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Agronomy
Special Issues
The Regulatory Functions of Epigenetic Mechanisms in Plants
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The Regulatory Functions of Epigenetic Mechanisms in Plants

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

Deadline for manuscript submissions: closed (31 December 2018) | Viewed by 32470

Special Issue Editors

Prof. Dr. Mieke Van Lijsebettens

E-Mail Website
Guest Editor
Center of Plant Systems Biology, Flanders Institute Biotechnology (VIB) and Ghent University (UGent), Technology Park 927, 9052 Gent, Belgium
Dr. Christopher Cazzonelli

E-Mail Website
Guest Editor
Hawkesbury Institute for the Environment, Western Sydney University, Richmond, NSW 2753, Australia
Interests: carotenoid biology; mechanical stress; epigenetics; plant physiology; molecular biology; crop nutrition; postharvest; horticulture; protected cropping; tree genomics; climate change; stress acclimation
Special Issues, Collections and Topics in MDPI journals
Dr. Marc De Block

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Guest Editor
BASF Agricultural Solutions Belgium NV, Technologiepark 38, 9052 Ghent, Belgium

Special Issue Information

Dear Colleagues,

The role of epigenetic and chromatin-related mechanisms in gene expression regulation is an emerging field of research in plant models, crops and natural accessions. DNA methylation, non-coding RNA, chromatin remodeling and modification add a level of transcriptional regulation in biological processes that underlie important agronomic traits such as imprinting, seed dormancy, vernalization, flowering time, disease resistance, micronutrient levels, pigmentation and fruit ripening. Transcriptional networks controlling complex traits such as abiotic and biotic stress tolerance, yield stability, energy homeostasis and secondary metabolism are under epigenetic regulation. Epigenome variation in epilines and generation of epialleles will provide insight and knowledge to further agronomical and agro-ecological research and might be translated in epigenetic or genetic approaches in plant breeding to optimize crop traits.

Prof. Dr. Mieke Van Lijsebettens
Dr. Chris Cazzonelli
Dr. Marc De Block

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

  • Simple trait
  • Complex trait
  • Epigenome
  • Transcriptional regulation
  • Crops
  • Chromatin
  • Epiallele
  • Transgenerational stability

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Published Papers (4 papers)

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Research

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14 pages, 2373 KiB  
Article
Selection of Salicylic Acid Tolerant Epilines in Brassica napus
by Sonja Klemme, Yorick De Smet, Bruno P. A. Cammue and Marc De Block
Agronomy 2019, 9(2), 92; https://doi.org/10.3390/agronomy9020092 - 18 Feb 2019
Cited by 4 | Viewed by 4189
Abstract
Two of the major pathways involved in induced defense of plants against pathogens include the salicylic acid (SA)- and jasmonic acid (JA)-mediated pathways that act mainly against biotrophs and necrotrophs, respectively. However, some necrotrophic pathogens, such as Botrytis cinerea, actively induce the [...] Read more.
Two of the major pathways involved in induced defense of plants against pathogens include the salicylic acid (SA)- and jasmonic acid (JA)-mediated pathways that act mainly against biotrophs and necrotrophs, respectively. However, some necrotrophic pathogens, such as Botrytis cinerea, actively induce the SA pathway, resulting in cell death that allows the pathogen to proliferate in the plant. Starting from an isogenic canola (Brassica napus) line, epilines were selected with a reduced sensitivity to SA. The genes belonging to the SA pathway had an altered transcription profile in the SA-tolerant lines, when treated with SA. Besides the already known genes of the SA pathway, new SA target genes were identified, creating possibilities to better understand the plant defense mechanism against pathogens. The SA-tolerant line with the lowest SA-induced gene expression is tolerant to Botrytis cinerea. When treated with SA, this line has also a reduced histone modification (histone H3 lysine 4 trimethylation) at the genes at the start of the SA pathway. Full article
(This article belongs to the Special Issue The Regulatory Functions of Epigenetic Mechanisms in Plants)
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21 pages, 1687 KiB  
Article
Methylome and Epialleles in Rice Epilines Selected for Energy Use Efficiency
by Martin Schmidt, Marina Byzova, Cindy Martens, Marrit Peeters, Yog Raj, Shailesh Shukla, Tom Verwulgen, Marc De Block and Mieke Van Lijsebettens
Agronomy 2018, 8(9), 163; https://doi.org/10.3390/agronomy8090163 - 24 Aug 2018
Cited by 8 | Viewed by 5510
Abstract
Epigenetics offers important opportunities in breeding to improve the potential yield in a wide variety of crops. Starting from a pure breeder seed lot of a rice (Oryza sativa ssp. indica) inbred population, repeated testing for improved cellular respiration rates and [...] Read more.
Epigenetics offers important opportunities in breeding to improve the potential yield in a wide variety of crops. Starting from a pure breeder seed lot of a rice (Oryza sativa ssp. indica) inbred population, repeated testing for improved cellular respiration rates and energy use efficiency (EUE) over three generations identified performant epilines with distinct epigenetic signatures and with improved seed yield in field trials. Epiline DNA methylomes were characterized by genome-wide bisulfite sequencing to discern cytosine methylation changes in relation to transcriptome and phenotype. Regional methylation changes were dispersed over the epiline genomes. A number of upstream-associated differentially methylated regions (DMRs) correlated with differentially expressed genes (DEGs) with a role in particular molecular functions like transmembrane transport and protein kinase activity. Targeted bisulfite sequencing confirmed epiline DMRs that anti-correlated with DEGs, identifying putative epialleles that were susceptible for cytosine methylation changes that might affect gene expression and contribute to the phenotype. Chromatin immunoprecipitation sequencing revealed the extensive enrichment of gene-associated histone H3 lysine-4 trimethylation (H3K4me3), which correlated with gene activation and reduced cytosine methylation. Our data indicate that seed formation is prone to epigenetic changes that might be used as a resource in crop improvement. Full article
(This article belongs to the Special Issue The Regulatory Functions of Epigenetic Mechanisms in Plants)
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Review

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17 pages, 1533 KiB  
Review
Shaping Plant Adaptability, Genome Structure and Gene Expression through Transposable Element Epigenetic Control: Focus on Methylation
by Leonardo Galindo-González, Felipe Sarmiento and Mauricio A. Quimbaya
Agronomy 2018, 8(9), 180; https://doi.org/10.3390/agronomy8090180 - 11 Sep 2018
Cited by 28 | Viewed by 7946
Abstract
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to [...] Read more.
In plants, transposable elements (TEs) represent a large fraction of the genome, with potential to alter gene expression and produce genomic rearrangements. Epigenetic control of TEs is often used to stop unrestricted movement of TEs that would result in detrimental effects due to insertion in essential genes. The current review focuses on the effects of methylation on TEs and their genomic context, and how this type of epigenetic control affects plant adaptability when plants are faced with different stresses and changes. TEs mobilize in response to stress elicitors, including biotic and abiotic cues, but also developmental transitions and ‘genome shock’ events like polyploidization. These events transitionally lift TE repression, allowing TEs to move to new genomic locations. When TEs fall close to genes, silencing through methylation can spread to nearby genes, resulting in lower gene expression. The presence of TEs in gene promoter regions can also confer stress inducibility modulated through alternative methylation and demethylation of the TE. Bursts of transposition triggered by events of genomic shock can increase genome size and account for differences seen during polyploidization or species divergence. Finally, TEs have evolved several mechanisms to suppress their own repression, including the use of microRNAs to control genes that promote methylation. The interplay between silencing, transient TE activation, and purifying selection allows the genome to use TEs as a reservoir of potential beneficial modifications but also keeps TEs under control to stop uncontrolled detrimental transposition. Full article
(This article belongs to the Special Issue The Regulatory Functions of Epigenetic Mechanisms in Plants)
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Other

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19 pages, 609 KiB  
Hypothesis
Towards the Understanding of Important Coconut Endosperm Phenotypes: Is there an Epigenetic Control?
by Jorge Gil C. Angeles, Jickerson P. Lado, Evangeline D. Pascual, Cristeta A. Cueto, Antonio C. Laurena and Rita P. Laude
Agronomy 2018, 8(10), 225; https://doi.org/10.3390/agronomy8100225 - 13 Oct 2018
Cited by 18 | Viewed by 13421
Abstract
The coconut is a major crop of many tropical countries, with the endosperm being one of its main products. The coconut soft-endosperm variants, the Makapuno and the Lono, are emerging as economically important. This review describes this crop, its salient endosperm phenotypes and [...] Read more.
The coconut is a major crop of many tropical countries, with the endosperm being one of its main products. The coconut soft-endosperm variants, the Makapuno and the Lono, are emerging as economically important. This review describes this crop, its salient endosperm phenotypes and the prevailing hypotheses associated with these. We also collate the literature on the Makapuno and provide a comprehensive review of the scarce information on the Lono. We review the current tenets of plant DNA methylation and provide examples of altered phenotypes associated with such methylation changes. We explore how the changes in the methylome affect endosperm development and the tissue culture process. We further cite the epigenetic basis of an altered endosperm phenotype of a closely related species to the coconut, the oil palm. We discuss how such modifications could affect coconut endosperm development, yielding the Makapuno and Lono phenotypes. Full article
(This article belongs to the Special Issue The Regulatory Functions of Epigenetic Mechanisms in Plants)
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