Natural and induced epigenetic variation for crop improvement

Lieberman‐Lazarovich, Michal; Kaiserli, Eirini; Bucher, Etienne; Mladenov, Velimir

doi:10.1016/j.pbi.2022.102297

Cited by 17 publications

(15 citation statements)

References 65 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This information has several applications for biotechnology and plant breeding. For example, this can expand to the transposon-mediated plant breeding as established in ERC project EVOBREED (https://cordis.europa.eu/project/id/322621/reporting/fr); which is particularly important from the regulation perspective since it is a transgene-free technology (Paszkowski, 2015;Lieberman-Lazarovich et al, 2022). Another interesting application for biotechnology is the development of helitron transposon system for cross-mobilizing the non-autonomous transposons, as displayed by a helitron-based system Helraiser (Kosek et al, 2021;Grabundzija et al, 2016).…”

Section: Discussionmentioning

confidence: 99%

Single molecule long-read eccDNA sequencing reveals unambiguous and selective transposon activation in Arabidopsis in response to stress, cellular state, and epigenetic processes

Vanderschuren

Zaidi

Shakir

et al. 2023

Preprint

View full text Add to dashboard Cite

Extrachromosomal circular DNA (eccDNA) has been described in a number of eukaryotic species, and their presence has been shown to enable gene amplification in phenomena as diverse as cancer and herbicide tolerance. A potential role for eccDNA is to serve as a means for transposon mobilization within the genome. However, most eccDNA studies in plants to date have been based on short-read sequencing data which fails at unambiguously identifying true eccDNA forms of genetic and transposable elements. Here, we report the first atlas of full-length eccDNAs for Arabidopsis using the Cider-Seq pipeline based on long-read sequencing of single molecules. Our dataset was validated by analysing eccDNAs of heat-stressed plants, thereby sequencing full-length eccDNA forms of the well-known heat-responsive ONSEN transposon. Our results show that more evolutionarily recent loci of ONSEN transposon produce greater numbers of eccDNAs upon heat-stress. We identified eccDNAs generated from loci of the transposon superfamily RC/Helitron as the most abundant eccDNAs in Arabidopsis. Profiling of eccDNAs from two cell types displaying altered DNA methylation patterns enabled the identification of new active TE loci such as VANDAL5A, ATCOPIA58 and ATREP19 in the shoot apical meristem, and ATCOPIA53, ENDOVIR1 and TA11 in calli tissues. Unexpectedly analysis of mutants in the DNA methylation pathways revealed that eccDNA formation from several retrotransposon loci is induced in the absence of active DNA demethylase ROS1. Together, our study provides an important resource to investigate the function of eccDNAs and the impact of DNA methylation in their regulation.

show abstract

Section: Discussionmentioning

confidence: 99%

Single molecule long-read eccDNA sequencing reveals unambiguous and selective transposon activation in Arabidopsis in response to stress, cellular state, and epigenetic processes

Vanderschuren

Zaidi

Shakir

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…This process includes consideration of the germplasm, length of the study, environments, and biological contexts. From the breeding perspective, schemes that consider, include, and manage epigenetic information (a la "epibreeding" by Lieberman-Lazarovich et al [2022]) are required and should be tailored for each specific breeding program. Epigenetic signatures may exist that respond to aspects such as biotic stress and address questions related to longevity and performance, which are relevant in the breeding and production of perennial crops.…”

Section: Concluding Remarks and Perspectivesmentioning

confidence: 99%

A review of plant epigenetics through the lens of almond

et al. 2023

View full text Add to dashboard Cite

While genomes were originally seen as static entities that stably held and organized genetic information, recent advances in sequencing have uncovered the dynamic nature of the genome. New conceptualizations of the genome include complex relationships between the environment and gene expression that must be maintained, regulated, and sometimes even transmitted over generations. The discovery of epigenetic mechanisms has allowed researchers to understand how traits like phenology, plasticity, and fitness can be altered without changing the underlying deoxyribonucleic acid sequence. While many discoveries were first made in animal systems, plants provide a particularly complex set of epigenetic mechanisms due to unique aspects of their biology and interactions with human selective breeding and cultivation. In the plant kingdom, annual plants have received the most attention; however, perennial plants endure and respond to their environment and human management in distinct ways. Perennials include crops such as almond, for which epigenetic effects have long been linked to phenomena and even considered relevant for breeding. Recent discoveries have elucidated epigenetic phenomena that influence traits such as dormancy and self‐compatibility, as well as disorders like noninfectious bud failure, which are known to be triggered by the environment and influenced by inherent aspects of the plant. Thus, epigenetics represents fertile ground to further understand almond biology and production and optimize its breeding. Here, we provide our current understanding of epigenetic regulation in plants and use almond as an example of how advances in epigenetics research can be used to understand biological fitness and agricultural performance in crop plants.

show abstract

“…Most studies of epigenetic variation in plants are based on stripping the methylation by chemicals such as 5-Azacytidine or genetic means ( i.e. mutants) and using the hypomethylated plants as a source of variation to study gene function and isolate new epialleles (Lieberman-Lazarovich et al, 2022). Our comprehension of the mechanisms involved in the creation and maintenance of epialleles was greatly advanced by the creation of epigenetic Recombinant Inbred Lines (epiRILs) which were generated by crossing wild-type Arabidopsis accessions with DNA hypomethylated mutants like met1 or decreased DNA methylation1 ( ddm1 ) (Reinders et al, 2009; Johannes et al, 2009).…”

Section: Introductionmentioning

confidence: 99%

Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase

Pavan Kumar,

Beaubiat,

Yadav

et al. 2024

Preprint

View full text Add to dashboard Cite

Epigenetic variation is mediated by epigenetic marks such as DNA methylation occurring in all cytosine contexts in plants. CG methylation plays a critical role in silencing transposable elements and regulating gene expression. The establishment of CG methylation occurs via the RNA-directed DNA methylation pathway and CG methylation maintenance relies on METHYLTRANSFERASE1, the homologue of the mammalian DNMT1. Here, we examined the capacity to stably alter the tomato genome methylome by a bacterial CG-specific M.SssI methyltransferase expressed through the LhG4/pOP transactivation system. Methylome analysis of M.SssI expressing plants revealed that their euchromatic genome regions are specifically hypermethylated in the CG context, and so are most of their genes. However, changes in gene expression were observed only with a set of genes exhibiting a greater susceptibility to CG hypermethylation near their transcription start site. Unlike gene rich genomic regions, our analysis revealed that heterochromatic regions are slightly hypomethylated at CGs only. Notably, some M.SssI-induced hypermethylation persisted even without the methylase or transgenes, indicating inheritable epigenetic modification. Collectively our findings suggest that heterologous expression of M.SssI can create new inherited epigenetic variations and changes in the methylation profiles on a genome wide scale. This open avenues for the conception of epigenetic recombinant inbred line populations with the potential to unveil agriculturally valuable tomato epialleles.

show abstract

Natural and induced epigenetic variation for crop improvement

Cited by 17 publications

References 65 publications

Single molecule long-read eccDNA sequencing reveals unambiguous and selective transposon activation in Arabidopsis in response to stress, cellular state, and epigenetic processes

Single molecule long-read eccDNA sequencing reveals unambiguous and selective transposon activation in Arabidopsis in response to stress, cellular state, and epigenetic processes

A review of plant epigenetics through the lens of almond

Genome wide inherited modifications of the tomato epigenome by trans-activated bacterial CG methyltransferase

Contact Info

Product

Resources

About