although research has shown that variable temperature treatments can accelerate the development process from vegetative to reproductive growth in Lilium, the molecular regulation mechanisms of this development are not clear. In this study, Lbr-miR171b and its target gene, LbrSCL6, were selected and validated using transgenic functional verification, subcellular localization, and transcriptional activation. This study also investigated the differential expression of Lbr-miR171b and LbrSCL6 in two temperature treatment groups (25 °C and 15 °C). Lbr-miR171b expression significantly increased after the temperature change, whereas that of LbrSCL6 exhibited the opposite trend. Through in situ hybridization experiments facilitated by the design of hybridization probes targeting LbrSCL6, a reduction in LbrSCL6 expression was detected following variable temperature treatment at 15 °C. The transgenic overexpression of Lbr-miR171b in plants promoted the phase transition, while LbrSCL6 overexpression induced a delay in the phase transition. In addition, LbrWOX4 interacted with LbrSCL6 in yeast two-hybrid and bimolecular fluorescence complementation assays. In conclusion, these results explain the molecular regulatory mechanisms governing the phase transition in Lilium. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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16 pages, 3346 KiB

Open AccessArticle

Gibberellin Signaling through RGA Suppresses GCN5 Effects on Arabidopsis Developmental Stages

by Christina Balouri, Stylianos Poulios, Dimitra Tsompani, Zoe Spyropoulou, Maria-Christina Ketikoglou, Athanasios Kaldis, John H. Doonan and Konstantinos E. Vlachonasios

Int. J. Mol. Sci. 2024, 25(12), 6757; https://doi.org/10.3390/ijms25126757 - 19 Jun 2024

Cited by 1 | Viewed by 1814

Abstract

Histone acetyltransferases (HATs) modify the amino-terminal tails of the core histone proteins via acetylation, regulating chromatin structure and transcription. GENERAL CONTROL NON-DEREPRESSIBLE 5 (GCN5) is a HAT that specifically acetylates H3K14 residues. GCN5 has been associated with cell division and differentiation, meristem function, root, stem, foliar, and floral development, and plant environmental response. The flowers of gcn5 plants display a reduced stamen length and exhibit male sterility relative to the wild-type plants. We show that these effects may arise from gibberellin (GA)-signaling defects. The signaling pathway of bioactive GAs depends on the proteolysis of their repressors, DELLA proteins. The repressor GA (RGA) DELLA protein represses plant growth, inflorescence, and flower and seed development. Our molecular data indicate that GCN5 is required for the activation and H3K14 acetylation of genes involved in the late stages of GA biosynthesis and catabolism. We studied the genetic interaction of the RGA and GCN5; the RGA can partially suppress GCN5 action during the whole plant life cycle. The reduced elongation of the stamen filament of gcn5–6 mutants is reversed in the rga–t2;gcn5–6 double mutants. RGAs suppress the GCN5 effect on the gene expression and histone acetylation of GA catabolism and GA signaling. Interestingly, the RGA and RGL2 do not suppress ADA2b function, suggesting that ADA2b acts downstream of GA signaling and is distinct from GCN5 activity. In conclusion, we propose that the action of GCN5 on stamen elongation is partially mediated by RGA and GA signaling. Full article

(This article belongs to the Special Issue Transcriptional Regulation in Plant Development: 2nd Edition)

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