14 ERA-CAPS: INvestigating TRiticeae EPIgenomes for Domestication (INTREPID)
Lead Research Organisation:
Earlham Institute
Department Name: Research Faculty
Abstract
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.
Technical Summary
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.
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.
Planned Impact
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.
Organisations
- Earlham Institute (Lead Research Organisation)
- University of Paris-Saclay (Collaboration)
- RAGT Seeds (Collaboration)
- KWS UK (Collaboration)
- Lancaster University (Collaboration)
- IBM (Collaboration)
- Australian National University (ANU) (Collaboration)
- LGC Ltd (Collaboration)
- Cold Spring Harbor Laboratory (CSHL) (Collaboration)
- Kansas State University (Collaboration)
- International Centre for Maize and Wheat Improvement (CIMMYT) (Collaboration)
- Helmholtz Zentrum München (Collaboration)
Publications
Concia L
(2020)
Wheat chromatin architecture is organized in genome territories and transcription factories.
in Genome biology
Gardiner L
(2017)
Hidden variation in polyploid wheat drives local adaptation
Gardiner LJ
(2020)
Understanding DNA Methylation Patterns in Wheat.
in Methods in molecular biology (Clifton, N.J.)
Gardiner LJ
(2018)
Hidden variation in polyploid wheat drives local adaptation.
in Genome research
Gardiner LJ
(2019)
Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.
in GigaScience
Gardiner LJ
(2016)
Mapping-by-sequencing in complex polyploid genomes using genic sequence capture: a case study to map yellow rust resistance in hexaploid wheat.
in The Plant journal : for cell and molecular biology
Olohan L
(2018)
A modified sequence capture approach allowing standard and methylation analyses of the same enriched genomic DNA sample.
in BMC genomics
| Description | First description of the wheat epigenome: • Developed technology/methodology advance combining sequence capture, bisulfite treatment and genome specific assignment of reads using homoeologous SNPs • Analysed genome wide methylation patterns including reports of genome specific methylation and conserved methylation patterns across the three genomes • Associating methylation of a single genome with genome specific gene expression • shown Non-CpG methylation is enriched in sub-genome specific methylation suggesting a potential association of sub-genome specific methylation with pseudo genes • Shown that tri-genome methylation is highly conserved with a diploid wheat progenitor while sub-genome specific methylation shows more variation i.e. context specific variation. Population epigenomic diversity across the A. E. Watkins bread wheat landrace cultivar collection There is a high level of genetic diversity in the A. E. Watkins bread wheat landrace collection and, we predict, also a high level of epigenetic diversity. This represents a dual source of variation not used in modern breeding that can be exploited for wheat improvement. Here, we analyze genotype and DNA methylation, an important mechanism of epigenetic gene expression control that can be passed between generations, across a core set of the Watkins collection. This core set includes 105 lines and captures the majority of the diversity in the Watkins collection. Using sodium bisulfite treatment and targeted gene enrichment we can survey genome-wide methylation and genotype across the three sub-genomes of allohexaploid wheat. Using a 12Mb capture probe set we were able to analyze an average of 48 Mb of the wheat genome per sample at a minimum depth of 10X. Methylation shows high variability within the Watkins collection with 42.1% of analyzed sites classified as single methylation polymorphism sites, or SMPs, between the samples. The vast majority of these SMPs (91.5%) are rare variants that were seen in less than 10% of the samples. Tri-genome methylation is more conserved between accessions than genome specific methylation and therefore likely to be the most stable form of methylation. Genome specific methylation sites show enrichment for homoeologous SNPs that differentiate the genome that is methylated from the other two sub-genomes and this SNP typically infers a CpG site from a non-CpG site. We have observed that methylation is a standalone source of variation in the absence of genetic variation, however, it is clear that if two wheat accessions show more closely related genotypes then their methylomes are more likely to be related. Both methylation and genotype are clearly influenced by the geographical origin of the sample, although it appears that genotypic profiles cluster across wider geographic regions while the methylation profiles of accessions tend to cluster into more local groups. These lines clustering locally by methylation may be more likely to have evolved with similar environmental conditions for growth and this may have influenced their methylation profiles. Therefore, we hypothesize that methylation acts as a fast-adaptive response to environmental stimulus that may later become 'hard coded' as SNPs. We are currently collaborating with Klaus Mayer's team in Munich to assess the gene networks that are targeted by methylation across the Watkins collection and how these vary between accessions. Furthermore, we are analyzing RNA-seq data for 12 of the samples from the Watkins collection to allow correlation of genotype, methylation and gene expression in this analysis. Finally, we are working with Cold Spring Harbor laboratories to sequence the full methylome of Chinese Spring wheat. Completion of Objectives 1. Defining the epigenome of Chinese Spring 42. Switch to Paragon and Elite UK cultivar a) We have generated a first survey of the epigenome of Chinese spring, identified differential methylation of the A, B and D sub-genomes and correlated this with changes in gene expression. (EI) b) We have built libraries and have generated shot gun Methyl-seq of the whole of Chinese Spring at 50X coverage at CSHL. While in the process of generating this data a similar data set was generated and published therefore we switched from Chinese Spring to Paragon a UK Elite cultivar. This data will be included in a publication later this year as part of the 10 plus Wheat genomes. 2. Development of capture probes for methylation analysis. Captures developed- single molecule sequencing tested. a) We have generated a 12MB capture probe set for re-sequencing the epigenome. This includes promoters, exons and introns but is incomplete, allow a survey across the genome. (MIPS, EI) b) In collaboration with Eduard Akhunov (KSU, USA) and Klaus Meyer/Manuel Spangel we have designed a new capture probe set based on the whole gene space identified in the latest NR-Gene Chinese spring assembly, this included 2kb of promoter space per gene and miRNA. (MIPS, EI) c) We have tested Pacific Biosciences RS II technology for identifying methylation in wheat based on polymerase enzyme kinetics. We currently have issues with sample volumes. 3. Epigenome variation in elite wheat cultivars. Our initial strategy was to look at variation in epigenome over 8 elite cultivars. During the review process and in our kick off meeting it was decided to expand to 105 cultivars, representing the Watkins core collection, an important wheat diversity collection. a) We have developed an approach were we genotype and epi-type from the same captured material using the 12MB capture probe set (EI) b) We have surveyed the epigenome and genotyped all 105 lines. (EI) c) We have identified conserved and variable epigenetic sites across the genome, we are currently identifying genes and processes that are being methylated (EI) d) We have analysed the data identifying differences between epi-type and genotype, with some cultivars sharing a common epi-type but different genotype. (EI) e) We have associated this material with geographical position and climatic data. (EI) f) Methylation in wheat appears to be playing a role in the rapid evolution of cultivars to specific agricultural environments. We are currently identifying the biological processes associated with these adaptions. (EI, MIPS) 4. Epigenetic variation in new synthetics a) The parents of new synthetics were tested in summer 2016 for compatibility and 4 pair-wise combinations of AABB and DD donors were selected according to the different efficiencies of hybrid formation. For the main crosses in 2017 the parents have been taken out of vernalisation and crossing will occur in the spring. A revised sampling scheme is described below that will sample new hybrids. (JIC) b) The data has been generated and analysed and a manuscript is currently in preparation (EI,MIPS) |
| Exploitation Route | Crop breeding is driven by genetic variation. It is likely that epigenetic variation significantly contributes to the phenotypic variation for some of the key traits breeders are interested in. We have already established that a huge amount of epi-genetic variation can be seen in a diverse global collection of bread wheat landraces. While this is of fundamental biological interest, it is not useful to wheat breeders. Our new EAGER proposal following on from INTREPID will turn this fundamental discovery into a breakthrough technology. To achieve this over the past few months we have worked with breeders to identify: genes and pathways controlling key traits relevant to them; a panel of relevant material and a clear understanding of how an assay could be developed that would integrate into existing genotyping pipelines. The EAGER project will also address many of the questions breeders are asking. Is there epigenetic variations in genes controlling traits they are interested in? How stable is the epigenetic variation? How is it inherited? Can I just follow a haplotype with existing SNP markers or are there methylated and unmethylated versions of the same haplotype. This EAGER project will address this questions and deliver them a KASP based assay to track epi-alleles. |
| Sectors | Agriculture, Food and Drink |
| Description | The results are now being translated as part of an EAGER proposal aiming to characterising epigenetic variation ok UK, US and CIMMYT material. We are also in discussion with LGC to take this forward. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink |
| Description | 18-BTT: A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES |
| Amount | £273,500 (GBP) |
| Funding ID | BB/S020942/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2019 |
| End | 03/2021 |
| Description | SEQUENCING THE GENIC PORTION OF SEEDS OF DISCOVERY ADVANCE PRE- BREEDING GERMPLASM TO UNCOVER THE GENETIC VARIATION |
| Amount | £330,000 (GBP) |
| Funding ID | BBS/OS/NW/000017 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2016 |
| End | 10/2019 |
| Title | Methyl-seq methods for wheat |
| Description | Background: Bread wheat has a large complex genome that makes whole genome resequencing costly. Therefore, genome complexity reduction techniques such as sequence capture make re-sequencing cost effective. With a high- quality draft wheat genome now available it is possible to design capture probe sets and to use them to accurately genotype and anchor SNPs to the genome. Furthermore, in addition to genetic variation, epigenetic variation provides a source of natural variation contributing to changes in gene expression and phenotype that can be profiled at the base pair level using sequence capture coupled with bisulphite treatment. Here, we present a new 12 Mbp wheat capture probe set, that allows both the profiling of genotype and methylation from the same DNA sample. Furthermore, we present a method, based on Agilent SureSelect Methyl-Seq, that will use a single capture assay as a starting point to allow both DNA sequencing and methyl-seq. Results: Our method uses a single capture assay that is sequentially split and used for both DNA sequencing and methyl-seq. The resultant genotype and epi-type data is highly comparable in terms of coverage and SNP/methylation site identification to that generated from separate captures for DNA sequencing and methyl-seq. Furthermore, by defining SNP frequencies in a diverse landrace from the Watkins collection we highlight the importance of having genotype data to prevent false positive methylation calls. Finally, we present the design of a new 12 Mbp wheat capture and demonstrate its successful application to re-sequence wheat. Conclusions: We present a cost-effective method for performing both DNA sequencing and methyl-seq from a single capture reaction thus reducing reagent costs, sample preparation time and DNA requirements for these complementary analyses. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | As yet not known |
| Title | promoter exon capture platform |
| Description | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an 'island strategy' can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Currently being used by DFW, CIMMYT and US CAPS projects |
| Title | A genome-wide DNA methylation survey of hexaploid wheat |
| Description | DNA methylation is an important mechanism of epigenetic gene expression control that can be passed between generations. Here, we use sodium bisulfite treatment and targeted gene enrichment to study genome-wide methylation across the three sub-genomes of allohexaploid wheat. While the majority of methylation is conserved across all three genomes we demonstrate that differential methylation exists between the sub-genomes in approximately equal proportions. We correlate sub-genome specific promoter methylation with decreased expression levels and show that altered growing temperature has a small effect on methylation state, identifying a small but functionally relevant set of methylated genes. Finally, we demonstrate long-term methylation maintenance using a comparison between the D sub-genome of hexaploid wheat and its progenitor Aegilops tauschii. We show that tri-genome methylation is highly conserved with the diploid wheat progenitor while sub-genome specific methylation shows more variation. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2016 |
| Provided To Others? | Yes |
| Impact | Differential methylation between homologous genomes in wheat, evidence for the stability of methylation in the genie portion of wheat |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB8762 |
| Title | Epigenomic variation across a polyploid wheat diversity collection |
| Description | We survey genotype and DNA methylation across the core Watkins bread wheat landrace collection. We observe high transposable element variability and expansion, most frequently in retrotransposons, alongside high epigenomic diversity; while there is an association between methylation and genotype, methylation is a standalone source of variation between closely related accessions. Both methylation and genotype are influenced by geographic origin. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Lead to an EAGER grant to translate the research |
| URL | https://www.ebi.ac.uk/ena/data/view/PRJEB23320 |
| Title | Watkins core collection re-sequencing data |
| Description | Re-sequence data for the Watkins collection |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | International collabration |
| URL | https://grassroots.tools/data/under_license/toronto/ |
| Title | promoter exon capture data |
| Description | The data contain the design space for the promoter and exon used in our capture |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. |
| URL | https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c... |
| Description | CIMMYT seeds of discovery |
| Organisation | Australian National University (ANU) |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Collaboration to provide Advance genetic approaches |
| Collaborator Contribution | Access to wheat material and phenotyping data |
| Impact | None yet |
| Start Year | 2016 |
| Description | CIMMYT seeds of discovery |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | Collaboration to provide Advance genetic approaches |
| Collaborator Contribution | Access to wheat material and phenotyping data |
| Impact | None yet |
| Start Year | 2016 |
| Description | EAGER - Eduard Akhunov |
| Organisation | Kansas State University |
| Country | United States |
| Sector | Academic/University |
| PI Contribution | Joint funding and publications, method development |
| Collaborator Contribution | Access to material and bioinformatics methods |
| Impact | EAGER -BBSRC grant A PATHWAY TO THE EXPLOITATION OF EPIGENETIC VARIATION IN UK, US AND INTERNATIONAL BREEDING PROGRAMMES Gardiner, L.-J., Brabbs, T., Akhunov, A., Jordan, K., Budak, H., Richmond, T., et al. (2019). Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat. GigaScience. http://doi.org/10.1093/gigascience/giz018 IWGS Consortium, Jordan, K. W., Wang, S., Lun, Y., Gardiner, L.-J., MacLachlan, R., et al. (2015). A haplotype map of allohexaploid wheat reveals distinct patterns of selection on homoeologous genomes. Genome Biology, 16(1), 680. http://doi.org/10.1186/s13059-015-0606-4 |
| Start Year | 2018 |
| Description | IBM |
| Organisation | IBM |
| Department | IBM UK Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | This project aims to leverage these new resources together with large gene expression data sets to reconstruct regulatory networks controlling important traits. With outputs feeding directly into UK and International wheat research and UK wheat breeding programmes. The collaboration focuses around two large data sets: the first, a high resolution time series data set for wheat and the second, a developmental time course for 16 international elite cultivars. The project aims to: 1. Develop normalisation methods for the transcriptome data sets (RNA-seq data), specific for dealing with the complexities of time course data and a complex polyploid genome. Benchmark these new approaches against existing tools. 2. Develop AI pattern matching algorithms to identify gene-expression modules and correlate these with biological processes. Use pattern matching algorithms to interrogate the high resolution data sets and to identify differences between regulatory networks in elite cultivars 3. Correlate changes in temporal or developmental expression patterns with changes in promoter architecture 4. Use network inference, co-expression and gene modules to reconstruct regulatory networks. Identify how network structure changes over time and between cultivars. This project will have impact for scientists as it will address fundamental questions about temporal regulation of processes in wheat and how a complex networks work across multiple genomes within a polyploid. By comparing networks across elite cultivars it will also have an impact for UK and international wheat breeders, identification of how breeding programmes have changed the architure of regulatory networks. This will have important impact for the selection of future networks for breeders to target or for assessing the selection of breeding material. It will allow breeders to make full use of the new resources and technologies. To ensure the impact to the UK industry is realised we aim to present this work a UK networking meeting and to visit and involve three private UK breeding companies RAGT, KWS and Elsoms seeds in early output from the project. |
| Collaborator Contribution | IBM have are involved in applying ML and AI approaches to analyse gene expression data in wheat and reconstruct gene networks. |
| Impact | https://github.com/AHallLab/PredictingCircadianTime Joint grant with the Alan Turing Institute https://doi.org/10.1101/2021.02.04.429826 |
| Start Year | 2017 |
| Description | INvestigating TRiticeae EPIgenomes for Domestication |
| Organisation | Cold Spring Harbor Laboratory (CSHL) |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | Development of approaches to sequence the epigenome and bioinformatics pipelines |
| Collaborator Contribution | access to material and expertise in systems genomic and bioinformatics. |
| Impact | not yet |
| Start Year | 2015 |
| Description | INvestigating TRiticeae EPIgenomes for Domestication |
| Organisation | Helmholtz Zentrum München |
| Country | Germany |
| Sector | Academic/University |
| PI Contribution | Development of approaches to sequence the epigenome and bioinformatics pipelines |
| Collaborator Contribution | access to material and expertise in systems genomic and bioinformatics. |
| Impact | not yet |
| Start Year | 2015 |
| Description | IWYP |
| Organisation | Australian National University (ANU) |
| Department | Division of Plant Sciences |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | My group lead this work, we are involved in the genotyping and bioinformatics |
| Collaborator Contribution | The three other groups are involved in generating the field phenotyping and plant physiology measurements. |
| Impact | none yet |
| Start Year | 2016 |
| Description | IWYP |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | My group lead this work, we are involved in the genotyping and bioinformatics |
| Collaborator Contribution | The three other groups are involved in generating the field phenotyping and plant physiology measurements. |
| Impact | none yet |
| Start Year | 2016 |
| Description | IWYP |
| Organisation | Lancaster University |
| Department | Lancaster Environment Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My group lead this work, we are involved in the genotyping and bioinformatics |
| Collaborator Contribution | The three other groups are involved in generating the field phenotyping and plant physiology measurements. |
| Impact | none yet |
| 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 | 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 | Moussa Benhamed |
| Organisation | University of Paris-Saclay |
| Country | France |
| Sector | Academic/University |
| PI Contribution | WE are collaborating with Moussa Benhamed to develop Next generation sequencing technology to explore the 3D structural organisation in the wheat nucleus and epigenetic regulation in wheat. |
| Collaborator Contribution | The have built sequencing libraries for design future wheat and are providing staff training |
| Impact | Production of sequencing libraries analysis of histone modification, 3D genome structural organisation and Chromatin accessibility. |
| Start Year | 2018 |
| 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 | Oral presentation and poster presentation at the Plant and Animal genome conference (PAG) San Diego |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Gave a talk entitled "Exploring epigenetic diversity in polyploid wheat" to an audience of scientists including; PIs, postdocs, students, industrial partners and breeders. This highlighted the findings of our epigenetic diversity study. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pag.confex.com/pag/xxvi/meetingapp.cgi/Session/4886 |
| Description | Oral presentation at conference: Training on Durum Wheat Genomics and Breeding, University of Bologna, Italy |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Oral presentation at training conference to educate and train breeders, farmers and students in bioinformatic techniques for the analysis of wheat genomics data |
| Year(s) Of Engagement Activity | 2017 |
| URL | http://www.wheatinitiative.org/events/durum-ewg-workshop-bioinformatics-advance-wheat-breeding |
| Description | Oral presentation at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attended and presented work at the Wheat and Barley Legacy for breeding improvement annual meeting at the University of Haifa, Israel. This built links with researchers in Italy, France and Israel for future collaboration and sparked their interest in epigenetic research. |
| Year(s) Of Engagement Activity | 2017 |
| Description | Oral presentation: Agilent User group meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | I presented my work analysing the methylation of wheat to many of the users of Agilent technology in the UK since I implemented Agilent technology for the study. Many PI's and postdoctoral researchers were present and were interested in how they could use this methodology for their own analyses. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://www.chem.agilent.com/edm/2017/06/Uk_Seminar_2017/Documents/GenUGM/Agenda_GUGM.pdf |
| Description | Talk and discussion with Elsoms seeds |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders. |
| Year(s) Of Engagement Activity | 2018 |