ijms-logo

Journal Browser

Journal Browser

Epigenomics and Crop Improvement

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Plant Sciences".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 11060

Special Issue Editor

Department of Bioscience and Bioinformatics, Myongji University, Yongin 17058, Korea
Interests: genomics; epigenomics; polyploidy; DNA methylation; RdDM; transposable element; soybean; legume
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Crop productivity and quality will need to increase as the human population continues to grow and consume more meat, while facing the challenges posed by global climate change. Plant breeding has played a significant role in global food security; nevertheless, the traditional approaches that rely solely on genetic diversity may not be sufficient to meet projected food demand.

The epigenetic mechanisms in plants are important in a wide range of biological processes, including development and response to the environment. Because of these fundamental roles, epigenetics has the potential to play a role in crop improvement, such as selecting for favorable epigenetic states, creating novel epialleles, and regulating transgene expression. Epigenetic diversity could provide additional sources of variation for breeders to use, allowing for more phenotypic variation to be captured or created for crop improvement. Since high-resolution epigenome profiling is now available, epigenome analysis and engineering in crop species could expand our understanding of the molecular mechanisms underlying epigenetic inheritance and open up new possibilities for utilizing epigenetics’ full potential in crop improvement.

Based on this background, we welcome eminent researchers working on crop epigenomics across the world to contribute their high-quality original research manuscripts, critical reviews, and opinion articles covering topics including but not limited to:

  • Epialleles associated with agronomic traits;
  • Epigenomic variation in response to the environment;
  • Dynamic nature of epigenome in polyploid crops;
  • Epigenetics in clonally propagated crops;
  • Artificial induction and stable inheritance of epigenomic changes;
  • Site-specific epigenetic engineering;
  • Predictive marker for hybrid performance.

Dr. Kyung Do Kim
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • epigenomics
  • crop improvement
  • DNA methylation
  • histone modification
  • cis-regulatory elements
  • epiallele
  • epigenetic inheritance
  • epigenome engineering

Published Papers (6 papers)

Order results
Result details
Select all
Export citation of selected articles as:

Research

Jump to: Review

19 pages, 3607 KiB  
Article
Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes
by Charlotte Ost, Hieu Xuan Cao, Thuy Linh Nguyen, Axel Himmelbach, Martin Mascher, Nils Stein and Klaus Humbeck
Int. J. Mol. Sci. 2023, 24(15), 12065; https://doi.org/10.3390/ijms241512065 - 27 Jul 2023
Cited by 1 | Viewed by 1201
Abstract
Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley [...] Read more.
Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach. Full article
(This article belongs to the Special Issue Epigenomics and Crop Improvement)
Show Figures

Figure 1

15 pages, 2246 KiB  
Article
WHIRLY1 Acts Upstream of ABA-Related Reprogramming of Drought-Induced Gene Expression in Barley and Affects Stress-Related Histone Modifications
by Minh Bui Manh, Charlotte Ost, Edgar Peiter, Bettina Hause, Karin Krupinska and Klaus Humbeck
Int. J. Mol. Sci. 2023, 24(7), 6326; https://doi.org/10.3390/ijms24076326 - 28 Mar 2023
Cited by 4 | Viewed by 1478
Abstract
WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated [...] Read more.
WHIRLY1, a small plant-specific ssDNA-binding protein, dually located in chloroplasts and the nucleus, is discussed to act as a retrograde signal transmitting a stress signal from the chloroplast to the nucleus and triggering there a stress-related gene expression. In this work, we investigated the function of WHIRLY1 in the drought stress response of barley, employing two overexpression lines (oeW1-2 and oeW1-15). The overexpression of WHIRLY1 delayed the drought-stress-related onset of senescence in primary leaves. Two abscisic acid (ABA)-dependent marker genes of drought stress, HvNCED1 and HvS40, whose expression in the wild type was induced during drought treatment, were not induced in overexpression lines. In addition, a drought-related increase in ABA concentration in the leaves was suppressed in WHIRLY1 overexpression lines. To analyze the impact of the gain-of-function of WHIRLY1 on the drought-related reprogramming of nuclear gene expression, RNAseq was performed comparing the wild type and an overexpression line. Cluster analyses revealed a set of genes highly up-regulated in response to drought in the wild type but not in the WHIRLY1 overexpression lines. Among these genes were many stress- and abscisic acid (ABA)-related ones. Another cluster comprised genes up-regulated in the oeW1 lines compared to the wild type. These were related to primary metabolism, chloroplast function and growth. Our results indicate that WHIRLY1 acts as a hub, balancing trade-off between stress-related and developmental pathways. To test whether the gain-of-function of WHIRLY1 affects the epigenetic control of stress-related gene expression, we analyzed drought-related histone modifications in different regions of the promoter and at the transcriptional start sites of HvNCED1 and HvS40. Interestingly, the level of euchromatic marks (H3K4me3 and H3K9ac) was clearly decreased in both genes in a WHIRLY1 overexpression line. Our results indicate that WHIRLY1, which is discussed to act as a retrograde signal, affects the ABA-related reprogramming of nuclear gene expression during drought via differential histone modifications. Full article
(This article belongs to the Special Issue Epigenomics and Crop Improvement)
Show Figures

Figure 1

9 pages, 1648 KiB  
Article
ENet-6mA: Identification of 6mA Modification Sites in Plant Genomes Using ElasticNet and Neural Networks
by Zeeshan Abbas, Hilal Tayara and Kil To Chong
Int. J. Mol. Sci. 2022, 23(15), 8314; https://doi.org/10.3390/ijms23158314 - 27 Jul 2022
Cited by 7 | Viewed by 1568
Abstract
N6-methyladenine (6mA) has been recognized as a key epigenetic alteration that affects a variety of biological activities. Precise prediction of 6mA modification sites is essential for understanding the logical consistency of biological activity. There are various experimental methods for identifying 6mA modification sites, [...] Read more.
N6-methyladenine (6mA) has been recognized as a key epigenetic alteration that affects a variety of biological activities. Precise prediction of 6mA modification sites is essential for understanding the logical consistency of biological activity. There are various experimental methods for identifying 6mA modification sites, but in silico prediction has emerged as a potential option due to the very high cost and labor-intensive nature of experimental procedures. Taking this into consideration, developing an efficient and accurate model for identifying N6-methyladenine is one of the top objectives in the field of bioinformatics. Therefore, we have created an in silico model for the classification of 6mA modifications in plant genomes. ENet-6mA uses three encoding methods, including one-hot, nucleotide chemical properties (NCP), and electron–ion interaction potential (EIIP), which are concatenated and fed as input to ElasticNet for feature reduction, and then the optimized features are given directly to the neural network to get classified. We used a benchmark dataset of rice for five-fold cross-validation testing and three other datasets from plant genomes for cross-species testing purposes. The results show that the model can predict the N6-methyladenine sites very well, even cross-species. Additionally, we separated the datasets into different ratios and calculated the performance using the area under the precision–recall curve (AUPRC), achieving 0.81, 0.79, and 0.50 with 1:10 (positive:negative) samples for F. vesca, R. chinensis, and A. thaliana, respectively. Full article
(This article belongs to the Special Issue Epigenomics and Crop Improvement)
Show Figures

Figure 1

Review

Jump to: Research

13 pages, 1024 KiB  
Review
Oligo—Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants
by Cezary Krasnodębski, Agnieszka Sawuła, Urszula Kaźmierczak and Magdalena Żuk
Int. J. Mol. Sci. 2023, 24(5), 4466; https://doi.org/10.3390/ijms24054466 - 24 Feb 2023
Cited by 3 | Viewed by 1701
Abstract
Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of [...] Read more.
Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides’ action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides. Full article
(This article belongs to the Special Issue Epigenomics and Crop Improvement)
Show Figures

Figure 1

39 pages, 2929 KiB  
Review
Genomic and Epigenomic Mechanisms of the Interaction between Parasitic and Host Plants
by Vasily V. Ashapkin, Lyudmila I. Kutueva, Nadezhda I. Aleksandrushkina, Boris F. Vanyushin, Denitsa R. Teofanova and Lyuben I. Zagorchev
Int. J. Mol. Sci. 2023, 24(3), 2647; https://doi.org/10.3390/ijms24032647 - 31 Jan 2023
Cited by 4 | Viewed by 2603
Abstract
Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible [...] Read more.
Parasitic plants extract nutrients from the other plants to finish their life cycle and reproduce. The control of parasitic weeds is notoriously difficult due to their tight physical association and their close biological relationship to their hosts. Parasitic plants differ in their susceptible host ranges, and the host species differ in their susceptibility to parasitic plants. Current data show that adaptations of parasitic plants to various hosts are largely genetically determined. However, multiple cases of rapid adaptation in genetically homogenous parasitic weed populations to new hosts strongly suggest the involvement of epigenetic mechanisms. Recent progress in genome-wide analyses of gene expression and epigenetic features revealed many new molecular details of the parasitic plants’ interactions with their host plants. The experimental data obtained in the last several years show that multiple common features have independently evolved in different lines of the parasitic plants. In this review we discuss the most interesting new details in the interaction between parasitic and host plants. Full article
(This article belongs to the Special Issue Epigenomics and Crop Improvement)
Show Figures

Figure 1

15 pages, 1017 KiB  
Review
Epigenetic Dynamics and Regulation of Plant Male Reproduction
by Quancan Hou, Tianye Zhang, Yuchen Qi, Zhenying Dong and Xiangyuan Wan
Int. J. Mol. Sci. 2022, 23(18), 10420; https://doi.org/10.3390/ijms231810420 - 09 Sep 2022
Cited by 8 | Viewed by 1926
Abstract
Flowering plant male germlines develop within anthers and undergo epigenetic reprogramming with dynamic changes in DNA methylation, chromatin modifications, and small RNAs. Profiling the epigenetic status using different technologies has substantially accumulated information on specific types of cells at different stages of male [...] Read more.
Flowering plant male germlines develop within anthers and undergo epigenetic reprogramming with dynamic changes in DNA methylation, chromatin modifications, and small RNAs. Profiling the epigenetic status using different technologies has substantially accumulated information on specific types of cells at different stages of male reproduction. Many epigenetically related genes involved in plant gametophyte development have been identified, and the mutation of these genes often leads to male sterility. Here, we review the recent progress on dynamic epigenetic changes during pollen mother cell differentiation, microsporogenesis, microgametogenesis, and tapetal cell development. The reported epigenetic variations between male fertile and sterile lines are summarized. We also summarize the epigenetic regulation-associated male sterility genes and discuss how epigenetic mechanisms in plant male reproduction can be further revealed. Full article
(This article belongs to the Special Issue Epigenomics and Crop Improvement)
Show Figures

Figure 1

Back to TopTop