From epigenetics to epigenomics and their implications in plant breeding (original) (raw)

Epigenetic mechanisms in plants and their implications in plant breeding

In the wake of the …, 2005

Higher organisms, including plants, use three systems to initiate and sustain epigenetic gene regulation: DNA methylation, histone modification and RNA-interference. Unraveling the relationships between these epigenetic components has led to surprising and rapidly evolving new concepts, showing how they interact and stabilize each other. These interacting systems can regulate expression or silencing of genes, resulting in epigenetically controlled phenotypes that can be meiotically or mitotically heritable. In this review we discuss issues relevant to the involvement of epigenetic inheritance as a source of polymorphism generating useful variation for selecting superior genotypes. The role of methylation in hybrid vigor and stability of performance, and aspects of epigenetic transgene silencing in elite transgenic varieties will also be addressed.

Heritable Epigenetic Variation and its Potential Applications for Crop Improvement

Plant Breeding and Biotechnology, 2013

Phenotypic variation within organisms is driven primarily by genetic diversity. However, there is a growing appreciation that epigenetic variation, resulting from a multitude of diverse chemical modifications to the DNA and chromatin, can have profound effects on phenotype. Heritable epigenetic marks persist through meiosis and can be stably transmitted to the next generation, resulting in transgenerational epigenetic inheritance. Importantly, when epigenetic changes occur near coding genes, affecting their transcriptional state, heritable epigenetic variation can result in heritable phenotypic variation. Large-scale interrogation of epigenome inheritance in Arabidopsis has revealed that spontaneous variation in DNA methylation occurs at a rate that is orders of magnitude greater than genetic mutation, indicating the key importance of epigenetic variation during evolution. Thus, there is a potential for epigenetics to play a role in crop improvement, including regulation of transgene expression and creation of novel epialleles. Here, we review cases of naturally occurring and genetically induced epialleles, and discuss how the studies from two epigenetic populations are rapidly increasing our understanding of epigenetic diversity.

Plant epigenetics: From genomes to epigenomes

Epigenetics is the study of heritable changes in gene expression that occur without a change in the DNA sequence. In recent years, this field has attracted increasing attention as more epigenetic mechanisms affecting gene activity are being discovered. Such processes involve a complex interplay between DNA methylation, histone modifications, and non-coding RNAs, notably small interfering RNAs (siRNAs) and micro RNAs (miRNAs). Epigenetic regulation is not only important for generating differentiated cell types during plant development, but also in maintaining the stability and integrity of their respective gene expression profiles. Although epigenetic processes are essential for normal development, they can become misdirected which leads to abnormal phenotypes and diseases, especially cancer. Sensing environmental changes and initiating a quick, reversible and appropriate response in terms of modified gene expression is of paramount importance for plants which are sessile autotrophs. Although epigenetic mechanisms help to protect plant cells from the activity of parasitic sequences such as transposable elements, this defense can complicate the genetic engineering process through transcriptional gene silencing. Epigenetic phenomena have economic relevance in the case of somaclonal variation: a genetic and phenotypic variation among clonally propagated plants from a single donor genotype. The success of sequencing projects on model plants has created widespread interest in exploring the epigenome in order to elucidate how plant cell decipher and execute the information stored and encoded in the genome. New high-throughput techniques are making it easier to map DNA methylation patterns on a large scale and results have already provided surprises.

Epigenetic Lessons from Transgenic Plants

Floriculture, Ornamental and Plant Biotechnology: Advances and Topical Issues Vol. II, 2006

Transgenic plant studies have lead to the breakthrough discovery of RNA silencing as a conserved mechanism for gene regulation across kingdoms. Recent molecular genetic studies have revealed a major role for RNA silencing in the formation of silent chromatin, characterized by histone modifications and dense DNA methylation. These epigenetic marks ensure stable, yet potentially reversible, transmission of the silent state of genetic elements such as transgenes and transposable elements through multiple cell divisions, and in some cases, through successive generations. It is now recognized that epigenetic control mechanisms play a fundamental role in preserving the integrity of the genome against invasive parasitic nucleic acid elements such as viruses and transposons. It is also becoming clear that epigenetic processes are of major evolutionary significance in plants by providing plasticity to the genome to adjust to environmental changes and by stabilizing the genome after polyploidization events. RNA silencing has become a powerful research tool to elucidate gene function in reverse genetics studies and has been applied in the production of virus resistant crops. An enhanced understanding of epigenetic processes is therefore not only of academic interest but will also provide new tools and techniques for plant scientists involved in conventional and biotechnology-based horticultural and agricultural crop improvement.

Epigenetics and plant genome evolution

Current Opinion in Plant Biology, 2014

Epigenetics was envisioned as a topic to inform evolutionary theory, but the interplay between epigenetics and evolution has received little attention. With the advent of high-throughput methods, it is now routine to measure the genome-wide distribution of epigenetic marks, and these genome-wide patterns are providing insights into evolutionary processes. For example, DNA methylation is associated with transposable element silencing but also with repression of the expression of nearby genes, perhaps caused by the spread of methylation into regulatory regions. This repressive effect, which is typically deleterious, is acted upon by purifying selection. These dynamics may also govern the outcome of hybridization and polyploid events by affecting homoeolog expression. Finally, genes are also often methylated, but the implications of genic methylation for plant gene and genome evolution are not yet characterized fully.

Plant Epigenetics: Mechanisms and Applications

Journal of Epigenetics , 2019

Plant epigenetic has become one of the key research topics not only as the subject of basic research, but also as a new source of useful traits for plant breeding. Epigenetic regulation is necessary for the production of differentiated cells throughout plant development, as well as maintaining the stability and integrity of the gene expression profiles. Although epigenetic processes are essential for natural growth, they can become misdirected led to abnormal phenotypes and diseases. Epigenetics is the study of heritable phenotype changes that do not involve alterations in the DNA sequence. The microstructure (not code) of DNA itself or the associated chromatin proteins may be modified, causing activation or silencing. This mechanism enables differentiated cells in a multicellular organism to express only the genes which are necessary for their own activity. In this review, our goal is to introduce epigenetics and its different applications in plants, especially in production of transgenic plants, plants tolerate to biotic and abiotic stresses and understanding the mechanisms of gene silencing. Also, in this review, we have referred to the role of transposons in epigenetic, epigenetic engineering methods, epigenetic fingerprinting and ultimately methods for epigenetic data analysis and related databases

Epigenetics Regulates Reproductive Development in Plants

Plants

Seed, resulting from reproductive development, is the main nutrient source for human beings, and reproduction has been intensively studied through genetic, molecular, and epigenetic approaches. However, how different epigenetic pathways crosstalk and integrate to regulate seed development remains unknown. Here, we review the recent progress of epigenetic changes that affect chromatin structure, such as DNA methylation, polycomb group proteins, histone modifications, and small RNA pathways in regulating plant reproduction. In gametogenesis of flowering plants, epigenetics is dynamic between the companion cell and gametes. Cytosine DNA methylation occurs in CG, CHG, CHH contexts (H = A, C, or T) of genes and transposable elements, and undergoes dynamic changes during reproduction. Cytosine methylation in the CHH context increases significantly during embryogenesis, reaches the highest levels in mature embryos, and decreases as the seed germinates. Polycomb group proteins are important...

Molecular Mechanisms of Epigenetic Variation in Plants

International Journal of Molecular Sciences, 2012

Natural variation is defined as the phenotypic variation caused by spontaneous mutations. In general, mutations are associated with changes of nucleotide sequence, and many mutations in genes that can cause changes in plant development have been identified. Epigenetic change, which does not involve alteration to the nucleotide sequence, can also cause changes in gene activity by changing the structure of chromatin through DNA methylation or histone modifications. Now there is evidence based on induced or spontaneous mutants that epigenetic changes can cause altering plant phenotypes. Epigenetic changes have occurred frequently in plants, and some are heritable or metastable causing variation in epigenetic status within or between species. Therefore, heritable epigenetic variation as well as genetic variation has the potential to drive natural variation.