Project: Investigating Triticeae Epigenomes for Domestication

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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Call ERA-CAPS 2nd Joint Call: Expanding the European Research Area in Molecular Plant Sciences II

Project partner

Number Name Role Country
Cold Spring Harbor Laboratory United States
German Research Center for Environmental Health Germany
John Innes Centre United Kingdom
University of Liverpool Coordinator United Kingdom