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Plants
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Unraveling Complex Traits and Developmental Pathways of Forest Trees
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Unraveling Complex Traits and Developmental Pathways of Forest Trees

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Development and Morphogenesis".

Deadline for manuscript submissions: closed (15 November 2025) | Viewed by 2549

Special Issue Editors

Prof. Dr. Zhong Chen

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Guest Editor
State Key Laboratory for Efficient Production of Forest Resources, Key Laboratory of Silviculture and Conservation of the Ministry of Education, National Energy R&D Center for Non-Food Biomass, College of Forestry, Beijing Forestry University, Beijing, China
Interests: functional genomics; tree physiology; plant molecular biology; plant biotechnology
Special Issues, Collections and Topics in MDPI journals
Dr. Guochun Zhao

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Guest Editor
Key Laboratory of Silviculture and Conservation of the Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
Interests: functional genomics; floral development; plant sex differentiation; tree physiology; plant molecular biology
Special Issues, Collections and Topics in MDPI journals
Dr. Shupei Rao

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Guest Editor
Jiangxi Provincial Key Laboratory of Native Tree Species Breeding and Efficient Utilization, Institute of Biological Resources, Jiangxi Academy of Sciences, Nanchang 330000, China
Interests: functional genomics; secondary metabolism; abiotic stress tolerance; plant molecular biology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Forest trees make a significant contribution to sustainability with renewable resources, forest foods, the supply of ecosystem services and the global economy. In the past 20 years, more and more tree genomes were deciphered, we have witnessed tremendous advances in forest tree physiology, genetics and molecular biology derived from genomic resources. With the rapid development of multi-omics technologies and novel bioinformatics tools, the complex traits and developmental pathways of forest trees has entered the functional genomics era. The challenge faced will be to identify genes underlying complex traits, to construct comprehensive gene regulatory networks, and to analyse the real functions of key candidate genes.

The present Special Issue entitled "Unraveling Complex Traits and Developmental Pathways of Forest Trees" encourages the submission of research articles as well as review papers dealing with new advances in functional genomics of forest trees. The main contents could be related to new perspectives in tree physiology, growth, development, and breeding, especially in wood formation and quality, floral development, sex differentiation, secondary metabolism, and stress tolerance. The topics covered include but are not limited to the identification and functional characterization of coding and non-coding features in genomes, multi-omics analysis, gene expression profiling, GWAS, genetic engineering approaches, such as transformation systems, or cutting-edge technologies, such as CRISPR/Cas9 gene editing and synthetic biology, as well as phenomics, bioinformatics, and quantitative genetics.

As the Guest Editors of this Special Issue, we would like to invite you to participate in this venture by contributing a paper on the topic of your choice within the broad area covered by "Unraveling Complex Traits and Developmental Pathways of Forest Trees". We look forward to receiving your contribution.

You may choose our Joint Special Issue in Forests.

Dr. Zhong Chen
Dr. Guochun Zhao
Dr. Shupei Rao
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 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

  • functional genomics
  • multi-omics analysis
  • synthetic biology
  • tree genetics and genomes
  • regulation of gene expression
  • gene regulatory networks
  • tree breeding

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Further information on MDPI's Special Issue policies can be found here.

Published Papers (2 papers)

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Research

17 pages, 3648 KB  
Article
Functional Characterization of Floral Gene Network Reveals a Critical FT1–AP1 Interaction in Flowering Regulation in Longan
by Yuru Tang, Yating Xu, Haoming Mao, Yawen Xu, Jianling Pan, Shaoquan Zheng, Guochun Zhao, Wenshun Hu and Ray Ming
Plants 2026, 15(1), 106; https://doi.org/10.3390/plants15010106 - 30 Dec 2025
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Abstract
Longan (Dimocarpus longan Lour.) is a commercially valuable tropical fruit crop that contains two antagonistic FLOWERING LOCUS T (FT) homologs involved in regulating flowering time. However, how these FT genes interact with flowering regulators FLOWERING LOCUS D (FD) [...] Read more.
Longan (Dimocarpus longan Lour.) is a commercially valuable tropical fruit crop that contains two antagonistic FLOWERING LOCUS T (FT) homologs involved in regulating flowering time. However, how these FT genes interact with flowering regulators FLOWERING LOCUS D (FD) and APETALA1 (AP1) remains unknown. Four flowering-related genes in longan, DlFT1, DlFT2, DlAP1 and DlFD, were successfully isolated. Expression profiling revealed that all four genes were expressed in leaves and buds across different stages of natural and KClO3-induced floral bud differentiation. Functional characterization through heterologous overexpression in Arabidopsis thaliana showed that DlAP1 significantly promotes early flowering under long-day conditions and induced morphological changes in floral organs and leaves. In contrast, DlFD overexpression had no effect on flowering time. Subcellular localization assays revealed that DlFT1 and DlFT2 localized to both the nucleus and the plasma membrane, while DlAP1 and DlFD localized exclusively to the nucleus. Yeast two-hybrid and bimolecular fluorescence complementation (BiFC) analyses revealed a novel regulatory node: DlFT1 directly interacts with DlAP1, a finding that expands the classical FT-FD-AP1 flowering model. Additionally, DlFD interacts more strongly with DlFT1 than with DlFT2, whereas DlFT1 only interacts with DlAP1, but not DlFT2. These results demonstrate that DlFT1 promotes flowering not only via the conserved FD-dependent pathway but also through direct association with AP1. These findings advance our understanding of the regulatory mechanisms of flowering in longan and provide valuable insights into flowering pathways of perennial woody species. Full article
(This article belongs to the Special Issue Unraveling Complex Traits and Developmental Pathways of Forest Trees)
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20 pages, 6814 KB  
Article
Characterization, Expression Profile Analysis, and Functional Prediction of UGP Gene Family in Dendrocalamus brandisii
by He Li, Chongyang Wu, Xiangyi Li, Junlei Xu, Zhanchao Cheng and Jian Gao
Plants 2025, 14(10), 1458; https://doi.org/10.3390/plants14101458 - 14 May 2025
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Abstract
UDP-glucose pyrophosphorylase (UGPase) is essential for carbohydrate metabolism, catalyzing UDP-glucose synthesis, a precursor for sucrose and cellulose biosynthesis. While UGP genes have been widely studied in plants, their functions in Dendrocalamus brandisii remain unclear. This study identified and characterized the DbUGP gene family [...] Read more.
UDP-glucose pyrophosphorylase (UGPase) is essential for carbohydrate metabolism, catalyzing UDP-glucose synthesis, a precursor for sucrose and cellulose biosynthesis. While UGP genes have been widely studied in plants, their functions in Dendrocalamus brandisii remain unclear. This study identified and characterized the DbUGP gene family using the whole genome and transcriptome data of D. brandisii, in conjunction with whole genome data from 10 additional species through sequence alignment, phylogenetic analysis, gene structure and motif exploration, protein structure prediction, and expression profiling. Phylogenetic analysis showed eight identified DbUGPs clustered with two OsUGPs in two clades. Gene structure, motif, and collinearity analyses indicate conservation with other bamboo UGPs. The gene family exhibited segmental duplications. Expression profiling revealed DbUGP1/5 were highly expressed in flowers, while others were enriched in shoots, buds, and culms. DbUGP1/4/8 were significantly downregulated during culm maturation. Protein structure prediction indicated two conformations with catalytic sites in disordered coil regions. WGCNA identified co-expression modules and protein interaction networks centered on DbUGP1/4, while KEGG enrichment indicated their functions in metabolism, signal transduction, and stress adaptation. Promoter analysis identified cis-regulatory elements responsive to light, MeJA, and ABA. This study suggests that the evolutionarily conserved DbUGPs exhibit mutual coordination and dynamic expression during D. brandisii growth, providing fresh insights into their functional roles. Full article
(This article belongs to the Special Issue Unraveling Complex Traits and Developmental Pathways of Forest Trees)
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