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Forests
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Epigenetic Variation: A Component of the Woody Plant Adaptation
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Epigenetic Variation: A Component of the Woody Plant Adaptation

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

Deadline for manuscript submissions: closed (9 September 2022) | Viewed by 6839

Special Issue Editors

Dr. María-Teresa Cervera

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Guest Editor
Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
Interests: forest trees; woody species; genomics; epigenetics; adaptation; natural variability; gene expression and regulation; organogenesis; biomass production; growth regulators
Special Issues, Collections and Topics in MDPI journals
Prof. Dr. Carmen Díaz-Sala

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Guest Editor
Department of Life Sciences, University of Alcalá, 28805 Alcalá de Henares, Madrid, Sapin
Interests: adventitious root formation; conifers; maturation; rooting competence; developmental reprogramming; conifer functional genomics; epigenetics/epigenomics
Special Issues, Collections and Topics in MDPI journals
Dr. María Ángeles Guevara

E-Mail Website
Guest Editor
Department of Forest Ecology and Genetics, INIA-CIFOR, Madrid, Spain
Interests: forest trees; woody species; genomics; epigenetics; adaptation; natural variability; gene expression and regulation; organogenesis; biomass production; growth regulators

Special Issue Information

Dear Colleagues,

Epigenetics refers to all molecular mechanisms that modify genome structure and/or activity without altering the DNA sequence. These changes may be heritable or non-heritable and result from chemical modifications such as DNA methylation, histone modifications, chromatin remodeling as well as other enzyme-driven changes (chromatin-modifying enzymes, signaling kinases). Non-coding RNA (ncRNA) molecules are also involved in regulating transcription at pre-transcriptional, transcriptional, and post-transcriptional levels.

In the last decades, a number of studies on epigenetic variation in plant species have documented environmentally driven effects on epigenetic variation which contribute to modulating stress response and plant growth plasticity. This study is particularly relevant as it showcases the potential role that epigenetic mechanisms may play in modulating rapid adaptive responses in long-lived woody species amidst increasingly changing environments.

This Special Issue “Epigenetic Variation: A Component of the Woody Plant Adaptation” will integrate original research and reviews related to all these aspects of woody plant epigenetics.

Dr. María-Teresa Cervera
Prof. Dr. Carmen Díaz-Sala
Dr. María Ángeles Guevara
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

  • epigenetics
  • epigenetic variation
  • abiotic stress
  • biotic stress
  • adaptation
  • plant development
  • fruit tree
  • forest trees

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Published Papers (3 papers)

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21 pages, 2142 KiB  
Article
Epigenetic and Genetic Variability in Contrasting Latitudinal Fagus sylvatica L. Provenances
by María Ángeles Guevara, David Sánchez-Gómez, María Dolores Vélez, Nuria de María, Luis Miguel Díaz, José Alberto Ramírez-Valiente, José Antonio Mancha, Ismael Aranda and María Teresa Cervera
Forests 2022, 13(12), 1971; https://doi.org/10.3390/f13121971 - 22 Nov 2022
Cited by 3 | Viewed by 1679
Abstract
The adaptive capacity of a species and its population is determined by both genetic and epigenetic variation, which defines the potential for adaptive evolution and plastic response to environmental changes. In this study, we used Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment [...] Read more.
The adaptive capacity of a species and its population is determined by both genetic and epigenetic variation, which defines the potential for adaptive evolution and plastic response to environmental changes. In this study, we used Methylation Sensitive Amplified Polymorphism (MSAP) and Amplified Fragment Length Polymorphism (AFLP), similar genome-wide profiling techniques, to analyze the epigenetic and genetic variability in European beech provenances from Germany (DE), Spain (ES) and Sweden (SE), representing the latitudinal distribution of the species. In addition, we evaluated the effect of moderate water stress on cytosine methylation dynamics by comparing two latitudinal contrasting provenances. Our analysis revealed that trees from ES showed lower values of epigenetic and genetic diversity than those from DE and SE. Analyses of molecular variance for MSAPs and AFLPs showed that 16% and 15% of the among population variations were associated with epigenetic and genetic variation, respectively. The study of the effect of water stress on cytosine methylation dynamics in seedlings from ES and SE revealed no significant levels of epigenetic differentiation between well-watered and stressed plants. Only 2% of the epigenetic variation was explained by the watering regime in ES without changes in SE. The results support that DNA methylation may play a role in the local adaptation of Fagus sylvatica to environmental variation. Full article
(This article belongs to the Special Issue Epigenetic Variation: A Component of the Woody Plant Adaptation)
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22 pages, 5687 KiB  
Article
Expression Patterns and Regulation of Non-Coding RNAs during Synthesis of Cellulose in Eucalyptus grandis Hill
by Ni Zhan, Zhen Wang, Yaojian Xie, Xiuhua Shang, Guo Liu and Zhihua Wu
Forests 2021, 12(11), 1565; https://doi.org/10.3390/f12111565 - 12 Nov 2021
Cited by 6 | Viewed by 2409
Abstract
Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of [...] Read more.
Cellulose, an essential structural component in the plant cell wall and a renewable biomass resource, plays a significant role in nature. Eucalyptus’s excellent timber tree species (including Eucalyptus grandis Hill) provide many raw materials for the paper and wood industries. The synthesis of cellulose is a very complex process involving multiple genes and regulated by various biological networks. However, research on regulating associated genes and non-coding RNAs during cellulose synthesis in E. grandis remains lacking. In this study, the wood anatomical characteristics and chemical indexes of E. grandis were analyzed by taking three different parts (diameter at breast height (DBH), middle and upper part of the trunk) from the main stem of E. grandis as raw materials. The role of non-coding RNAs (Long non-coding RNA, lncRNA; Micro RNA, miRNA; Circle RNA, circRNA) on regulating candidate genes was presented, and the network map of ceRNA (Competing endogenous RNA) regulation during wood cellulose biosynthesis of E. grandis was constructed. The transcriptome sequencing of nine samples obtained from the trunk of the immature xylem in E. grandis at DBH, middle and upper parts had a 95.81 G clean reading, 57,480 transcripts, 7365 lncRNAs, and 5180 circRNAs. Each sample had 172–306 known miRNAs and 1644–3508 new miRNAs. A total of 190 DE-lncRNAs (Differentially expressed long non-coding RNAs), 174 DE-miRNAs (Differentially expressed micro RNAs), and 270 DE-circRNAs (Differentially expressed circle RNAs) were obtained by comparing transcript expression levels. Four lncRNAs and nine miRNAs were screened out, and the ceRNA regulatory network was constructed. LncRNA1 and lncRNA4 regulated the genes responsible for cellulose synthesis in E. grandis, which were overexpressed in 84K (Populus Alba × Populus glandulosa) poplar. The cellulose and lignin content in lncRNA4-oe were significantly higher than wild type 84K poplar and lncRNA1-oe. The average plant height, middle and basal part of the stem diameter in lncRNA4-oe were significantly higher than the wild type. However, there was no significant difference between the growth of lncRNA1-oe and the wild type. Further studies are warranted to explore the molecular regulatory mechanism of cellulose biosynthesis in Eucalyptus species. Full article
(This article belongs to the Special Issue Epigenetic Variation: A Component of the Woody Plant Adaptation)
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13 pages, 3852 KiB  
Article
Genomic Methylated Cytosine Level during the Dedifferentiation and Cellular Competence in Coffea arabica Lines: Insights about the Different In Vitro Responses
by João Paulo de Morais Oliveira, Natália Arruda Sanglard, Adésio Ferreira and Wellington Ronildo Clarindo
Forests 2021, 12(11), 1536; https://doi.org/10.3390/f12111536 - 8 Nov 2021
Cited by 4 | Viewed by 1920
Abstract
Coffea arabica genotypes present distinct responses in vitro, and somaclonal variation occurrence has been reported. Global cytosine methylation is one of the epigenetic mechanisms that influences the Coffea in vitro responses. We aimed to establish the indirect somatic embryogenesis in C. arabica ‘Catuaí [...] Read more.
Coffea arabica genotypes present distinct responses in vitro, and somaclonal variation occurrence has been reported. Global cytosine methylation is one of the epigenetic mechanisms that influences the Coffea in vitro responses. We aimed to establish the indirect somatic embryogenesis in C. arabica ‘Catuaí Vermelho’, ‘Caturra’ and ‘Oeiras’, associate the distinct responses to the methylated cytosine genomic level, and check the ploidy stability. Leaf explants were cultured in callus induction and proliferation medium. The resulted calli were transferred to the regeneration medium, and the mature cotyledonary somatic embryos were transferred to the seedling medium. ‘Oeiras’ exhibited the highest number of responsive leaf explants, followed by ‘Caturra’ and ‘Catuaí Vermelho’. Global methylated cytosine level increased over time in the ‘Catuaí Vermelho’ and ‘Caturra’ friable calli, remaining constant in ‘Oeiras’. ‘Oeiras’ did not regenerate somatic embryos, while ‘Catuaí Vermelho’ exhibited the highest number. Somatic embryo regeneration was associated with the increase of the methylated cytosine level. However, the ‘Catuaí Vermelho’ embryogenic calli showed a lower methylated cytosine level than ‘Caturra’. Recovered plantlets exhibited the same 2C value and chromosome number to the explant donors. Therefore, cytosine hypermethylation occurred during C. arabica indirect somatic embryogenesis, influencing cell competence and somatic embryos regeneration. Full article
(This article belongs to the Special Issue Epigenetic Variation: A Component of the Woody Plant Adaptation)
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