Joint Calls

Investigating Triticeae Epigenomes for Domestication

  • Acronym INTREPID
  • Duration 36
  • Project leader Hall, Anthony (PL), UK, Department of Functional Genomics
  • Other project participants Bevan, Michael, UK, John Innes Centre
    Mayer, Klaus, Germany, Helmholtz Zentrum München
    McCombie, W. Richard, USA, Cold Spring Harbor Laboratory
  • Funding NSF awards are pending
  • Total Granted budget ca. € 2.228.675


The production of new hybrids is a centrally important way of improving crops as they exhibit novel
traits directly after hybrid formation, which are not found in progenitor parents. Growing evidence
points to possible epigenetic origins for these emergent phenotypes. Our recent genome-wide map of
methylation in maize (Regulski et al 2013) revealed extensive cytosine methylation variation that can
alter gene functions and be stably inherited in ways reminiscent of paramutation. The scale and
heritability of epigenetic modifications therefore needs to be measured, related to potential changes in
gene and chromosome function (for example recombination), and then taken into account in breeding
as a source of variation in breeding.
Here we aim to build on our collective experience in plant epigenetics and genomics to map the
epigenome of bread wheat, which, together with maize and rice, provides most human nutrition.
Outputs of this project will be of immediate value for breeders for understanding the extent and
contribution of epi-allelic variation to traits and in the choice of parental epi-allelic variation in
making new hybrids. The project will also exploit experimental advantages of wheat to understand
how epigenetic marks are re-programmed during the formation of new wheat hybrids, and how their
independently maintained genomes influence each other during stabilization of the new hexaploid
genomes. We have established four key foundations for mapping and understanding the wheat
epigenome: the first genome sequence assembly of wheat (Brenchley et al 2012); an efficient method
for the cost-effective sequencing of the gene space of multiple wheat genomes and for determining
genome- wide DNA methylation patterns (Gardiner et al submitted); an improved understanding of the
mechanisms of epigenetic inheritance (Calarco et al 2012); and evidence of altered gene expression in
wheat hybrids (Pfeifer et al 2014).
The project brings together world- leading expertise in crop genome sequencing, bioinformatics and
genome analysis to work in four comprehensive linked research projects: defining the complete
epigenome of the wheat including repetitive regions; surveying the epigenomes of 8 diverse elite
wheat lines; identifying how epigenetic marks are re-set and stabilized during the formation of new
wheat hybrids and how these marks influence gene expression; and determining if environmental
conditions can influence the stabilization of epigenetic marks.
This project will generate new knowledge of how epi-alleles are formed and maintained, how the
genomes of polyploid wheat influence each other, and how they influence gene function. It will have a
fundamentally important impact on wheat breeding by establishing the extent of epigenetic variation
in wheat lines and its consequences on genome function and predicted phenotypes. Such information
can guide the choice of parents for hybrid formation and explain aspects of missing heritability.
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