Harnessing cytosine DNA hypomethylation to explore the potential for crop improvement in wheat

 

Our overall aim is to generate genome-wide DNA hypomethylated wheat to study i) synthetic remodeling of meiotic recombination as a tool to reduce linkage drag and facilitate introgression of economically important traits and ii) epigenetic control of wheat heterosis, i.e. hybrid vigor between wheat parents with synthetically induced DNA methylation differences.

The Idea

Background

Present-day wheat research is aimed at improving yield and performance under variable environmental conditions. Several approaches can lead to improved yields, including i) introgression of economically valuable traits from wild relatives and ii) exploitation of hybrid vigour or heterosis. The main limitation of trait introgression is the low number and uneven distribution of meiotic recombination events along chromosomes. This leads to a phenomenon called ‘linkage drag’ whereby desirable traits, for example, abiotic and biotic stress resistances are introgressed together with genetically linked deleterious traits, for example, disease susceptibility. Heterosis, or hybrid vigour, a phenomenon where progeny outperforms either parent, can lead to a dramatic yield increase in wheat. However, the molecular basis of heterosis is not yet fully understood making it a haphazard strategy.

Cytosine DNA methylation (hereinafter, DNA methylation) is an important epigenetic mark that contributes to genome integrity via transcriptional silencing of transposable elements (TE). In addition, in a model plant Arabidopsis, DNA methylation is implicated in shaping meiotic recombination landscape and heterosis. Specifically, a genome-wide loss of DNA methylation leads to increased crossover frequencies in gene-rich regions, whereas offspring of genetically identical parents with synthetically induced variation in DNA methylation levels can display hybrid vigor.

Our overall aim is to generate genome-wide DNA hypomethylated wheat to study i) synthetic remodeling of meiotic recombination as a tool to reduce linkage drag and facilitate introgression of economically important traits and ii) epigenetic control of wheat heterosis, i.e. hybrid vigor between wheat parents with synthetically induced DNA methylation differences.

Specific project aims

In Arabidopsis, tomato and rice, DDM1, a SNF2-family nucleosome remodeler, is essential for normal DNA methylation. Among multiple factors required for initiation and maintenance of DNA methylation, including several DNA methyltransferases, DDM1 is unique in that its loss affects both meiotic recombination and hybrid vigor. Therefore, in our proposal we will disrupt the function of putative DDM1 in wheat and thus develop a platform to study the effects of synthetically DNA hypomethylated wheat genomes on meiotic crossovers and heterosis.

We have identified putative wheat DDM1 homologues (TaDDM1, Fig. 1) and will use OpenPlant funding to mutate TaDDM1 via CRISPR/Cas9. Specifically, we will identify and test gene editing efficiencies of a number of guide RNAs targeting putative TaDDM1 homologues in vitro and, using a transient protoplast assay, in vivo. This will dramatically increase the efficiency and success rates of generating taddm1 mutants in wheat via stable transformation, our aim immediately beyond the OpenPlant project.

The Team

Dr Natasha Elina,
Senior Research Associate and a Broodbank post-doctoral fellow, Department of Plant Sciences, University of Cambridge

Dr Ian Henderson,
Reader , Department of Plant Sciences, University of Cambridge

Dr Alison Bentley,
Director of Genetics and Breeding, National Institute of Agricultural Botany

Prof. Keith Edwards,
Professor of Cereal Functional Genomics, University of Bristol


Project Outputs

Project Report

Summary of the project's achievements and future plans

Project Proposal

Figure 1

Original proposal and application

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Project Resources


Jim Haseloff