Exploiting induced and natural epigenetic variation for crop improvement

KEY POINTS * 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. ABSTRACT 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. Access through your

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INTROGRESSION OF UNTAPPED DIVERSITY INTO ELITE WHEAT LINES Article 07 October 2021 MULTI-PARENT POPULATIONS IN CROPS: A TOOLBOX INTEGRATING GENOMICS AND GENETIC MAPPING WITH BREEDING Article

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references ACKNOWLEDGEMENTS 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. AUTHOR INFORMATION AUTHORS AND AFFILIATIONS * Department of Plant and

Microbial Biology, University of Minnesota, Saint Paul, 55108, Minnesota, USA Nathan M. Springer * Department of Genetics, The University of Georgia, Athens, 30602, Georgia, USA Robert J.

Schmitz Authors * Nathan M. Springer View author publications You can also search for this author inPubMed Google Scholar * Robert J. Schmitz View author publications You can also search for

this author inPubMed Google Scholar CORRESPONDING AUTHORS Correspondence to Nathan M. Springer or Robert J. Schmitz. ETHICS DECLARATIONS COMPETING INTERESTS The authors declare no competing

financial interests. POWERPOINT SLIDES POWERPOINT SLIDE FOR FIG. 1 POWERPOINT SLIDE FOR FIG. 2 POWERPOINT SLIDE FOR FIG. 3 POWERPOINT SLIDE FOR FIG. 4 GLOSSARY * Traits Any measurable

aspect of an organism, including morphological, biochemical and molecular properties. * Transgressive segregation The situation in which offspring (F1, F2 or later generations) exhibit

phenotypes that transgress (are outside of) the parental phenotypic range. * Heritable variation Information in the genome that is transmitted to offspring or daughter cells. * Genomic

selection The use of genetic markers that are spread throughout the genome to select individuals with desired predicted breeding values. * Paramutation An interaction between alleles in

which one alleles triggers a heritable change at the other allele, resulting in altered expression or chromatin state. * Imprinting Differential expression of alleles depending on

parent-of-origin of the allele. * Wide crosses Crosses between very distantly related members of the same species or between individuals of related species. * RNA-directed DNA methylation

(RdDM). The mechanism by which 24-nt small interfering RNAs can direct DNA methylation to specific genomic loci. * Accessions Individuals isolated from a single geographical area. An ecotype

comprises many accessions from a similar ecological range. * Differentially methylated regions (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. * Epialleles 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.

* Epigenetic recombinant inbred line (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. * Polyploidization

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). * Linkage disequilibrium 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. * Scions Shoot or branch of a plant that is grafted to a

rootstock. * Grafting 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. * Rootstock The root system of a plant with the shoot removed onto which another variety is grafted. * Epigenetic quantitative trait loci (epiQTL).

Epigenetic variants that are associated with a trait and that do not have any changes in the DNA sequence. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS

ARTICLE Springer, N., Schmitz, R. Exploiting induced and natural epigenetic variation for crop improvement. _Nat Rev Genet_ 18, 563–575 (2017). https://doi.org/10.1038/nrg.2017.45 Download

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