18-BTT: A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES
Lead Research Organisation:
Earlham Institute
Department Name: Research Faculty
Abstract
Epigenetic modification represents a potential source of variation that can be used in breeding programmes, contributing to trait variation. In wheat, we have evidence for wide spread and stable epigenetic variation across global landraces. However, this represents a source of variation that has not to date impacted breeding programmes. In this project we aim to accelerate the translation of this basic knowledge, investigating variation in DNA methylation over a set of agronomically important genes across a panel of UK, US and CIMMYT derived wheat germplasm. This will uncover important information about epigenetic inheritance, stability and its role in adaptation. We will develop an enabling technology for breeders to track epi-alleles. We will use this technology to track epi-alleles that we identify in genes controlling agriculturally important traits and associate them with phenotypic changes.
Technical Summary
Crop breeding is driven by genetic variation. Identifying, understanding and introducing this variation into elite material is critical for the development of new high performance cultivars. There is growing evidence that epigenetic variation presents another important source of variation for breeders to exploit. Epigenetic variation has been associated with agronomically important traits. Our recent work has pioneered the developed methodology for analysing epigenetic variation in hexaploid bread wheat. This has allowed us to uncover a massive amount of untapped and stable epigenetic variation across a diverse collection of wheat.
This two year collaborative EAGER project between the Earlham Institute and Kansas State University offers a breakthrough advance in translation of our fundamental work on DNA methylation to a technology that is transformative, relevant and accessible to wheat breeders for the development of new cultivars. To achieve this we will focus on generating a complete description of the epigenetic state of pathways controlling important adaptive traits relevant to wheat breeders, in material that is relevant to them.
The project will identify 500 wheat genes across pathways controlling adaptive traits relevant to breeders, to design, build and test capture probe sets and investigate methylation state across these genes. The developed probes will be used to characterize methylation state of 500 genes across 288 lines relevant to UK, US and CIMMYT breeding programs. This dataset will be used to address specific biological question: a) Is variation in methylation seen across elite material? b) How is methylation inherited and how stable is it? c) How do different breeding methods and plant biotechnology approaches effect methylation patterns? Then, in collabration with industry, we will develop an assay to track these changes.
This two year collaborative EAGER project between the Earlham Institute and Kansas State University offers a breakthrough advance in translation of our fundamental work on DNA methylation to a technology that is transformative, relevant and accessible to wheat breeders for the development of new cultivars. To achieve this we will focus on generating a complete description of the epigenetic state of pathways controlling important adaptive traits relevant to wheat breeders, in material that is relevant to them.
The project will identify 500 wheat genes across pathways controlling adaptive traits relevant to breeders, to design, build and test capture probe sets and investigate methylation state across these genes. The developed probes will be used to characterize methylation state of 500 genes across 288 lines relevant to UK, US and CIMMYT breeding programs. This dataset will be used to address specific biological question: a) Is variation in methylation seen across elite material? b) How is methylation inherited and how stable is it? c) How do different breeding methods and plant biotechnology approaches effect methylation patterns? Then, in collabration with industry, we will develop an assay to track these changes.
Planned Impact
N/A
Description | We have worked with NEB to test and develop a protocol, however the protocol fails to allow us to multiple samples. We have tested various solutions without success. We are therefore going back to the protocol we previously published ( We have generated genotype data for 30 UK wheat cultivars We have built and tested bioinformatics workflows for comparing methylation between cultivars We have generated SNP data for 36 IK cultivars. we are now generating methyl seq data for these cultivars and 14 international cultivars. |
Exploitation Route | The data will be useful for KWS and RAGT as the data is for line important for their breeding programmes |
Sectors | Agriculture Food and Drink |
Description | Dr Spannagl and Prof. Meyer |
Organisation | Helmholtz Association of German Research Centres |
Department | Helmholtz Zentrum Munchen |
Country | Germany |
Sector | Academic/University |
PI Contribution | We work in collaboration to analyse and annotate complex plant genomes |
Collaborator Contribution | The have supplied expertise and staff time to collabrative projects |
Impact | Rabanus-Wallace, M. T., Hackauf, B., Mascher, M., Lux, T., Wicker, T., Gundlach, H., et al. (2019). Chromosome-scale genome assembly provides insights into rye biology, evolution, and agronomic potential. bioRxiv, 5, 2019.12.11.869693. http://doi.org/10.1101/2019.12.11.869693 L.-J. Gardiner, R. Joynson, J. Omony, R. Rusholme-Pilcher, L. Olohan, D. Lang, C. Bai, M. Hawkesford, D. Salt, M. Spannagl, K. F. X. Mayer, J. Kenny, M. Bevan, N. Hall, and A. Hall, "Hidden variation in polyploid wheat drives local adaptation.," Genome Res, http://doi.org/10.1101/gr.233551.117 Walkowiak, S., Gao, L., Monat, C. et al. Multiple wheat genomes reveal global variation in modern breeding. Nature 588, 277-283 (2020). https://doi.org/10.1038/s41586-020-2961-x |
Start Year | 2016 |
Description | KWS |
Organisation | KWS UK |
Country | United Kingdom |
Sector | Private |
PI Contribution | Generated double haploid population for the IWYP project and provide material for INTREPID and the BBSRC/EAGER work |
Collaborator Contribution | Know of the techniques and approaches we are using, early access to the data we generate |
Impact | Double haploid seed population |
Start Year | 2017 |
Description | KWS methylation collabration |
Organisation | KWS UK |
Country | United Kingdom |
Sector | Private |
PI Contribution | We are generating genome wide methylation data and genotype data for key KWS lines |
Collaborator Contribution | Identified lines to use |
Impact | Not yet |
Start Year | 2019 |
Description | LGC |
Organisation | LGC Ltd |
Department | Genotyping facility |
Country | United Kingdom |
Sector | Private |
PI Contribution | We have identified potential targets for generating Epi-SNPs |
Collaborator Contribution | LGC have been working to combine BS conversion of DNA with a KASP assay to develop a method of tracking epigenetic modifications |
Impact | No output yet |
Start Year | 2019 |
Description | RAGT |
Organisation | RAGT Seeds |
Country | United Kingdom |
Sector | Private |
PI Contribution | Identify key material for our EAGER project and Design future wheat. Support for collaboration with IBM. |
Collaborator Contribution | Discussion of methods and analysis of material relevant to RAGT. |
Impact | none yet |
Start Year | 2018 |
Description | PAG2024 Trticeae Genetics and Genomics |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Title: Using pangenomes in Anger to Reduce reference bias in transcriptomic experiments |
Year(s) Of Engagement Activity | 2024 |