Exploiting induced and natural epigenetic variation for crop improvement

Substantial natural variation in DNA methylation patterns exists within many plant species. This variation can influence gene expression and plant traits.

Variation in DNA methylation can arise through a range of mechanisms and is often inherited in the progeny of plants.

Clonal propagation can lead to epigenetic alleles, which can be stably inherited by regenerated plants. This phenomenon has potential applications for agricultural species that are

propagated through grafting or tissue culture.

New epigenome editing tools will generate opportunities for creating novel epiallelic variants by alteration of DNA methylation or other chromatin modifications. These tools can be used for

crop improvement through epigenome engineering.

Plant breeding has traditionally relied on combining the genetic diversity present within a species to develop combinations of alleles that provide desired traits. Epigenetic diversity may

provide additional sources of variation within a species that could be captured or created for crop improvement. It will be important to understand the sources of epigenetic variation and

the stability of newly formed epigenetic variants over generations to fully use the potential of epigenetic variation to improve crops. The development and application of methods for

widespread epigenome profiling and engineering may generate new avenues for using the full potential of epigenetics in crop improvement.

The authors are grateful to the vibrant community of epigenetic researchers and acknowledge that only a subset of critical works is cited in this article owing to space limitations. The

authors are grateful to J. Noshay for assistance with figure preparation. C. Hirsch, S. Anderson and S. Eichten provided valuable feedback on the manuscript. The authors also appreciate the

constructive feedback from several anonymous reviewers that helped to improve the article.

Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, 55108, Minnesota, USA

Department of Genetics, The University of Georgia, Athens, 30602, Georgia, USA

Any measurable aspect of an organism, including morphological, biochemical and molecular properties.

The situation in which offspring (F1, F2 or later generations) exhibit phenotypes that transgress (are outside of) the parental phenotypic range.

Information in the genome that is transmitted to offspring or daughter cells.

The use of genetic markers that are spread throughout the genome to select individuals with desired predicted breeding values.

An interaction between alleles in which one alleles triggers a heritable change at the other allele, resulting in altered expression or chromatin state.

Differential expression of alleles depending on parent-of-origin of the allele.

Crosses between very distantly related members of the same species or between individuals of related species.

(RdDM). The mechanism by which 24-nt small interfering RNAs can direct DNA methylation to specific genomic loci.

Individuals isolated from a single geographical area. An ecotype comprises many accessions from a similar ecological range.

(DMRs). Genomic regions that have different levels of methylation between sample groups. Can be context specific (CG, CHG or CHH) or can refer to overall methylcytosine content.

Chromatin differences at a locus between different individuals or cells. Note that an epiallele may be due to genetic differences (at cis-genomic or trans-genomic locations). Thus, some

epialleles may reflect epigenetic variation but others may reflect genetic variation.

(epiRIL). A quasi-homozygous line that is almost identical at the genetic level but that segregates at the DNA methylation level. Produced from an initial cross between two individuals with

few DNA sequence differences but with contrasting DNA methylation profiles, followed by 6–8 generations of self-pollination.

Whole-genome duplication events that can occur through the doubling of the chromosomes in a single species (autopolyploidization) or through a cross between related species followed by

chromosome doubling (allopolyploidization).

A measure of whether alleles at two loci coexist in a population in a nonrandom manner. Alleles that are in linkage disequilibrium are found together on the same haplotype more often than

would be expected under a random combination of alleles.

The joining of living material from two individuals to generate a chimaera. In plants this generally is performed through grafting of a scion (a branch or bud) from one plant to a rootstock

from another plant.

The root system of a plant with the shoot removed onto which another variety is grafted.

(epiQTL). Epigenetic variants that are associated with a trait and that do not have any changes in the DNA sequence.

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