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Horticulturae
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Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants
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Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants

A special issue of Horticulturae (ISSN 2311-7524). This special issue belongs to the section "Floriculture, Nursery and Landscape, and Turf".

Deadline for manuscript submissions: 31 October 2025 | Viewed by 2576

Special Issue Editors

Prof. Dr. Chao Ma

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Guest Editor
Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing 100193, China
Interests: ornamental horticulture; flowering regulation; flower development; phytohormone; postharvest physiology
Dr. Daofeng Liu

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Guest Editor
Chongqing Engineering Research Center for Floriculture, Key Laboratory of Agricultural Biosafety and Green Production of Upper Yangtze River (Ministry of Education), College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
Interests: genetic breeding; biotechnology; abiotic stresses; hormonal crosstalk
Special Issues, Collections and Topics in MDPI journals
Dr. Wen Chen

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Guest Editor
College of Horticulture Science, Zhejiang A&F University, Hangzhou 311300, China
Interests: ornamental plants; abiotic stress; plant physiology; genetic breeding
Special Issues, Collections and Topics in MDPI journals
Dr. Lin Ouyang

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Guest Editor
Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences (CAAS), Chengdu 610213, China
Interests: ornamental plants; abiotic stress; plant physiology; plant biotechnology

Special Issue Information

Dear Colleagues,

Ornamental plants include landscape trees, flowers and other ground cover.

With the recent advancements in omics sciences, such as genomics, transcriptomics, proteomics, metabolomics and phenomics, these modern technologies provide new methods for studying plant molecular mechanisms. For ornamental plants, the study usually focused on the regulatory mechanism analysis using omics technologies.

The scope of this Special Issue includes a series of contents, such as genomics, transcriptomics, proteomics, metabolomics and phenomics, single omics or multi omics analysis of ornamental plants, as well as epiomics (epigenomics, epitranscriptomics and epiproteomics) and interactomics (e.g., DNA–RNA interactomics, RNA–RNA interactomics, DNA–protein interactomics, RNA–protein interactomics, protein–protein interactomics and protein–metabolite interactomics), immunomics and microbiomics related to the regulatory mechanisms of ornamental plants. This Special Issue focuses on genetic traits related to flower color, floral fragrance, abiotic and biotic stress, and other characteristics of ornamental plants. This Special Issue also encourages experimental verification of the physiological mechanisms and molecular regulatory mechanisms of ornamental plants.

Prof. Dr. Chao Ma
Dr. Daofeng Liu
Dr. Wen Chen
Dr. Lin Ouyang
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 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. Horticulturae is an international peer-reviewed open access monthly 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 2200 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

  • ornamental plants
  • genomics
  • transcriptomics
  • proteomics
  • metabolomics
  • regulatory mechanisms

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Published Papers (5 papers)

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Research

18 pages, 14476 KiB  
Article
Functional Characterization of CpPIP1;1 and Genome-Wide Analysis of PIPs in Wintersweet (Chimonanthus praecox (L.) Link)
by Fei Ren, Zhu Feng, Guo Wei, Yimeng Lv, Jia Zhao, Yeyuan Deng, Shunzhao Sui and Jing Ma
Horticulturae 2025, 11(6), 581; https://doi.org/10.3390/horticulturae11060581 (registering DOI) - 24 May 2025
Abstract
Plant aquaporin proteins (AQPs) are categorized into seven distinct families, among which, plasma membrane intrinsic proteins (PIPs) play pivotal roles in plant growth and physiological processes. In this study, we identified 11 CpPIP genes in wintersweet (Chimonanthus praecox (L.) Link) based on [...] Read more.
Plant aquaporin proteins (AQPs) are categorized into seven distinct families, among which, plasma membrane intrinsic proteins (PIPs) play pivotal roles in plant growth and physiological processes. In this study, we identified 11 CpPIP genes in wintersweet (Chimonanthus praecox (L.) Link) based on bioinformatic characterization of gene structural organization, chromosomal localization, and phylogenetic relationships. Subsequent phylogenetic reconstruction resolved two evolutionarily distinct CpPIP subclasses. We focused on the isolation and characterization of CpPIP1;1, which showed the highest expression in floral organs. During flowering, a significant increase was observed in the expression of the CpPIP1;1 gene in response to a gradual reduction in environmental temperature. Moreover, the overexpression of CpPIP1;1 in Arabidopsis thaliana resulted in early flowering and an enhanced tolerance to salt, drought, and cold stress. We subsequently transcriptionally fused the CpPIP1;1 promoter containing MYC and MYB low-temperature response elements to the β-glucuronidase (GUS) reporter gene and introduced this construct into Nicotiana tabacum. GUS activity assays of the transgenic plants revealed that the CpPIP1;1 promoter was effectively expressed in flowers. Furthermore, the promoter transcriptional activity was enhanced in response to salt, drought, cold, gibberellic acid, and methyl jasmonate treatments. Collectively, our findings in this study revealed that CpPIP1;1 plays a key role in the regulation of flowering and stress tolerance in wintersweet plants. Full article
(This article belongs to the Special Issue Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants)
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28 pages, 27429 KiB  
Article
Comparative Transcriptome Profiling Reveals Differential Defense Responses of Resistant and Susceptible Phalaenopsis to Dickeya fangzhongdai
by Jingjing Xin, Jiyong Tang, Ying Mao, Dongdong Ren, Ping Luo and Yongyi Cui
Horticulturae 2025, 11(5), 534; https://doi.org/10.3390/horticulturae11050534 - 15 May 2025
Viewed by 209
Abstract
Soft rot caused by Dickeya fangzhongdai is a destructive disease in Phalaenopsis production that seriously impacts the quality and yield of Phalaenopsis. To explore the molecular mechanisms underlying disease resistance, transcriptome analysis was conducted on resistant and susceptible Phalaenopsis varieties. By comparing [...] Read more.
Soft rot caused by Dickeya fangzhongdai is a destructive disease in Phalaenopsis production that seriously impacts the quality and yield of Phalaenopsis. To explore the molecular mechanisms underlying disease resistance, transcriptome analysis was conducted on resistant and susceptible Phalaenopsis varieties. By comparing the transcriptomes of the resistant variety ‘ES L20’ and the susceptible variety ‘Zishuijing’ after D. fangzhongdai infection, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses were performed. The results revealed that the differentially expressed genes were mainly enriched in pathways related to plant–pathogen interaction, plant hormone signal transduction, and the phenylpropanoid biosynthetic pathway. In the resistant variety ‘ES L20’, some genes in the Ca2+ pathway, PAMP-triggered immunity pathway, and Effector-triggered immunity pathway were significantly up-regulated. Analysis of the transcriptome levels of genes in the phytohormone-related pathways showed that genes associated with IAA (indole-3-acetic acid), salicylic acid, and jasmonic acid signal transduction pathways were all up-regulated in the resistant variety after inoculation. Furthermore, the analysis of genes in the phenylpropanoid biosynthesis pathway demonstrated significant up-regulation in the resistant variety. The determination of lignin content validated this result, confirming the crucial role of lignin synthesis in Phalaenopsis defense against soft rot. These findings suggest that the differentially expressed genes in phytopathogenic interaction pathways, along with those involved in hormone-related and lignin synthesis pathways, play important roles in Phalaenopsis resistance to soft rot. This study provides valuable insights into the molecular basis of Phalaenopsis resistance to soft rot and may contribute to the development of effective disease control strategies. Full article
(This article belongs to the Special Issue Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants)
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14 pages, 4208 KiB  
Article
The Transcription Factor LoTDF1 Plays a Role in Early Anther Development in Lily (Lilium Oriental Hybrids)
by Juanjuan Sui, Yan Tang, Xing Cao and Jingxia Yang
Horticulturae 2025, 11(4), 398; https://doi.org/10.3390/horticulturae11040398 - 9 Apr 2025
Viewed by 348
Abstract
Lilies are one of the most popular ornamental flowers in the world. However, the abundant pollen produced in their anthers causes significant inconvenience for producers and consumers. Pollen abortion induced by molecular breeding techniques is one of the effective ways to solve this [...] Read more.
Lilies are one of the most popular ornamental flowers in the world. However, the abundant pollen produced in their anthers causes significant inconvenience for producers and consumers. Pollen abortion induced by molecular breeding techniques is one of the effective ways to solve this problem. In this study, the LoTDF1 gene, which is involved in regulating lily anther development, was identified and cloned from lily anthers based on transcriptome data. The open reading frame of LoTDF1 is 936 bp and encodes a protein with 311 amino acids. Multiple sequence alignment and phylogenetic tree analysis revealed that the LoTDF1 protein contained a conserved R2R3 domain, belonging to the MYB transcription factor family. Subcellular localization and transcriptional activation assays demonstrated that LoTDF1 localized to the nucleus and functioned as a transcription activator. The transcriptional activation domain was located within the last 195 amino acids (117–311a) of the C-terminus, and there may be more than one transcriptional activation domain in the region. The expression level of the LoTDF1 gene was highest during the pollen mother cell (PMC) stage of lily anther development (2 cm anther), followed by the tetrad stage (4 cm anther). In situ hybridization experiments further confirmed that LoTDF1 transcripts were predominantly localized in PMCs, tapetal cells, middle layer cells, dyads, and tetrads. The experiment data suggest that LoTDF1 plays a critical role in regulating early anther development in lily. LoTDF1 could be a promising candidate gene for molecular breeding strategies aimed at developing pollen-free lily cultivars to enhance commercial and consumer appeal. Full article
(This article belongs to the Special Issue Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants)
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17 pages, 8048 KiB  
Article
Transcription Factor RhCUC3 Regulates Petal Numbers in Rose Flowers
by Yan Fang, Zixin Zhao, Yuanji Shen, Zheyuan Ding, Yongyi Cui and Wen Chen
Horticulturae 2025, 11(2), 170; https://doi.org/10.3390/horticulturae11020170 - 5 Feb 2025
Viewed by 648
Abstract
Rose is one of the most popular ornamental plants worldwide. The double-flower trait, referring to flowers with extra petals, has been a key focus in rose breeding history. However, the genetic mechanisms regulating petal number in roses are still not fully understood. Here, [...] Read more.
Rose is one of the most popular ornamental plants worldwide. The double-flower trait, referring to flowers with extra petals, has been a key focus in rose breeding history. However, the genetic mechanisms regulating petal number in roses are still not fully understood. Here, we identified the CUP-SHAPED COTYLEDON 3 (RhCUC3) gene in the miniature rose (Rosa hybrida ‘Eclair’). The expression of RhCUC3 was high during the petal and stamen primordium differentiation stages but declined sharply during pistil primordium development. RhCUC3 belongs to the NAM/CUC3 subgroup of NAC transcription factors and is localized in the nucleus. The transcript level of RhCUC3 increased significantly with ABA and GA treatments and was inversely down-regulated with MeJA and 6-BA treatments. Silencing RhCUC3 using virus-induced gene silencing (VIGS) in rose ‘Eclair’ significantly decreased the number of petaloid stamens and normal petals while slightly increasing the number of stamens. Additionally, the expression of RhAG and RhAGL, two MADS-box genes associated with floral organ identity, was significantly higher in TRV-RhCUC3 compared to the TRV control. These findings suggest that RhCUC3 enhances stamen petaloidy and petal number, potentially by modulating the expression of RhAG and RhAGL, providing new insights into the function of NAC transcription factors in plants. Full article
(This article belongs to the Special Issue Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants)
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18 pages, 7846 KiB  
Article
Genome-Wide Identification and Expression Analysis of bZIP Transcription Factors Under Salt Stress in Chrysanthemum
by Yanchao Guo, Kexin Ji, Zhongqi Jia, Palinuer Aiwaili, Lin Liu, Haoran Ren, Qinglin Liu, Yunhe Jiang, Junping Gao and Yanjie Xu
Horticulturae 2024, 10(12), 1327; https://doi.org/10.3390/horticulturae10121327 - 11 Dec 2024
Viewed by 796
Abstract
Chrysanthemum is one of the most important ornamental plants in the world. Its yield and quality are greatly affected by abiotic stress. The basic leucine zipper (bZIP) transcription factors play crucial roles in abiotic stress response; however, there has been no [...] Read more.
Chrysanthemum is one of the most important ornamental plants in the world. Its yield and quality are greatly affected by abiotic stress. The basic leucine zipper (bZIP) transcription factors play crucial roles in abiotic stress response; however, there has been no genome-wide investigation of the bZIP family in Chrysanthemums. Here, we identified 71 bZIP family proteins in the Chrysanthemum nankingense genome and classified them into 12 subgroups using phylogenetic analysis, including subgroups S, A, D, and G, and further performed a conserved motif, gene structure, and protein interaction network analysis for these subgroups. The results indicated that the members from the same subgroup often possess similar gene structures and motif organization, and the genes of the S subgroup are highly conservative during their evolution. The protein interaction network indicated that members of CnbZIP-S dominate the central position of the protein network. In addition, the expression of the CmbZIP genes in ‘Jinba’ was analyzed in root tissue via RNA-Seq after salt stress treatment. We found that 11 CmbZIP genes were down-regulated by salt treatment, and the bZIP-S genes, which were down-regulated, are more prevalent than other subgroups, indicating that the S subgroup genes may play an important role in the salt stress response in Chrysanthemum. Our research provides useful information for breeding new chrysanthemum cultivars with strong salt tolerance. Full article
(This article belongs to the Special Issue Advanced Omics Technologies and Regulatory Mechanisms of Ornamental Plants)
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