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Forests
Special Issues
Genomics of Growth Traits and Stress Acclimation in Forest Trees
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Genomics of Growth Traits and Stress Acclimation in Forest Trees

A special issue of Forests (ISSN 1999-4907). This special issue belongs to the section "Genetics and Molecular Biology".

Deadline for manuscript submissions: closed (31 August 2023) | Viewed by 8270

Special Issue Editors

Dr. Tao Su

E-Mail Website
Guest Editor
College of Life Sciences, Nanjing Forestry University, Nanjing 210037, China
Interests: molecular ecophysiology; stress biology; genomic diversity
Special Issues, Collections and Topics in MDPI journals
Dr. Su Chen

E-Mail Website
Guest Editor
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
Interests: functional genome; signaling in seed dormancy; transcriptional regulation of cold and salinity stress in trees
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Nan Liu

E-Mail Website
Guest Editor
South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
Interests: ecophysiology and stress-responsive mechanisms; environmental restoration and reconstruction of land; N and C composition in forests

Special Issue Information

Dear Colleagues,

The forest ecology and sustainable utilization of timber sources are crucial owing to the concomitant influence of a variety of stress cues (e.g., drought, salinity, osmosis, extreme temperature, and climate change) and biotic stimuli (e.g., pathogenic invaders). Molecular patterns of genetic resilience and resistance in correlation with favorable environments and nutrients are postulated to collectively impact survival and evolution in forest-tree species. Tree growth, stress adaptation, and defense priming are mounted concurrently with a profound deployment of genomic traits and metabolic and signaling genes underlying the transcriptional/translational mechanisms.

Recent technique innovation in functional genomics, genetics, and omics (e.g., transcriptome, proteome, and metabolome) accelerates optimizing growth performance and alternative strategies for stresses and quality/biomass-related traits in forest trees. Specific QTL/gene identification and experimental evaluation for major genomic traits within the regulatory crosstalk between metabolism, defense, and signaling pathways make the molecular breeding and development of stress-resilient and high-biomass energy trees incredibly important. Thus, an in-depth perception and unveiling of cellular and metabolic processes in trees are expected to pave the way toward novel strategies based on the reorientation of growth traits and stress acclimation.

[*] Aim and scope:

This Special Issue aims to stimulate comprehensive research, presenting a collection of the latest fundamental discoveries in the field of genomic and genetic regulatory mechanisms in tree growth, tolerance, and immune defense to various stressors. Additionally, the novel demonstration of genome editing, genetic transformation, and the advances and application in forest tree improvement are of interest, as are omics study to identify candidate genes and families affecting growth traits, biomass quality, stress tolerance, etc., the development of high-efficiency transformation and genome editing systems for tree species, and the application of synthetic biology strategies to produce valuable metabolites in engineered plants. All types of submissions, including original research, high-quality reviews, methodologies, perspectives, and opinion articles in this field, are welcome.

Dr. Tao Su
Dr. Su Chen
Prof. Dr. Nan Liu
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. Forests 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 2600 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

  • genome
  • C and N metabolism
  • apoplast
  • stress adaptation
  • omics
  • tree

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Published Papers (5 papers)

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Research

20 pages, 6180 KiB  
Article
Genome-Wide Identification and Expression Analysis of Salt Tolerance-Associated WRKY Family Genes in Cyclocarya paliurus
by Zhengting Yang, Fayin He, Yin An, Nannan Zhang, Sixian Fan, Ming Tang and Kun Li
Forests 2023, 14(9), 1771; https://doi.org/10.3390/f14091771 - 31 Aug 2023
Cited by 3 | Viewed by 1126
Abstract
WRKY proteins are key transcription factors involved in a range of physiological processes and environmental adaptations. Yet, little is known about the role WRKY genes play in Cyclocarya paliurus (Batal.) Iljinskaja (C. paliurus) a significant medicinal plant belonging to [...] Read more.
WRKY proteins are key transcription factors involved in a range of physiological processes and environmental adaptations. Yet, little is known about the role WRKY genes play in Cyclocarya paliurus (Batal.) Iljinskaja (C. paliurus) a significant medicinal plant belonging to the Juglandaceae family. Leveraging the recently released whole-genome sequence of C. paliurus, we conducted an in-depth, genome-wide study on the expression of WRKY genes under environmental stresses. We identified 80 CpWRKY genes, classifying them into distinct groups and subgroups based on their structural and phylogenetic characteristics. Synteny analysis and phylogenetic comparison provided insights into the evolutionary traits of these genes. We further investigated the response of the WRKY gene family to salinity stress in combination with the following specific stressors: Methyl jasmonate (MeJA), sodium hydrosulfide (NaHS), and sodium nitroprusside (SNP), which induce the production of signaling molecules jasmonates (JA), hydrogen sulfide (H2S), and nitric oxide (NO), respectively. Our comprehensive analysis of CpWRKY gene expression patterns under various conditions revealed that combined treatments were more effective in inducing up-regulation of CpWRKY gene expression than individual treatments. Full article
(This article belongs to the Special Issue Genomics of Growth Traits and Stress Acclimation in Forest Trees)
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15 pages, 3313 KiB  
Article
Transcriptomic Response to Drought Stress in Populus davidiana Dode
by Meng Yang, Lili Wang, Xinyu Wang, Yijie Li and Haijiao Huang
Forests 2023, 14(7), 1465; https://doi.org/10.3390/f14071465 - 17 Jul 2023
Cited by 1 | Viewed by 1493
Abstract
Plants are often exposed to drought stress, and decreases in the soil water content can prevent plants from reaching their full genetic potential. Populus davidiana Dode belongs to the genus Populus, and it is a temperate deciduous tree that is cold and drought [...] Read more.
Plants are often exposed to drought stress, and decreases in the soil water content can prevent plants from reaching their full genetic potential. Populus davidiana Dode belongs to the genus Populus, and it is a temperate deciduous tree that is cold and drought tolerant. To investigate the mechanism of P. davidiana response to drought stress, transcriptome analysis was performed on drought and control treatments of P. davidiana. We identified 10230 differentially expressed genes (DEGs). Most DEGs were enriched in pathways related to transcriptional regulation and hormone signal transduction, ROS metabolism, lignin synthesis, and the sugar metabolism process in two contrasting groups. Compared with the control condition, soluble sugars, proline, and POD activity were all increased under drought stress. In addition, Na+, K+, and Ca2+ were all higher under drought stress than in the control. These results not only revealed the mechanism of tolerance to drought stress in P. davidiana, but also promoted the development and application of drought-tolerant genetic resources in P. davidiana. Full article
(This article belongs to the Special Issue Genomics of Growth Traits and Stress Acclimation in Forest Trees)
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17 pages, 3873 KiB  
Article
Identification of ApbHLH1 as a Partner Interacting with ApMYB1 to Promote Anthocyanin Biosynthesis during Autumnal Leaf Coloration in Acer palmatum
by Long Chen, Sujing Sun, Gengcheng Qiu and Jiading Yang
Forests 2023, 14(6), 1262; https://doi.org/10.3390/f14061262 - 19 Jun 2023
Viewed by 1327
Abstract
Anthocyanin biosynthesis determines the leaf color of Acer palmatum as a widely-planted landscape tree. Previously, ApMYB1 has been characterized as a positive regulator of anthocyanin biosynthesis. To further elucidate the mechanism of leaf coloration, the present study identified a basic helix-loop-helix (bHLH) transcription [...] Read more.
Anthocyanin biosynthesis determines the leaf color of Acer palmatum as a widely-planted landscape tree. Previously, ApMYB1 has been characterized as a positive regulator of anthocyanin biosynthesis. To further elucidate the mechanism of leaf coloration, the present study identified a basic helix-loop-helix (bHLH) transcription factor (ApbHLH1) through the phylogenetic analysis of 156 putative bHLH proteins in Acer palmatum and eight reference bHLHs which were known to be involved in the anthocyanin biosynthesis of selected plants. Protein structure comparison showed that ApbHLH1 has a conserved bHLH domain, and its N-terminal contains an MYB-interacting region. The expression of ApbHLH1 in leaves was found to not be correlated with anthocyanin contents either in green, semi-red leaves or during leaf autumnal senescence when anthocyanin content increased. ApbHLH1 expression in detached leaves was induced by exogenous senescence-promoting chemicals, including H2O2, SA, MeJA, ACC and ABA, with certain durations. In particular, either high light or low temperature induced ApbHLH1 expression significantly, and combination of high light and low temperatures seemed more effective in inducing ApbHLH1 expression. Luciferase complementation imaging assays confirmed the physical interaction between ApbHLH1 and ApMYB1, which could be abolished by either the truncating MYB-interacting region of ApbHLH1 or the deleting bHLH interacting domain of ApMYB1. The transient expression of ApbHLH1 could not induce anthocyanin production, while the co-expression of ApbHLH1 and ApMYB1 resulted in a higher accumulation of anthocyanins compared to the expression of ApMYB1 alone in tobacco leaves. Collectively, our results revealed that ApbHLH1 participated in leaf coloration through binding with ApMYB1 and enhancing the ApMYB1 function of promoting anthocyanin biosynthesis during leaf autumnal reddening in Acer palmatum. ApbHLH1 could have the potential for breeding color-leafed plants through co-transformation with ApMYB1. Full article
(This article belongs to the Special Issue Genomics of Growth Traits and Stress Acclimation in Forest Trees)
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15 pages, 1793 KiB  
Article
GWAS on the Attack by Aspen Borer Saperda calcarata on Black Cottonwood Trees Reveals a Response Mechanism Involving Secondary Metabolism and Independence of Tree Architecture
by Sebastián L. Sepúlveda, David B. Neale, Jason A. Holliday, Randi Famula, Oliver Fiehn, Brian J. Stanton and Fernando P. Guerra
Forests 2023, 14(6), 1129; https://doi.org/10.3390/f14061129 - 30 May 2023
Cited by 2 | Viewed by 1563
Abstract
Black cottonwood (Populus trichocarpa) is a species of economic interest and an outstanding study model. The aspen borer (Saperda calcarata) causes irreversible damage to poplars and other riparian species in North America. The insect can produce multiple effects ranging [...] Read more.
Black cottonwood (Populus trichocarpa) is a species of economic interest and an outstanding study model. The aspen borer (Saperda calcarata) causes irreversible damage to poplars and other riparian species in North America. The insect can produce multiple effects ranging from the presence of some galleries in the stem to tree death. Despite the ecological and commercial importance of this tree–insect interaction, the genetic mechanisms underlying the response of P. trichocarpa to S. calcarata are scarcely understood. In this study, a common garden trial of P. trichocarpa provenances, established in Davis, California, was assessed at the second year of growth, regarding the infestation of S. calcarata from a natural outbreak. A genome-wide association study (GWAS) was conducted using 629k of exonic SNPs to assess the relationship between genomic variation and insect attack. Tree architecture, in terms of stem number per plant, and the wood metabolome were also included. Insect attack was independent of the number of stems per tree. The performed GWAS identified three significantly associated SNP markers (q-value < 0.2) belonging to the same number of gene models, encoding proteins involved in signal transduction mechanisms and secondary metabolite production, including that of R-mandelonitrile lyase, Chromodomain-helicase-DNA-binding family protein, and Leucine-rich repeat protein. These results are aligned with the current knowledge of defensive pathways in plants and trees, helping to expand the understanding of the defensive response mechanisms of black cottonwood against wood borer insects. Full article
(This article belongs to the Special Issue Genomics of Growth Traits and Stress Acclimation in Forest Trees)
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14 pages, 10028 KiB  
Article
Genome-Wide Identification and Expression Analysis of the R2R3-MYB Gene Family in Rubber Trees
by Mingyang Liu, Hong Yang, Songle Fan, Bingbing Guo, Longjun Dai, Lifeng Wang and Meng Wang
Forests 2023, 14(4), 710; https://doi.org/10.3390/f14040710 - 30 Mar 2023
Cited by 1 | Viewed by 1940
Abstract
The plant MYB transcription factor family featured as highly conserved DNA-binding domains consisting of 1 to 4 imperfect repeats (R). Increasing evidence indicates that MYB genes participates in growth, differentiation, metabolism, and biotic and abiotic stress responses. However, the functions of MYB genes [...] Read more.
The plant MYB transcription factor family featured as highly conserved DNA-binding domains consisting of 1 to 4 imperfect repeats (R). Increasing evidence indicates that MYB genes participates in growth, differentiation, metabolism, and biotic and abiotic stress responses. However, the functions of MYB genes in the rubber tree remain to be deeply elucidated, especially R2R3-MYB gene family. In this study, molecular biology, bioinformatics, and qRT-PCR were used to identify and analyze HbR2R3-MYB gene family members in the rubber tree. A total of 132 members of the R2R3-MYB gene family were identified in the rubber tree based on genome-wide level. Most of the HbR2R3-MYBs were mapped to 17 rubber tree chromosomes except four genes. A phylogenetic analysis divided all the HbR2R3-MYBs into 20 subgroups with Arabidopsis thaliana. MEME analysis showed that the protein of HbR2R3-MYBs was characterized by 9 conserved motifs. Twenty-six representative R2R3 HbMYBs from different subgroups were selected for expression profiles analysis and the results revealed that the HbR2R3-MYBs members showed various expression patterns in different tissues, powdery mildew-infected and ethylene treatment, implying the diversity of their functions in rubber trees. These results provide fundamental knowledge for further studying the response of the HbR2R3-MYB family to stress and regulation latex flow in rubber tree. Full article
(This article belongs to the Special Issue Genomics of Growth Traits and Stress Acclimation in Forest Trees)
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