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Agronomy
Special Issues
Crop Epigenetics and Epigenomics
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Crop Epigenetics and Epigenomics

A special issue of Agronomy (ISSN 2073-4395). This special issue belongs to the section "Crop Breeding and Genetics".

Deadline for manuscript submissions: closed (15 December 2022) | Viewed by 5578

Special Issue Editors

Prof. Dr. Haifeng Wang

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Guest Editor
College of Agriculture, Guangxi University, Nanning 530004, China
Interests: polyploidy; epigenetics; bioinformatics; plant evolution
Special Issues, Collections and Topics in MDPI journals
Dr. Qingxin Song

E-Mail Website
Co-Guest Editor
State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, 1 Weigang Road, Nanjing 210095, China
Interests: polyploidy; epigenetics; bioinformatics; plant evolution
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Epigenetics refers to the study of heritable changes in gene expression caused by DNA methylation, histone modification, and non-coding RNAs, without involving any changes in the DNA sequence. Advances in high-throughput techniques have revealed a genome-wide epigenetic landscape (epigenome). In recent decades, extensive evidence has shown epigenetic regulation of gene expression and its effect on crop growth, development, and response to biotic/abiotic stress. As epigenetic modification variations are plastic, dynamic, and environmentally responsive, epigenetic modification of trait variation is more attractive for crop breeding and the operation of important agronomic traits. This Special Issue will cover a broad range of studies on epigenetics and epigenomics of a wide range of plant species. Therefore, we invite submissions of any types of manuscripts related to crop epigenetics and epigenomics, including original research, methods, and reviews.

Dr. Haifeng Wang
Dr. Qingxin Song
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. Agronomy 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

  • DNA methylation
  • histone modification
  • non-coding RNAs
  • epigenetics
  • epigenomics

Published Papers (2 papers)

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Research

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15 pages, 23291 KiB  
Article
Epigenetic and Genetic Contribution for Expression Bias of Homologous Alleles in Polyploid Sugarcane
by Yajie Xue, Yan Shi, Yuchuan Qi, Hang Yu, Chengwu Zou, Xueying Cao, Cuimin Sun, Baoshan Chen and Haifeng Wang
Agronomy 2022, 12(11), 2852; https://doi.org/10.3390/agronomy12112852 - 15 Nov 2022
Cited by 2 | Viewed by 1557
Abstract
DNA methylation regulates gene expression in eukaryotes, but their roles in gene expression changes in polyploids are poorly understood. Here, we comparatively analyzed the DNA methylation profiles and transcriptome maps of four tissues (leaf, rind, pith, and root) in autopolyploid sugarcane (Saccharum [...] Read more.
DNA methylation regulates gene expression in eukaryotes, but their roles in gene expression changes in polyploids are poorly understood. Here, we comparatively analyzed the DNA methylation profiles and transcriptome maps of four tissues (leaf, rind, pith, and root) in autopolyploid sugarcane (Saccharum spontaneum). The overall DNA methylation levels were relatively equal and were consistent with the similar genome-wide expression levels of homologous alleles among different homologous chromosomes. However, tetrad alleles showed a large proportion of non-balanced alleles (85–89%) compared with balanced alleles (11–15%). For tetrad alleles, highly-expressed alleles showed lower Ka/Ks values than those in lowly-expressed alleles, indicating that dominant (and non-suppressed) alleles were under strong purifying selection pressure compared to non-dominant (and suppressed) alleles. Specifically, higher DNA methylation levels were found in non-balanced alleles compared to balanced alleles, as well as a higher CG to TG substitution rate, suggesting epigenetic and genetic variation associated with transcription divergence. Moreover, among non-balanced alleles, which were associated with DNA methylation changes, many were involved in several processes relevant to agronomic traits, such as responses to stress and carbohydrate transport. Taken together, our results provide unique epigenetic insights into the transcriptional regulation of homologous alleles, which contribute to the key agronomic traits in sugarcane and facilitate epigenetic studies in other polyploid crops. Full article
(This article belongs to the Special Issue Crop Epigenetics and Epigenomics)
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Review

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34 pages, 3482 KiB  
Review
Plant Immunity Is Regulated by Biological, Genetic, and Epigenetic Factors
by Ali Movahedi, Soheila Aghaei-Dargiri, Bahram Barati, Saeid Kadkhodaei, Hui Wei, Sirous Sangari, Liming Yang and Chen Xu
Agronomy 2022, 12(11), 2790; https://doi.org/10.3390/agronomy12112790 - 9 Nov 2022
Cited by 2 | Viewed by 3571
Abstract
An immune system is a protective mechanism that shields plants from environmental stresses. This primary function is to maintain optimal circumstances for the growth and development of plant tissues while avoiding harm from biotic and abiotic stress factors. Plants subjected to various stressors [...] Read more.
An immune system is a protective mechanism that shields plants from environmental stresses. This primary function is to maintain optimal circumstances for the growth and development of plant tissues while avoiding harm from biotic and abiotic stress factors. Plants subjected to various stressors initiate stress signaling cascades that affect multiple gene expressions and induce adaptation. These signaling pathways are coordinated by transcription factors, non-coding RNAs, RNA-binding proteins, and protein–protein interaction networks. Several studies have focused on various immune systems, but no study has collected all of them together to illustrate them efficiently. According to this review, stress-responsive genes encode ion and water transporters, enzymes, and transcription factors, making plants more resistant to biological and abiotic challenges. Plants have also evolved anti-pathogen defense systems such as regulatory hormone pathways, reactive oxygen species generation, gene expression, programmed cell death, and cell survival. Plants produce short RNAs in response to a viral attack, which silences the offensive genome and creates complex epigenetic regulatory mechanisms such as histone changes, chromatin remodeling, and DNA methylation to protect plants from pathogens. This review provides an in-depth description of proteins, effectors, and pathways included in plant resistance against environmental stresses and offers details on future trends, such as metabolic pathways and genetic engineering, to improve the protection of plants against stress-induced responses. Full article
(This article belongs to the Special Issue Crop Epigenetics and Epigenomics)
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