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Forests
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Advances in Ecological Genomics of Forest Trees
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Advances in Ecological Genomics of 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 9736

Special Issue Editors

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. Xi-Yang Zhao

E-Mail Website
Guest Editor
State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China
Interests: forestry; forestry research; forest ecology; chlorophyll fluorescence; cloning salt stress; plant salt-tolerance; transgenics; chlorophyll
Dr. Andrea Coppi

E-Mail Website
Guest Editor
Department of Biology, University of Florence, Via la Pira 4 – 50121, Florence, Italy
Interests: molecular phylogeny; community phylogenetics; population genetics; plant functional traits; ecosystem services
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Filippos A. Aravanopoulos

E-Mail Website
Guest Editor
Faculty of Agriculture, Forestry & Natural Environment, Aristotle University of Thessaloniki, P.O. Box 278, University Campus, Thessaloniki 54124, Greece
Interests: forest genetics; conservation of genetic resources-genetic monitoring; population genetics; epigenetics-epigenomics; molecular breeding-QTL mapping-MAS; coevolution; fluctuating asymmetry & allometry
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Forest trees form unparalleled biomes in terms of their combined ecological, economic and social importance. Due to their wide distribution, largely random mating systems and large population sizes, most tree species present extensive genetic variation within and between populations. Although the genomic resources of various forest trees have proliferated, forest trees are still a difficult genetic system to study in many respects. For example, multigenerational evolutionary studies are often not possible due to their long generation times, their underlying biological systems are vastly different (e.g. conifers vs. angiosperms), but the availability of genomics lowers the barrier to high-quality ecological and evolutionary genomic studies in less-studied forest tree taxa. With the development and improvement of even more genomic technologies, progressively more studies on the ecological genomics of non-model organisms will provide an important theoretical and practical basis for the development of landscape and molecular ecology. For this Special Issue, we welcome research contributions from all areas, including experimental studies, genomic research methods and models, and critical reviews of pertinent literature to advance the development of forest tree ecological genomics.

Dr. Su Chen
Prof. Dr. Xi-Yang Zhao
Dr. Andrea Coppi
Prof. Dr. Filippos Aravanopoulos
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
  • ecological genomics
  • forestry genomics

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Published Papers (5 papers)

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17 pages, 4921 KiB  
Article
Genome-Wide Identification of miR169 Family in Response to ABA and Salt Stress in Poplar
by Ruiqi Wang, Yuting Wang, Yongmei Gu, Pingyu Yan, Wenna Zhao and Tingbo Jiang
Forests 2023, 14(5), 961; https://doi.org/10.3390/f14050961 - 6 May 2023
Cited by 5 | Viewed by 1836
Abstract
The miR169 family is one of the largest families of known miRNAs, which performs important functions in plant growth, development, and responses to biotic/abiotic stresses. However, its functions in response to abiotic stresses are still unclear in poplar. In present study, a total [...] Read more.
The miR169 family is one of the largest families of known miRNAs, which performs important functions in plant growth, development, and responses to biotic/abiotic stresses. However, its functions in response to abiotic stresses are still unclear in poplar. In present study, a total of 33 precursor MIR169s were identified from poplar and divided into 3 groups by evolutionary analysis and multiple sequence alignment, with the members in same group sharing similar motifs. Collinearity analysis revealed miR169s in other species that are homologous to poplar miRNAs. Cis-acting elements predication showed that miR169s may respond to ABA (Abscisic acid) and salt stress, which was verified by qRT-PCR. In addition, 12 pairs of miR169/target gene modules were identified by degradome sequencing and most of these modules responded to ABA and salt stress. Specifically, a part of miRNAs showed opposite expression trends with their targets at a certain period, demonstrating a repressive effect on the target genes. All the results suggest that miR169s perform important functions in response to abiotic stresses in poplar. Full article
(This article belongs to the Special Issue Advances in Ecological Genomics of Forest Trees)
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18 pages, 1843 KiB  
Article
De Novo SNP Discovery and Genotyping of Masson Pine (Pinus massoniana Lamb.) via Genotyping-by-Sequencing
by Peng-Le Li, Mo-Hua Yang, Xiao-Long Jiang, Huan Xiong, Hui-Liang Duan, Feng-Lan Zou, Qian-Yu Xu, Wei Wang, Yong-Hui Hong and Neng-Qing Lin
Forests 2023, 14(2), 387; https://doi.org/10.3390/f14020387 - 14 Feb 2023
Cited by 1 | Viewed by 1863
Abstract
Masson pine (Pinus massoniana Lamb.) is an important tree species in China, but its genomic research has been hindered due to a large genome size. Genotyping-by-sequencing (GBS) has been a powerful approach to revolutionize the field of genomic research by facilitating the [...] Read more.
Masson pine (Pinus massoniana Lamb.) is an important tree species in China, but its genomic research has been hindered due to a large genome size. Genotyping-by-sequencing (GBS) has been a powerful approach to revolutionize the field of genomic research by facilitating the discovery of thousands of single nucleotide polymorphisms (SNPs) and genotyping in non-model organisms, at relatively low cost. Here, we performed de novo SNP discovery and genotyping in 299 trees via the genotyping-by-sequencing (GBS) approach. The effort produced 9.33 × 109 sequence reads, 265,525 SNP-associated contigs, and 6,739,240 raw SNPs. Further filtering and validation of the SNP-associated contigs for reliable SNPs were performed using blasting against the Pinus tabuliformis reference genome, functional annotation, technical replicates, and custom parameter settings for the optimization. The 159,372 SNP-associated contigs were aligned and validated for SNP prediction, in which 60,038 contigs were searched with hits in the NCBI nr database. We further improved the SNP discovery and genotyping with multiple technical replicates and custom parameter settings filtering. It was found that the use of blasting, annotation, technical replicates, and specific parameter settings removed many unreliable SNPs and identified 20,055 more precise and reliable SNPs from the 10,712 filtered contigs. We further demonstrated the informativeness of the identified SNPs in the inference of some genetic diversity and structure. These findings should be useful to stimulate genomic research and genomics-assisted breeding of Masson pine. Full article
(This article belongs to the Special Issue Advances in Ecological Genomics of Forest Trees)
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12 pages, 4527 KiB  
Article
Response and Regulatory Network Analysis of Roots and Stems to Abiotic Stress in Populus trichocarpa
by Ran Tao, Yaqiu Liu and Weipeng Jing
Forests 2022, 13(8), 1300; https://doi.org/10.3390/f13081300 - 16 Aug 2022
Cited by 3 | Viewed by 1545
Abstract
Abiotic stress is one of the environmental conditions that effects plant survival and growth. As a vital model plant and papermaking raw material, it is very important to identify the differentially expressed genes of Populus trichocarpa Torr. & A.Gray ex Hook under abiotic [...] Read more.
Abiotic stress is one of the environmental conditions that effects plant survival and growth. As a vital model plant and papermaking raw material, it is very important to identify the differentially expressed genes of Populus trichocarpa Torr. & A.Gray ex Hook under abiotic stress in order to cultivate stress-tolerant plants. We analyzed the whole transcription spectrum and potential differentially expressed genes of 54 groups of roots and stem-xylem sequencing sample data under cold, drought, heat and salt stress for different durations. Gene Ontology (GO) enrichment analysis showed that molecular function played a stronger role in stems’ response to abiotic stress, and genes in roots could barely respond to both cold stress and heat stress. Degree and betweenness centrality were used to identify transcription factors. It was considered that intermediate centrality is more suitable to determine whether the transcription factor is a hub gene. DNA binding was the biggest enrichment, while transcription factors responded to the abiotic stress. The multipronged approach identified in the roots and stems provides a genetic basis for resistance and more targeted genetic improvement of Populus trichocarpa. The comparison of two centralities can more effectively analyze the importance of complex gene network nodes in plants under corresponding abiotic stresses. Full article
(This article belongs to the Special Issue Advances in Ecological Genomics of Forest Trees)
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10 pages, 1293 KiB  
Brief Report
Conservation Genetics of the Only Honeysuckle Azalea (Rhododendron luteum) Population Present in Greece
by F. A. Aravanopoulos, N. Tourvas, S. Fotsinos, C. Michailidou and A. Antoniadi
Forests 2024, 15(1), 5; https://doi.org/10.3390/f15010005 - 19 Dec 2023
Viewed by 1180
Abstract
Honeysuckle azalea (Rhododendron luteum) has only a single population occurrence in Greece, on Lesvos Island of the north-eastern Aegean Sea. The genetic diversity of this population was studied in a population of n = 37 individuals randomly sampled in a transect [...] Read more.
Honeysuckle azalea (Rhododendron luteum) has only a single population occurrence in Greece, on Lesvos Island of the north-eastern Aegean Sea. The genetic diversity of this population was studied in a population of n = 37 individuals randomly sampled in a transect spanning between the highest and lowest natural altitudinal distribution limits in Mt. Ordymnos, SW Lesvos. A modified DNA extraction and isolation protocol was used to overcome problems of DNA quality due to secondary metabolite activity. Genetic variation was investigated based on molecular Inter Simple Sequence Repeat (ISSR) markers. Results showed the presence of a sufficient amount of genetic diversity for the maintenance of adaptive potential. Genetic diversity was lower but comparable to that of other Rhododendron species sampled from the centre of their natural distribution, despite the relatively small population size, negative anthropogenic pressure and population isolation due to the island environment. Some structuring of genetic diversity was indicated based on a PCoA analysis and the genetic distance dendrogram, while spatial autocorrelation was highly significant. Results point towards the need to assign a protection status to the whole area of the species’ natural distribution on Lesvos Island. Moreover, it is proposed that an in situ Gene Conservation Unit (GCU) be established in the core of this population in Lesvos as part of the Network of the European Forest Genetic Resources Programme, while the establishment of ex situ conservation is also advised. Full article
(This article belongs to the Special Issue Advances in Ecological Genomics of Forest Trees)
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17 pages, 5492 KiB  
Brief Report
WGCNA Reveals Genes Associated with Lignification in the Secondary Stages of Wood Formation
by Ruiqi Wang, Miaomiao Xie, Wenna Zhao, Pingyu Yan, Yuting Wang, Yongmei Gu, Tingbo Jiang and Guanzheng Qu
Forests 2023, 14(1), 99; https://doi.org/10.3390/f14010099 - 4 Jan 2023
Cited by 3 | Viewed by 2164
Abstract
The lignified tissue in the secondary stem is the main source of wood. In this study, we applied RNA-Seq analysis to the poplar stems in three developmental stages, including primary stem (PS), transitional stem (TS), and secondary stem (SS), to identify a total [...] Read more.
The lignified tissue in the secondary stem is the main source of wood. In this study, we applied RNA-Seq analysis to the poplar stems in three developmental stages, including primary stem (PS), transitional stem (TS), and secondary stem (SS), to identify a total of 2028 genes that were highly expressed in the SS. Gene annotation indicated that the functions of these genes are mainly involved in cell wall biosynthesis, xylem development, and programmed cell death (PCD) processes. Subsequently, we explored the expression pattern of these genes at various developmental stages in the horizontal direction of the wood by ASPwood. The expression of these genes was modularized and correlated with the percentage of lignified xylem, using weighted gene co-expression network analysis (WGCNA). Among the genes, as many as 690 were identified as directly associated with lignification in the SS. In addition, the gene promoter cis-elements and protein interactions were predicted by PlantRegMap and STRING, respectively. The results were introduced into a co-expression network to confirm their relationship. We eventually found 54 TFs dominating this network, of which ADOF1, ATMYB3, AtbZIP44 (Potri.005G231300), ANAC043, ATWRKY40, ATEBP (Potri.010G006800), ARF5, anac075, RAP2.1, ARF16, AT- HSFB3, Potri.014G050000 (from WRKY family), HAT22, AT-HSFB2B, and AtWRKY20 had extremely high connectivity, which may play an important role in the lignification of wood formation at secondary stages. Full article
(This article belongs to the Special Issue Advances in Ecological Genomics of Forest Trees)
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