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Genomic Perspective on Forest Genetics and Phytopathobiomes
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Genomic Perspective on Forest Genetics and Phytopathobiomes

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: closed (20 February 2025) | Viewed by 6634

Special Issue Editor

Dr. Giang Thi Ha Vu

E-Mail Website
Guest Editor
Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Büsgenweg 2, D-37077 Göttingen, Germany
Interests: population genetics; plant genome evolution; epigenetics; DNA damage repair; phytopathology
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

In the face of evolving environmental challenges, understanding the genetic foundations of forest health becomes crucial. Genomic approaches, by accelerating our comprehension of the genetic and evolutionary underpinnings of nonmodel tree species, are indispensable in addressing challenges faced by forest ecosystems. They play a pivotal role in informing strategies to enhance adaptive capacities, improve conservation decisions, and advance breeding programs for resilient trees.

This Special Issue, entitled ‘Genomic Perspective on Forest Genetics and Phytopathobiomes’, aims to explore the complex interplay of genetic factors shaping the resilience of forests, with a particular focus on genomics. We invite submissions covering various topics, including investigating genetic variations in different tree species and their adaptive responses to changing environments, understanding interactions between tree hosts and pathogens, and presenting cutting-edge genomic tools for conservation to facilitate sustainable forest management. We especially encourage contributions that illuminate the genetic aspects of emerging diseases, offering insights into the adaptive capacity of forests facing climate change-induced challenges.

Dr. Giang Thi Ha Vu
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • genomic diversity
  • adaptive responses
  • genetic variation
  • forest pathology
  • environmental stress
  • microbiome
  • plant–pathogen interactions

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Published Papers (5 papers)

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Research

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15 pages, 5911 KiB  
Article
Genome-Wide Identification and Expression Analysis of GASA Genes in Hevea brasiliensis Reveals Their Involvement in Response to Cold Stress
by Yuying Cong, Yanshi Hu, Zhi Deng, Wenguan Wu, Tingkai Wu, Yanhong Zhao and Zewei An
Int. J. Mol. Sci. 2025, 26(7), 3454; https://doi.org/10.3390/ijms26073454 - 7 Apr 2025
Viewed by 384
Abstract
The Gibberellic Acid Stimulated in Arabidopsis (GASA) gene family is regulated by gibberellins and plays a crucial role in regulating plant growth and development. Based on rubber tree genome data, 18 HbGASA genes, designated HbGASA1 to HbGASA18, were identified in Hevea brasiliensis [...] Read more.
The Gibberellic Acid Stimulated in Arabidopsis (GASA) gene family is regulated by gibberellins and plays a crucial role in regulating plant growth and development. Based on rubber tree genome data, 18 HbGASA genes, designated HbGASA1 to HbGASA18, were identified in Hevea brasiliensis. Comprehensive bioinformatics analyses were performed to characterize gene structures, chromosomal distributions, syntenic relationships, protein architectures, phylogenetic evolution, and expression profiles. The expression patterns of HbGASA genes under low-temperature stress were further validated by quantitative real-time polymerase chain reactions (qRT-PCR). The results demonstrated that the 18 HbGASA genes were unevenly distributed across 10 chromosomes. The encoded proteins ranged from 88 to 253 amino acids in length, and the number of exons varied from 2 to 4. Phylogenetic analysis clustered these genes into three distinct clades. Conserved motif analysis identified 10 conserved motifs, with Motif 1 and Motif 2 being highly conserved across all members. Promoter analysis revealed multiple hormone-responsive and stress-related regulatory cis-acting elements. Transcripts of the 18 HbGASA genes were detected in various tissues, and significant differences were observed in their expression levels. Under cold stress, qRT-PCR results showed that multiple HbGASA genes were significantly up-regulated. This study provides valuable insights into the structure, evolution, and functional diversification of GASA genes in the important tropical crop, H. brasiliensis. Full article
(This article belongs to the Special Issue Genomic Perspective on Forest Genetics and Phytopathobiomes)
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16 pages, 2853 KiB  
Article
Monoclonality and Low Genetic Diversity in Vanilla shenzhenica: Highlighting Urgent Need for Genetic Preservation of China’s Only Endangered Vanilla
by Li Xiao, Ai-Qun Hu, Mei-Na Wang, Zhuo Cheng, Kuan-Bo Chi, Chun-Lin Long and Jin-Gang Liu
Int. J. Mol. Sci. 2025, 26(7), 3451; https://doi.org/10.3390/ijms26073451 - 7 Apr 2025
Viewed by 387
Abstract
Long-term clonality has profound consequences for genetic structure despite offering an alternative means of reproductive assurance under unfavorable conditions for sexual reproduction. Vanilla shenzhenica Z. J. Liu & S. C. Chen (Orchidaceae), the only endangered Vanilla species in China, exhibits a clear tendency [...] Read more.
Long-term clonality has profound consequences for genetic structure despite offering an alternative means of reproductive assurance under unfavorable conditions for sexual reproduction. Vanilla shenzhenica Z. J. Liu & S. C. Chen (Orchidaceae), the only endangered Vanilla species in China, exhibits a clear tendency towards asexual propagation, as evidenced by its small, fragmented wild populations. To develop effective conservation strategies for this species, it is essential to assess the extent of clonality and evaluate genetic diversity both within and among populations. In this study, we sampled 43 individuals from cultivated and wild populations of V. shenzhenica and analyzed their phylogenetic relationships, genetic structure, and diversity based on single-nucleotide polymorphisms (SNPs). Our results indicate that all the studied wild populations are predominantly sustained by vegetative growth, each forming a monoclonal patch with a single genotype. The overall genetic diversity within V. shenzhenica is low likely due to a combination of factors, including clonality, reduced effective population size, and environmental disturbances. These findings underscore the urgent need for the conservation management of this species. Conservation plans should prioritize ex situ conservation efforts, focusing on promoting assisted sexual reproduction to produce viable seeds and offspring that combine diverse genotypes from different populations. This study provides valuable insights in relation to effective conservation planning for endangered clonal species. Full article
(This article belongs to the Special Issue Genomic Perspective on Forest Genetics and Phytopathobiomes)
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11 pages, 2756 KiB  
Article
Identification and Transcriptome Analysis of Bursaphelenchus xylophilus with Excellent Low Temperature Resistance
by Yue Zhang, Ruiwen Zhao, Tingting Jing, Sixi Lin and Xiaolei Ding
Int. J. Mol. Sci. 2024, 25(24), 13732; https://doi.org/10.3390/ijms252413732 - 23 Dec 2024
Cited by 1 | Viewed by 656
Abstract
Bursaphelenchus xylophilus is one of the most destructive quarantine pests, causing irreversible damage to pine trees. However, the unexpected identification of pine wilt disease in Northern China indicates that Bursaphelenchus xylophilus can survive under low temperatures. In this study, we analyzed the reproductivity [...] Read more.
Bursaphelenchus xylophilus is one of the most destructive quarantine pests, causing irreversible damage to pine trees. However, the unexpected identification of pine wilt disease in Northern China indicates that Bursaphelenchus xylophilus can survive under low temperatures. In this study, we analyzed the reproductivity variations among 18 different isolates, and SC13 was identified to have excellent low temperature resistance. Subsequent molecular analysis of SC13 indicated its distinct gene expression under low temperatures. The epidermal growth factor, nematode cuticle collagen and G-protein-coupled receptor genes with environmental adaptation functions were demonstrated to be differentially expressed under low temperatures. Meanwhile, morphological observations also indicated that SC13 contained significantly more lipid drops in low-temperature treatments. Generally, the identification of representative Bursaphelenchus xylophilus isolates will facilitate relevant studies in the future, and the discovery of the gene expression and morphological changes of Bursaphelenchus xylophilus under low temperatures could expand the current understanding of the environmental adaption abilities of such invasive nematodes. Full article
(This article belongs to the Special Issue Genomic Perspective on Forest Genetics and Phytopathobiomes)
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21 pages, 4693 KiB  
Article
Study of the Genetic Mechanisms of Siberian Stone Pine (Pinus sibirica Du Tour) Adaptation to the Climatic and Pest Outbreak Stresses Using Dendrogenomic Approach
by Serafima V. Novikova, Natalia V. Oreshkova, Vadim V. Sharov, Dmitry A. Kuzmin, Denis A. Demidko, Elvina M. Bisirova, Dina F. Zhirnova, Liliana V. Belokopytova, Elena A. Babushkina and Konstantin V. Krutovsky
Int. J. Mol. Sci. 2024, 25(21), 11767; https://doi.org/10.3390/ijms252111767 - 1 Nov 2024
Viewed by 1446
Abstract
A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate [...] Read more.
A joint analysis of dendrochronological and genomic data was performed to identify genetic mechanisms of adaptation and assess the adaptive genetic potential of Siberian stone pine (Pinus sibirica Du Tour) populations. The data obtained are necessary for predicting the effect of climate change and mitigating its negative consequences. Presented are the results of an association analysis of the variation of 84,853 genetic markers (single nucleotide polymorphisms—SNPs) obtained by double digest restriction-site associated DNA sequencing (ddRADseq) and 110 individual phenotypic traits, including dendrophenotypes based on the dynamics of tree-ring widths (TRWs) of 234 individual trees in six natural populations of Siberian stone pine, which have a history of extreme climatic stresses (e.g., droughts) and outbreaks of defoliators (e.g., pine sawfly [Neodiprion sertifer Geoff.]). The genetic structure of studied populations was relatively weak; samples are poorly differentiated and belong to genetically similar populations. Genotype–dendrophenotype associations were analyzed using three different approaches and corresponding models: General Linear Model (GLM), Bayesian Sparse Linear Mixed Model (BSLMM), and Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK), respectively. Thirty SNPs were detected by at least two different approaches, and two SNPs by all three. In addition, three SNPs associated with mean values of recovery dendrophenotype (Rc) averaged across multiple years of climatic stresses were also found by all three methods. The sequences containing these SNPs were annotated using genome annotation of a very closely related species, whitebark pine (P. albicaulis Engelm.). We found that most of the SNPs with supposedly adaptive variation were located in intergenic regions. Three dendrophenotype-associated SNPs were located within the 10 Kbp regions and one in the intron of the genes encoding proteins that play a crucial role in ensuring the integrity of the plant’s genetic information, particularly under environmental stress conditions that can induce DNA damage. In addition, we found a correlation of individual heterozygosity with some dendrophenotypes. Heterosis was observed in most of these statistically significant cases; signs of homeostasis were also detected. Although most of the identified SNPs were not assigned to a particular gene, their high polymorphism and association with adaptive traits likely indicate high adaptive potential that can facilitate adaptation of Siberian stone pine populations to the climatic stresses and climate change. Full article
(This article belongs to the Special Issue Genomic Perspective on Forest Genetics and Phytopathobiomes)
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Review

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25 pages, 1356 KiB  
Review
Applications of CRISPR Technologies in Forestry and Molecular Wood Biotechnology
by Hieu Xuan Cao, David Michels, Giang Thi Ha Vu and Oliver Gailing
Int. J. Mol. Sci. 2024, 25(21), 11792; https://doi.org/10.3390/ijms252111792 - 2 Nov 2024
Viewed by 2976
Abstract
Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer [...] Read more.
Forests worldwide are under increasing pressure from climate change and emerging diseases, threatening their vital ecological and economic roles. Traditional breeding approaches, while valuable, are inherently slow and limited by the long generation times and existing genetic variation of trees. CRISPR technologies offer a transformative solution, enabling precise and efficient genome editing to accelerate the development of climate-resilient and productive forests. This review provides a comprehensive overview of CRISPR applications in forestry, exploring its potential for enhancing disease resistance, improving abiotic stress tolerance, modifying wood properties, and accelerating growth. We discuss the mechanisms and applications of various CRISPR systems, including base editing, prime editing, and multiplexing strategies. Additionally, we highlight recent advances in overcoming key challenges such as reagent delivery and plant regeneration, which are crucial for successful implementation of CRISPR in trees. We also delve into the potential and ethical considerations of using CRISPR gene drive for population-level genetic alterations, as well as the importance of genetic containment strategies for mitigating risks. This review emphasizes the need for continued research, technological advancements, extensive long-term field trials, public engagement, and responsible innovation to fully harness the power of CRISPR for shaping a sustainable future for forests. Full article
(This article belongs to the Special Issue Genomic Perspective on Forest Genetics and Phytopathobiomes)
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