14 ERA-CAPS: INvestigating TRiticeae EPIgenomes for Domestication (INTREPID)
Lead Research Organisation:
John Innes Centre
Department Name: Crop Genetics
Abstract
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Planned Impact
Please refer to the Lead Applicant JeS form.
People |
ORCID iD |
| Michael Bevan (Principal Investigator) |
Publications
Gardiner L
(2017)
Hidden variation in polyploid wheat drives local adaptation
Bevan MW
(2017)
Genomic innovation for crop improvement.
in Nature
Gardiner LJ
(2018)
Hidden variation in polyploid wheat drives local adaptation.
in Genome research
Gardiner LJ
(2019)
Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency.
in Genome biology
Gardiner LJ
(2019)
Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.
in GigaScience
Gardiner LJ
(2020)
A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene.
in PloS one
| Description | Work is progressing well. Initial analyses suggest a prominent role for epigenetic variation in the adaptation of wheat landraces to growth in different environments. Progress in analysing differences between the D genomes of diploid progenitor and hexaploid wheat are advanced we have shown that gene expression in the diploid context (the Ae tauschii DD genome) is reduced in the hexaploid AABBDD genome context. This was validated by quantitative methods and we showed that chromatin compaction occurs that is known to reduce gene expression. Current work aims to assess how quickly this compaction happens after formation of a new polyploid, and we also aim to assess different histone modifications that mark active and inactive genes The data generation is complete: RNAseq; small RNAs; ATAC-seq; HiC proximity ligation coupled to ChIP, and ChIP for active histone marks; bisulphite sequencing for DNA methylation analyses, skim sequencing to assess genome integrity; karyotyping; and RNAseq of deletion lines. We have concluded the data generation phase of this project and developed a genomics framework for comparing gene expression and chromatin states between different lines. Initial analyses show the rapid imposition of new patterns of dominant and repressed gene expression. Some patterns are conserved between different crosses, which some appear to be specific to each cross, suggesting stochastic events may be occurring. Chromatin accessibility patterns are rapidly altered. Our work is starting to demonstrate a central role for chromatin states in imposing and maintaining new patterns of gene expression in newly formed polyploid lines Over the past year we have made excellent progress, despite Covid-19 curtailing lab work and meetings. We have devised new ways of quantifying absolute transcript levels and used this to establish different categories of gene expression changes in newly formed wheat synthetic lines. DNA methylation analyses reveal extensive changes linked to gene expression and histone marks. Finally we have completed chromatin proximity assays that are starting to reveal large scale changes in chromosome organisation in new synthetic lines, such as differential compaction of the D genome |
| Exploitation Route | Yes, epigenetic markers could be developed to provide tools for selecting desirable epigenetic states in wheat lines. Also, our work may provide some predictability for selecting lines for new synthetic wheat production. |
| Sectors | Agriculture, Food and Drink |
| Description | We have just started the grant so this question is irrelevant. However, excellent progress is being made, with two consortium meetings setting up a detailed research plan, which is now well underway. The importance and novelty of this work is now very apparent. UPDATE: new hybrids have been made and RNA and DNA extracted from multiple triploid lines. Related lines have been treated to double chromosome numbers and these will soon be sampled. Sequencing of small RNA, ribo-depleted RNA and gene capture bisulphite sequence is ongoing. ATAC sequencing is being optimised in wheat to map any changes in chromatin accessibility upon polyploidisation. We are well advanced into the project and have taken a new approach that explores the role of chromatin in establishing and maintaining new patterns of gene expression in wheat hybrids. This is turning out to be be productive and is providing fundamental new insights into polyploidy. Work has been delayed and made more difficult to coordinate by Covid. Final analyses and integration of data will occur over the summer of 2021, and a draft manuscript is being written that we hope to submit at the end of 2021 at the earliest We have completed the extensive data-generation phase of this project and established a genome bioinformatics framework for data integration and analyses. The initial results look very exciting and we anticipate a high impact publication to be ready by the end of 2020. Due to Covid and the desire to improve the quality fo work new data sets have been incorporated into the analyses, including HiC, HiChIP and ChIP-seq data. Our analytical procedures now permit multiple combinations of gene modifications to be related to gene expression and orthologous relationships. WE hope that these analyses will be sufficiently advanced to write a high impact paper towards the end of 2022 |
| First Year Of Impact | 2022 |
| Sector | Agriculture, Food and Drink |
| Impact Types | Economic |
| Title | ATAC-seq for wheat |
| Description | ATAC-seq is a sequence- based assay for measuring the accessibility of chromatin to proteins. Chromatin accessibility locates regions of DNA in genomes that can regulate gene expression, and the extent of chromatin accessibility indicates the potential of an adjacent gene for expression. This method was developed for use in human cell lines. We adapted the method for plants- specifically wheat. This involved substantial work on rapid purification of clean nuclei and downstream data processing to remove contaminating reads of organellar origin. This method provided new insights into chromosomes in newly formed polyploid wheat lines. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | We have been able to provide evidence that rapid changes in chromatin states underly changes in gene expression caused by very recent polyploidisation. This is an important finding with respect with new synthetic wheat lines, which often exhibit new and useful traits |
| Title | eHiC "Easy proximity ligation assay" for wheat |
| Description | Proximity ligation is a powerful method for mapping the relative locations of DNA stands in intact chromatin. Such interactions are increasingly seen as important for understanding the interactions between chromosomes and how these relate to gene expression. There have been several variant methods developed for human cell lines, each with improvements and specialisations. We wished to apply this method to wheat in order to test the hypothesis that newly formed homoeologous genes and regulatory loci have a common regulation due to physical interactions, and to measure any changes in chromosome- scale compaction. In wheat proximity ligation needs to be very efficient due to the large size of the genome. We have adapted a recently published method from human cells that promised to be more efficient in recovering the desired types of ligation products. Our adaptations have substantially improved the recovery of inter-locus ligation events. This means the method can be coupled to chromatin IP to enrich for different chromatin states. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | We are using the new eHiC method on new wheat synthetic lines to assess the role of very recent polyploidisation on chromosome interactions. Specifically we are assaying genes whose expression is dominant or repressed in particular genomes. The outcomes of this work will provide fundamental new insights into the emergence of new traits in polyploid crops such as wheat and into whether and how gene regulatory loci interact |
| Title | Supporting data for "Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat" |
| 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. 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. 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 | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| Title | Supporting data for "Reduced chromatin accessibility underlies gene expression differences in homologous chromosome arms of diploid Aegilops tauschii and hexaploid wheat" |
| Description | Polyploidy is centrally important in the evolution and domestication of plants as it leads to major genomic-scale changes, such as altered patterns of gene expression, which are thought to underlie the emergence of new traits. Despite the common occurrence of these globally altered patterns of gene expression in polyploids, the mechanisms involved are currently not well understood.
Using a precisely defined framework of highly conserved syntenic genes on hexaploid wheat chromosome 3DL and its progenitor 3L chromosome arm of diploid Aegilops tauschii, we show that 70% of these gene pairs exhibited proportionately reduced gene expression, in which expression in the hexaploid context of the 3DL genes was approximately 40% of the levels observed in diploid Ae. tauschii.. Approximately 30% of genes were differentially expressed, including several genes with elevated expression during the later stages of grain development in wheat compared to Ae. tauschii. Gene sequence and methylation differences accounted for approximately 11% of the differences in gene expression. In contrast, over 80% of genes with differential expression exhibited altered patterns of chromatin accessibility of genes in the hexaploid chromosome arm compared to its diploid progenitor. An overall reduction in chromatin accessibility across regulatory regions of genes was observed in the hexaploid context compared to the diploid Ae. tauschii context. These chromosome arm analyses show that differential chromatin accessibility may underlie differences in gene expression in hexaploid chromosome arm of wheat compared to its diploid progenitor chromosome arm. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2020 |
| Provided To Others? | Yes |
| URL | http://gigadb.org/dataset/100737 |
| Description | Cold Spring Harbor Laboratory |
| Organisation | Cold Spring Harbor Laboratory (CSHL) |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | CSHL partnership provides access to their sequencing laboratory and expertise in sequencing small RNAs |
| Collaborator Contribution | sequencing RNA and small RNA from new wheat hybrids |
| Impact | RNAseq data sets for analyses |
| Start Year | 2017 |
| Description | Wheat eipgenomics |
| Organisation | Cold Spring Harbor Laboratory (CSHL) |
| Country | United States |
| Sector | Charity/Non Profit |
| PI Contribution | This project started in July 2016, and aims to study the epigenomes of wheat and progenitor species. Current work involves 1. methyl-sequence of the complete CS42 reference genome. This sequencing has almost been completed at CSHL 2. Create new hybrids of wheat and study how genome interactions influence genome methylation patterns and gene expression 3. Relate methylation patterns to histone methylation patterns and chromatin conformation |
| Collaborator Contribution | 1. CSHL are carrying out bisulphite sequencing, experimental design and data interpretation 2. EI are carrying our exome capture, bisulphite sequencing and chromatin IP 3. NIAB are creating new hybrids |
| Impact | too early for completion of analyses of large datasets |
| Start Year | 2016 |
| Description | Wheat eipgenomics |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | This project started in July 2016, and aims to study the epigenomes of wheat and progenitor species. Current work involves 1. methyl-sequence of the complete CS42 reference genome. This sequencing has almost been completed at CSHL 2. Create new hybrids of wheat and study how genome interactions influence genome methylation patterns and gene expression 3. Relate methylation patterns to histone methylation patterns and chromatin conformation |
| Collaborator Contribution | 1. CSHL are carrying out bisulphite sequencing, experimental design and data interpretation 2. EI are carrying our exome capture, bisulphite sequencing and chromatin IP 3. NIAB are creating new hybrids |
| Impact | too early for completion of analyses of large datasets |
| Start Year | 2016 |
| Description | Wheat eipgenomics |
| Organisation | National Institute Of Agricultural Botany |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | This project started in July 2016, and aims to study the epigenomes of wheat and progenitor species. Current work involves 1. methyl-sequence of the complete CS42 reference genome. This sequencing has almost been completed at CSHL 2. Create new hybrids of wheat and study how genome interactions influence genome methylation patterns and gene expression 3. Relate methylation patterns to histone methylation patterns and chromatin conformation |
| Collaborator Contribution | 1. CSHL are carrying out bisulphite sequencing, experimental design and data interpretation 2. EI are carrying our exome capture, bisulphite sequencing and chromatin IP 3. NIAB are creating new hybrids |
| Impact | too early for completion of analyses of large datasets |
| Start Year | 2016 |
| Description | Attendance at ERA-CAPs coordination meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Prof Bevan attended the ERA-CAPs coordination meeting in Lisbon for discussions on how to address major challenges to secure future food supplies and a viable bio-economy in Europe. |
| Year(s) Of Engagement Activity | 2015 |
| Description | Presentation at PAG conference San Diego USA |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | I presented our latest data on comparative gene expression between diploid and hexaploid wheat lines |
| Year(s) Of Engagement Activity | 2019 |
| Description | planning wheat genome analyses |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | An annual meeting to plan multiple aspects of wheat genome and epigenome sequencing |
| Year(s) Of Engagement Activity | 2018 |