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Role of Epigenetics and Epigenomics in Plant Development and Their...
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Role of Epigenetics and Epigenomics in Plant Development and Their Association with Abiotic Environmental Stresses

A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 8430

Special Issue Editors

Prof. Dr. Lijia Li

E-Mail Website
Guest Editor
College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: molecular cytogenetics; molecular biology; genetic engineering
Dr. Mayank Gautam

E-Mail Website
Guest Editor
College of Life Sciences, Wuhan University, Wuhan 430072, China
Interests: epigenetics; epigenomics; cell death; transcriptome; nucleolar structure

Special Issue Information

In this Special Issue, we focus on the current understanding of the regulation and function of the epigenetic modifications, including DNA methylation, histone modification, histone variants, some non-coding RNAs (ncRNAs) and epigenomics, in plant development, such as stomatal development, vernalization, fruit ripening and other developmental processes. This Special Issue also covers the tight associations between epigenetic modifications and a wide range of abiotic environmental stresses, including heat, cold, drought, high salinity, pesticides, climate change and other conditions. During the past two decades, epigenetic and epigenomic investigations have been carried out on a number of plant species, such as Arabidopsis thaliana, Zea mays, Oryza sativa and Brassica rapa. We are still far away from elucidating the crosstalk among the underlying epigenetic molecular mechanisms and epigenomic regulators.

Authors are invited to submit original research and review articles on the following areas and related areas that are not mentioned here:

  • Role of epigenetics and epigenomics in plant growth and development;
  • Dynamic regulation of epigenetics and epigenomics in response to abiotic environmental stresses in plants, and in epigenetic transgeneration stress adaptation;
  • Epigenetics and its association with gene regulation, transposon silencing and chromosomal interaction;
  • Crosstalk among distinct epigenetic regulatory pathways.

Prof. Dr. Lijia Li
Dr. Mayank Gautam
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. Plants is an international peer-reviewed open access semimonthly 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 2700 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

  • DNA methylation
  • histone modifications
  • non-coding RNA
  • chromatin remodeling
  • plant development
  • abiotic environmental stresses
  • epigenetic mechanisms

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Published Papers (3 papers)

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Research

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22 pages, 6089 KiB  
Article
Identification and Functional Analysis of Long Non-Coding RNA (lncRNA) in Response to Seed Aging in Rice
by Yixin Zhang, Fan Fan, Qunjie Zhang, Yongjian Luo, Qinjian Liu, Jiadong Gao, Jun Liu, Guanghui Chen and Haiqing Zhang
Plants 2022, 11(23), 3223; https://doi.org/10.3390/plants11233223 - 24 Nov 2022
Cited by 9 | Viewed by 2631
Abstract
Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice [...] Read more.
Many lncRNAs have been shown to play a vital role in aging processes. However, how lncRNAs regulate seed aging remains unknown. In this study, we performed whole transcriptome strand-specific RNA sequencing of samples from rice embryos, analyzed the differences in expression of rice seed lncRNAs before and after artificial aging treatment (AAT), and systematically screened 6002 rice lncRNAs. During the AAT period, the expression levels of most lncRNAs (454) were downregulated and only four were upregulated among the 458 differentially expressed lncRNAs (DELs). Cis- or trans-regulated target genes of the four upregulated lncRNAs were mainly related to base repair, while 454 downregulated lncRNAs were related to plant–pathogen interaction, plant hormones, energy metabolism, and secondary metabolism. The pathways of DEL target genes were similar with those of differentially expressed mRNAs (DEGs). A competing endogenous RNA (ceRNA) network composed of 34 lncRNAs, 24 microRNAs (miRNA), and 161 mRNAs was obtained. The cDNA sequence of lncRNA LNC_037529 was obtained by rapid amplification of cDNA ends (RACE) cloning with a total length of 1325 bp, a conserved 5′ end, and a non-conserved 3′ end. Together, our findings indicate that genome-wide selection for lncRNA downregulation was an important mechanism for rice seed aging. LncRNAs can be used as markers of seed aging in rice. These findings provide a future path to decipher the underlying mechanism associated with lncRNAs in seed aging. Full article
(This article belongs to the Special Issue Role of Epigenetics and Epigenomics in Plant Development and Their Association with Abiotic Environmental Stresses)
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20 pages, 4850 KiB  
Article
Determining the Effects of Light on the Fruit Peel Quality of Photosensitive and Nonphotosensitive Eggplant
by Zhaoze Sang, Jinhua Zuo, Qing Wang, Anzhen Fu, Yanyan Zheng, Yonghong Ge, Zongwei Qian and Yanling Cui
Plants 2022, 11(16), 2095; https://doi.org/10.3390/plants11162095 - 12 Aug 2022
Cited by 3 | Viewed by 1776
Abstract
With the development of facility agriculture, low-light stress is a prominent problem and a popular research topic currently. In this study, transcriptome analysis was used to analyze the genes in the fruit peel of photosensitive and nonphotosensitive eggplant and to explore the mechanism [...] Read more.
With the development of facility agriculture, low-light stress is a prominent problem and a popular research topic currently. In this study, transcriptome analysis was used to analyze the genes in the fruit peel of photosensitive and nonphotosensitive eggplant and to explore the mechanism of changes in fruit color, texture, hormone content, aroma, and taste of these two different types of eggplant. We identified 51, 65, 66, and 66 genes involved in synthesizing anthocyanins, texture, hormone content, and aroma and flavor, respectively, in the two different types of eggplant based on the variation in gene expression trends in the fruit peel. These results provide a basis for further analysis of the molecular mechanism underlying the regulatory processes in eggplant fruits under low-light stress. Full article
(This article belongs to the Special Issue Role of Epigenetics and Epigenomics in Plant Development and Their Association with Abiotic Environmental Stresses)
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Review

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16 pages, 670 KiB  
Review
DNA Methylation in Algae and Its Impact on Abiotic Stress Responses
by Michele Ferrari, Antonella Muto, Leonardo Bruno and Radiana Cozza
Plants 2023, 12(2), 241; https://doi.org/10.3390/plants12020241 - 5 Jan 2023
Cited by 6 | Viewed by 3052
Abstract
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved [...] Read more.
Epigenetics, referring to heritable gene regulatory information that is independent of changes in DNA sequences, is an important mechanism involved both in organism development and in the response to environmental events. About the epigenetic marks, DNA methylation is one of the most conserved mechanisms, playing a pivotal role in organism response to several biotic and abiotic stressors. Indeed, stress can induce changes in gene expression through hypo- or hyper-methylation of DNA at specific loci and/or in DNA methylation at the genome-wide level, which has an adaptive significance and can direct genome evolution. Exploring DNA methylation in responses to abiotic stress could have important implications for improving stress tolerance in algae. This article summarises the DNA methylation pattern in algae and its impact on abiotic stress, such as heavy metals, nutrients and temperature. Our discussion provides information for further research in algae for a better comprehension of the epigenetic response under abiotic stress, which could favour important implications to sustain algae growth under abiotic stress conditions, often related to high biosynthesis of interesting metabolites. Full article
(This article belongs to the Special Issue Role of Epigenetics and Epigenomics in Plant Development and Their Association with Abiotic Environmental Stresses)
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