• Research

Investigating Triticeae epigenomes for domestication (INTREPID)

Exploring the wheat epigenome.

Plant breeding uses DNA sequence variation to make new allelic combinations for crop improvement. Our creation of the first wheat gene sequence assemblies (Brenchley et al Nature) has enabled new levels of high throughput precise genotyping for breeding this globally important crop. Nevertheless, there are other levels of heritable variation, such as epigenetic modifications, that are widely thought to play a key role in shaping genomes and creating new variation.

We have recently developed highly efficient re-sequencing technologies for wheat that can measure DNA methylation in genes of multiple lines. This provides an outstanding opportunity to assess epigenetic variation in a major polyploid crop and understand how it may influence traits.

The overall objective of this project is to use newly available wheat genome resources, together with  our innovative application of exome capture and bisulphite sequencing, to measure epigenetic modifications in wheat genes, and relate these to gene expression and the acquisition of new phenotypes, and how they may contribute to genetic changes such as gene loss during polyploid formation.


A genome-wide survey of DNA methylation in hexaploid wheat

Laura-Jayne Gardiner, Mark Quinton-Tulloch, Lisa Olohan, Jonathan Price, Neil Hall, Anthony Hall

Genome Biology201516:273


John Kenny

University of Liverpool

Micheal Bevan

John Innes Centre

Klaus Mayer

Helmholtz-Zentrum Muenchen, Germany

Dick McCombie


Rob Martienssen


Impact statement.

The research programme will take a comprehensive approach to defining the epigenome of bread wheat, the functional consequences of epigenetic modifications, how the genome is re-shaped, stabilized and inherited in  newly formed hybrids, and how the environment may influence patterns of epigenetic modification. These are fundamentally important questions in biology and are necessary for understanding trait variation in wheat hybrids. This project will reveal new sources of potentially useful variation for crop improvement. The collaboration draws on the best expertise worldwide in epigenetics and wheat genomics to work in two integrated Work Programmes. All data will be managed in an open iPlant cyberinfrastructure, integrated with wheat genome resources  and provided in publicly accessible formats.

The specific objectives of this integrated research programme are to:

  1. Define the epigenome of the genome reference Chinese Spring 42, correlate epigenetic modifications to changes in gene expression and chromosome dynamics such as recombination, and establish a community standard for future work
  2. Survey the epigenomes of 8 elite wheat varieties to map variation in the epigenomes, identify epi-alleles and make markers to a subset of these, and assess the influence of breeding on the epigenome and its contribution to key traits
  3. Define epigenome variation in two tetraploid (AABB) and four diploid (DD) progenitors of bread wheat that will be used to make new hybrids.
  4. Establish how epigenetic marks are placed down in newly created synthetic hybrid wheat (SHW), how these are stabilised in subsequent generations, and how this affects gene structure and expression;
  5. Determine if environmental conditions such as elevated temperatures can influence patterns of epigenetic modifications during the stabilization of newly formed hybrids.