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14 ERA-CAPS: INvestigating TRiticeae EPIgenomes for Domestication (INTREPID)

ReferenceBB/N005104/2
Principal Investigator / Supervisor Professor Anthony Hall
Co-Investigators /
Co-Supervisors		 Professor Neil Hall, Dr John Kenny
Institution Earlham Institute
DepartmentResearch Faculty
Funding typeResearch
Value (£) 309,763
StatusCompleted
TypeResearch Grant
Start date 01/10/2016
End date 30/03/2019
Duration30 months

Abstract

The production of new hybrids is an 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. The scale and heritability of epigenetic modifications therefore needs to be measured, related to potential changes in gene and chromosome function 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. 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; an efficient method for the cost-effective sequencing of the gene space of multiple wheat genomes and for determining genome-wide DNA methylation patterns an improved understanding of the mechanisms of epigenetic inheritance and evidence of altered gene expression in wheat hybrids. This 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 an 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.

Summary

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 491, 705) 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 proposal 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.

Impact Summary

Wheat is one of the three global crops providing the bulk of human nutrition. Large-scale coordinated research programmes are aiming to increase yields and reduce agricultural inputs in order to meet future consumption patterns and to mitigate the predicted effects of a changed growing climate. This project will have a fundamentally important impact on wheat breeding by understanding, for the first time, the extent of inherited epigenetic variation in wheat lines, and its consequences on genome function and predicted phenotypes. Such variation has been predicted to contribute to creating new phenotypes and heterotic yield increases in hybrids, but it has not yet been assessed at a genome scale in wheat. Such variation may explain aspects of missing or low heritability and could be used in breeding programmes. The project will show how new epigenetic variation is generated in hybrids, how such variation is stabilized, how new patterns of gene expression are created and stabilized; and how patterns of epi-alleles and traits can be influenced by the environment. This can guide crop improvement strategies by determining the choice of parents for hybrid formation, and by identifying subsequent epigenetic variation and measuring its stability across generations before incorporation into breeding programmes. In addition to these basic and applied outputs of this project, we will develop bioinformatic tools for identifying and analysing epigenetic marks and tracking their potential phenotypic consequences through gene expression network analyses. These impacts will be delivered through the open cyber-infrastructure provided by iPlant and through databases such as Ensembl genomes, through close engagement with breeders, and through publications and training programmes.
Committee Not funded via Committee
Research TopicsCrop Science, Plant Science
Research PriorityX – Research Priority information not available
Research Initiative ERA-NET on Coordinating Action in Plant Sciences (ERA-CAPS) [2013-2014]
Funding SchemeX – not Funded via a specific Funding Scheme
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