Heritable Epigenetic Variation and its Potential Applications for Crop Improvement (original) (raw)

From epigenetics to epigenomics and their implications in plant breeding

2012

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.

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.

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.

Unlocking the Arabidopsis epigenome

Epigenetics, 2009

T he patterns of DNA methylation, referred to as the "methylome," must be faithfully propagated for proper development of plants and mammals. 1-4 However, it has been unclear to which extent transgenerational epigenetic inheritance will be affected after DNA methylation distribution has been altered. Recently, three reports have addressed this issue in the model plant Arabidopsis thaliana. 5-7 Here we revisit the results of these experiments addressing the stability of epigenetic inheritance within two populations of epigenetic recombinant inbred lines (epiRILs), in which mosaic epigenomes were subjected to inbreeding for multiple generations. The manner in which the epigenetic variation was induced differed between the two populations, one by adversely affecting chromatin remodeling and the second by impairing the maintenance of DNA methylation, yet the comparison of the results provides a broader view of transgenerational epigenetic inheritance that may find parallels in other organisms.

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.

Will epigenetics be a key player in crop breeding?

Frontiers in Plant Science

If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and iden...

Epigenetics and its role in effecting agronomical traits

Frontiers in Plant Science

Climate-resilient crops with improved adaptation to the changing climate are urgently needed to feed the growing population. Hence, developing high-yielding crop varieties with better agronomic traits is one of the most critical issues in agricultural research. These are vital to enhancing yield as well as resistance to harsh conditions, both of which help farmers over time. The majority of agronomic traits are quantitative and are subject to intricate genetic control, thereby obstructing crop improvement. Plant epibreeding is the utilisation of epigenetic variation for crop development, and has a wide range of applications in the field of crop improvement. Epigenetics refers to changes in gene expression that are heritable and induced by methylation of DNA, post-translational modifications of histones or RNA interference rather than an alteration in the underlying sequence of DNA. The epigenetic modifications influence gene expression by changing the state of chromatin, which under...

Can Epigenetics Guide the Production of Better Adapted Cultivars?

Agronomy

As the global population continues to grow, food demand will be reaching levels which current agricultural practices cannot meet. This projected demand combined with the negative impacts of climate change on crop production calls for more careful breeding efforts to develop better adapted plants more tolerant to climate fluctuations. Fortunately, the development of molecular biology techniques like genome, transcriptome and epigenome sequencing now offer new approaches to help classical breeding meet these challenges. This review focuses on the potential of epigenetic approaches, particularly the creation of epigenetic markers (epi-markers) for guiding the selection process in breeding programs. Many studies have indeed successfully linked stable epigenetic modifications to different plant traits of interest but research on the applicability of using epi-markers in breeding programs is still scarce. This review emphasises the current progress that has been made with regards to the u...