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Forests
Special Issues
Latest Progress in Research on Forest Tree Genomics
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Latest Progress in Research on Forest Tree Genomics

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

Deadline for manuscript submissions: 28 February 2025 | Viewed by 4291

Special Issue Editors

Dr. Meng Li

E-Mail Website
Guest Editor
College of Life Science and Technology, Central South University of Forestry and Technology, Changsha 410004, China
Interests: specific organ development of woody plants; organ abortion and abscission
Dr. Hao Chen

E-Mail Website
Guest Editor
College of Forestry, wildlife, and environment, Auburn University, Auburn, AL 36849, USA
Interests: transcriptional and translational regulation; genetic and genomic basis of wood formation; tissue culture and genetic engineering
Special Issues, Collections and Topics in MDPI journals
Dr. Ting Wang

E-Mail Website
Guest Editor
College of Life Science, Beijing Normal University, Beijing 100875, China
Interests: plant cell wall synthesis; plant development

Special Issue Information

Dear Colleagues,

Forests are the main body of terrestrial ecosystems, which provide the basic material foundation and living environment for humans. Global climate change and sustained population growth are increasingly threatening the stability of forest ecosystems. Thus, there is a dire need to improve forest productivity, adaptability, resilience and sustainability to challenge this situation. Forest genomics is believed to play a crucial role in this process. As with agriculture, genomics-based methods have the potential to significantly facilitate genetic breeding in tree species. The productivity and adaptability of woody plants can be improved by modifying one or more genes in their genome.

Forest genomic has identified a number of effective genetic markers and genes in molecular breeding, especially the key genes regulating forest-specific traits. Increasing information concerning forest genomics can answer many unique and interesting biological questions about tree species, including their unusual reproductive characteristics, woody and perennial growth habits, and their response mechanisms to abiotic and biotic stresses. Moreover, forest tree genomics will provide new insights into organ development, carbon sink, longevity and population genetics, which is critical for developing the pertinent strategies to protect and utilize forest resources.

In this Special Issue, we aim to provide an overview of the latest progress in research on forest tree genomics from around the world, which will highlight the important theoretical and practical significance of genomics and molecular biology in forestry.

Potential topics include, but are not limited to, the following:

  • Wood formation;
  • Genetic improvement in forest trees mediated via gene editing technique;
  • Genome, transcriptome, metabolome and proteome analysis in tree species;
  • Establishment of genetic transformation and regeneration system of forest trees;
  • Molecular marker-assisted breeding of tree species.

Dr. Meng Li
Dr. Hao Chen
Dr. Ting Wang
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

  • tree
  • genomics
  • wood formation
  • transcriptome
  • forest ecology
  • genetic diversity of tree species
  • molecular markers of tree species

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

Published Papers (4 papers)

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Research

17 pages, 3964 KiB  
Article
Characterization of the Expansin Gene Promoters in Populus trichocarpa
by Junkang Zhang, Xiaoyu Li, Lei Wang, Longfeng Gong, Mengtian Li and Jichen Xu
Forests 2024, 15(9), 1485; https://doi.org/10.3390/f15091485 - 24 Aug 2024
Viewed by 595
Abstract
The expansin genes are commonly expressed in plant cells, and the encoded proteins influence plant growth and stress resistance by loosening the structure and increasing the flexibility of the cell wall. The objective of this study was to characterize expansin gene promoters in [...] Read more.
The expansin genes are commonly expressed in plant cells, and the encoded proteins influence plant growth and stress resistance by loosening the structure and increasing the flexibility of the cell wall. The objective of this study was to characterize expansin gene promoters in Populus trichocarpa to clarify the regulatory mechanisms underlying gene expression and evolution. Sequence alignments revealed that the similarity among 36 poplar expansin genes was greater for the coding sequences than for the promoter sequences, which suggested these promoter sequences evolved asynchronously. The bases flanking the start codon exhibited a usage bias, with sites +3, +4, and +5 biased toward GC, whereas the other sites were biased toward AT. The flanking sites were significantly correlated with gene expression, especially sites −10 and −17, in which C and G are the bases positively associated with gene expression. A total of 435 regulatory elements (61 types) were identified on the promoters of the poplar expansin genes; Skn-1 was the most common element in 23 promoters. Some expansin genes had more regulatory elements on their promoters (e.g., PtrEXPA4, PtrEXPA3, PtrEXPB3, and PtrEXPB1), whereas some others had less (e.g., PtrEXLA2, PtrEXLB1, and PtrEXPA23). Furthermore, 26 types of elements were involved in expansin gene expression, 25 of which positively affected expression in all analyzed samples. The exception was the endosperm expression-related element Skn-1, which negatively regulated expression in four tissues or treatments. Expression analysis showed that the expansin genes in Populus trichocarpa performed much differently under regular and abiotic stress conditions, which well matched the diversity of their promoter sequences. The results show that expansin genes play an important role in plant growth and development and stress resistance through expression adjustment. Full article
(This article belongs to the Special Issue Latest Progress in Research on Forest Tree Genomics)
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17 pages, 4725 KiB  
Article
Genome-Wide Profiling of the Genes Related to Leaf Discoloration in Zelkova schneideriana
by Yuhan Sun, Longfeng Gong, Xiao Liu, Jiayu Hu, Xiaoxiong Lu and Jichen Xu
Forests 2024, 15(7), 1146; https://doi.org/10.3390/f15071146 - 1 Jul 2024
Viewed by 815
Abstract
Zelkova schneideriana is a landscaping flowering and deciduous plant whose leaf color changes in the fall season. In the discoloration period, the anthocyanin content in the red lines of Z. schneideriana is 3.52 times greater than that in the green lines, whereas the [...] Read more.
Zelkova schneideriana is a landscaping flowering and deciduous plant whose leaf color changes in the fall season. In the discoloration period, the anthocyanin content in the red lines of Z. schneideriana is 3.52 times greater than that in the green lines, whereas the chlorophyll content in the red lines is 20.10 times lower. To understand the molecular mechanism of the leaf discoloration, transcriptome sequencing was performed. A total of 3965 differentially expressed genes (DEGs) were identified between the red and green lines in the discoloration period. These DEGs were mainly involved in plant–pathogen interactions, the MAPK signaling pathway, plant hormone signal transduction, flavonoid biosynthesis, and anthocyanin biosynthesis. Among them, three downregulated genes were involved in chlorophyll synthesis; these genes exhibited a maximum decrease in the red lines that was 11.13 times greater than their expression in the green lines. In contrast, 33 upregulated genes were involved in anthocyanin biosynthesis; they exhibited a maximum increase in the red lines 4645.33 times greater than their expression in the green lines. The results of an association analysis revealed that four transcription factors, including ZeBHLH42, ZeMYB123, ZeMYB113, and ZeWRKY44, positively regulated the anthocyanin synthesis genes. These results explained the mechanism underlying the discoloration of Zelkova leaves and provided a basis for molecular breeding programs of colorful plants. Full article
(This article belongs to the Special Issue Latest Progress in Research on Forest Tree Genomics)
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17 pages, 7178 KiB  
Article
CsAFS2 Gene from the Tea Plant Intercropped with Chinese Chestnut Plays an Important Role in Insect Resistance and Cold Resistance
by Jianzhao Wang, Mei Dao, Ziyun Yang, Yan Bai, Ying Qin and Tian Wu
Forests 2024, 15(2), 380; https://doi.org/10.3390/f15020380 - 18 Feb 2024
Viewed by 1207
Abstract
α-Farnesene, a crucial secondary metabolite in sesquiterpenes, is crucial for plant biotic and abiotic stress resistance. In this study, we screened an AFS gene from transcriptome data of tea plants (Camellia sinensis) intercropped with Chinese chestnut (Castanea mollissima), resulting [...] Read more.
α-Farnesene, a crucial secondary metabolite in sesquiterpenes, is crucial for plant biotic and abiotic stress resistance. In this study, we screened an AFS gene from transcriptome data of tea plants (Camellia sinensis) intercropped with Chinese chestnut (Castanea mollissima), resulting in the cloning of CsAFS2. CsAFS2 expression increased following treatment with MJ (Methyl jasmonate), SA (Salicylic acid), GA3 (Gibberellin A3), and various plant growth regulators, as well as under high-salt, drought, and low-temperature conditions. The heterologous genetic transformation of tobacco with CsAFS2 led to an enhanced resistance to low-temperature stress and aphid feeding, evident from elevated levels of osmotic regulatory substances, increased protective enzyme activity, and the upregulation of cold and insect resistance-related genes. Trichomes, crucial in cold and insect resistance, exhibited significantly greater length and density in transgenic tobacco as compared to control plants. These results confirm the vital role of CsAFS2 in enhancing cold and insect resistance, providing comprehensive insights into stress regulation mechanisms in tea plants and advancing stress-resistant tea plant breeding. Full article
(This article belongs to the Special Issue Latest Progress in Research on Forest Tree Genomics)
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11 pages, 5385 KiB  
Communication
A Type A Response Regulator Is Involved in Growth in Salix Matsudana Koidz
by Peng Yin, Lei Wang, Junkang Zhang, Xue Wang, Di Wu and Jichen Xu
Forests 2024, 15(1), 4; https://doi.org/10.3390/f15010004 - 19 Dec 2023
Viewed by 1069
Abstract
The cytokinin signaling pathway is important for plant growth and development. To understand the regulatory process, a type A response regulator, SmRR5, in Salix matsudana Koidz., was characterized and functionally analyzed. Gene expression tests showed that SmRR5 was distinctly higher in the [...] Read more.
The cytokinin signaling pathway is important for plant growth and development. To understand the regulatory process, a type A response regulator, SmRR5, in Salix matsudana Koidz., was characterized and functionally analyzed. Gene expression tests showed that SmRR5 was distinctly higher in the leaves and roots of the fast-growing S. matsudana variety 9901 than in those of the slow-growing variety Yanjing (YJ). The transcript abundance was highest in the meristem zone (MEZ), followed by the elongation zone (EZ) and maturation zone (MAZ) in 9901 roots, but it was identically low in YJ roots. Overexpression of SmRR5 in tobacco plants significantly improved plant height, maximum root length (MRL), lateral root number (LRN), fresh weight (FW), dry weight (DW), and flowering time compared with wild-type plants. Transcript profiling revealed that multiple genes associated with flowering (SWEET1, FPF1, and COL12), plant growth (YUCCA8, PIN5, and ARF9a), and adventitious root (AR) formation (Hox3, MYC2, and AGL46) were highly expressed in the overexpression of leaves and roots. Thus, SmRR5 effectively facilitated plant growth and development. Full article
(This article belongs to the Special Issue Latest Progress in Research on Forest Tree Genomics)
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