Australia Partnering Award: International pooling for advanced cereal science - IPAC
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Organisations
- University of Dundee (Lead Research Organisation)
- Commonwealth Scientific and Industrial Research Organisation (Collaboration)
- Australian National University (ANU) (Collaboration)
- Universidade de São Paulo (Collaboration)
- Nanjing Agricultural University (Collaboration)
- La Trobe University (Collaboration, Project Partner)
- University of Southampton (Collaboration)
- Australian National University (Project Partner)
- University of Adelaide (Project Partner)
Publications
Jayakodi M
(2024)
Structural variation in the pangenome of wild and domesticated barley
in Nature
| Description | We have developed precise isolation techniques to understand how different genes are expressed in barley grain. We hope this understanding will help us learn more about how to control grain formation in cultivated cereals. |
| Exploitation Route | We will publish our methods and findings in future open-access publications. |
| Sectors | Agriculture Food and Drink |
| Description | Visits from the team helped develop a spin out company based on their computational advances in developing user-friendly software to analyse RNAseq datasets |
| First Year Of Impact | 2024 |
| Sector | Other |
| Impact Types | Economic |
| Description | Membership on BBSRC Response Mode Funding Panel |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Impact | Contribute to the operation of BBSRC |
| Description | contribute to Scottish Science Advisory Council consultation on Engineering Biology |
| Geographic Reach | National |
| Policy Influence Type | Contribution to a national consultation/review |
| Impact | Feedbacks are provided at this stage. No decisions have been made. |
| Description | China Scholarship Council - Wenhao Wu |
| Amount | £80,000 (GBP) |
| Organisation | Government of China |
| Sector | Public |
| Country | China |
| Start | 08/2023 |
| End | 08/2027 |
| Description | Facing Forwards - Understanding epidermal development in cereals |
| Amount | £1,164,671 (GBP) |
| Funding ID | BB/Y001850/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2024 |
| End | 12/2026 |
| Description | Follow on fund |
| Amount | £249,956 (GBP) |
| Funding ID | APP2126 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 12/2023 |
| End | 11/2025 |
| Description | High Growth Spinout Programme (HGSP) company creation |
| Amount | £200,000 (GBP) |
| Organisation | Scottish Enterprise |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 07/2025 |
| Description | Machine learning based image analysis for phenotyping to speed up barley breeding |
| Amount | £117,839 (GBP) |
| Funding ID | BB/Y513659/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 08/2023 |
| End | 09/2027 |
| Description | Pioneer award |
| Amount | £199,727 (GBP) |
| Funding ID | BB/Y513192/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 02/2024 |
| End | 06/2025 |
| Description | SCAnDi: Single-cell and single molecule analysis for DNA identification |
| Amount | £511,898 (GBP) |
| Funding ID | ES/Y010655/1 |
| Organisation | Economic and Social Research Council |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 03/2025 |
| Description | Sainsbury PhD Studentship - Alanna McCutcheon |
| Amount | £138,000 (GBP) |
| Organisation | Gatsby Charitable Foundation |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 08/2024 |
| End | 08/2028 |
| Description | Syngenta UK Life Sciences Studentship Programme |
| Amount | £40,000 (GBP) |
| Organisation | Syngenta International AG |
| Sector | Private |
| Country | Switzerland |
| Start | 09/2025 |
| End | 09/2029 |
| Description | The Generation Gap - Mechanisms of maternal control on grain |
| Amount | £588,538 (GBP) |
| Funding ID | BB/W003074/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 03/2022 |
| End | 09/2025 |
| Description | The development and evolution of grain abscission in the Triticeae |
| Amount | £1,768,228 (GBP) |
| Funding ID | MR/Y016149/1 |
| Organisation | United Kingdom Research and Innovation |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2024 |
| End | 06/2028 |
| Description | The regulatory role of alternative splicing in response to Zinc deficiency in rice, International Exchanges 2023 Cost Share (NSFC) |
| Amount | £12,000 (GBP) |
| Organisation | The Royal Society |
| Sector | Charity/Non Profit |
| Country | United Kingdom |
| Start | 03/2024 |
| End | 03/2026 |
| Title | Generation of genetic resources to study grain development in barley |
| Description | Our partners at the University of Adelaide are generating gene-edited lines in targets selected based on our research findings. These materials will be available for our study during and following a planned research visit to the University of Adelaide in 2024 |
| Type Of Material | Biological samples |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | Impacts are still to be determined and will depend on the lines. |
| Title | single nuclei isolation for barley in preparation for droplet-based sequencing |
| Description | We developed a protocol to isolate nuclei from developing grain in preparation for sequencing ensuring high quality and concentration. |
| Type Of Material | Biological samples |
| Year Produced | 2024 |
| Provided To Others? | No |
| Impact | We used this method to generate single nuclei transcriptomes from barley grain and are analysing these data now to understand more about different cell types within grain. We will make this method available in planned publications. |
| Title | snRNAseq and RNAseq of developing barley grain |
| Description | These sequencing data describe single cell transcriptomes in developing barley grain |
| Type Of Material | Database/Collection of data |
| Year Produced | 2025 |
| Provided To Others? | No |
| Impact | We are developing new computational approaches to work with these data and hope to complete our analyses in the coming months. Once published, the dataset will be publicly available. |
| Description | 3D RNA-seq training workshop |
| Organisation | Australian National University (ANU) |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We have carried out a 3D RNA-seq training workshop at the Australian National University. (https://www.eventbrite.com.au/e/3d-rna-seq-workshop-tickets-556207510637) |
| Collaborator Contribution | The participants have provided feedbacks on how to improve the 3D RNA-seq tool as well as the training. |
| Impact | not available yet |
| Start Year | 2023 |
| Description | Alternative splicing for rare paediatric diseases |
| Organisation | University of Southampton |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are applying our developed computational methods to detect alternative splicing more accurately and sensitively in short-and long-read data in rare paediatric diseases. |
| Collaborator Contribution | Prof Dianna Barrelle generated the RNA-seq and long read data for a cohort of patients. Her team will evaluate and validate the results from our method. Advice and discussions are carried out around the limitations of our methods and new progress on the method development and improvements are made. |
| Impact | Several possible grant proposals to GOSH and BBSRC |
| Start Year | 2022 |
| Description | Collaboration with Australian National University |
| Organisation | Australian National University (ANU) |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Our team (Runxuan Zhang and Wenbin Guo) visited Dr. Eduardo Eryas' group at Australian National University (ANU) in February 2023. Our team conducted training sessions on our 3D RNA-seq transcriptomic pipeline (described in another collaboration/partner outcome provided by Runxuan Zhang). The team established the pipeline for using the computational tool developed in his group "rattle (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-022-02715-w)" to process an sample nanopore sequencing dataset on barley RNAs. We also discussed about the future developments on RNA analysis. We also established contacts with other colleagues from ANU, including Ashley Jones (https://biology.anu.edu.au/people/professional-staff/ashley-jones) and Aude Fahrer (https://biology.anu.edu.au/people/academics/aude-fahrer). Runxuan Zhang also delivered a seminar talk entitled "Innovative advanced computational solutions for -omics data" |
| Collaborator Contribution | open invitation and arranged the visit |
| Impact | none yet |
| Start Year | 2023 |
| Description | Collaboration with La Trobe for Bioinformatics |
| Organisation | La Trobe University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Our team (Runxuan Zhang and Wenbin Guo) visited La Trobe University and conducted training sessions on our 3D RNA-seq transcriptomic pipeline. Runxuan Zhang also delivered a talk with a title "Computational solutions for tools and resources for accurate transcriptomics". Connections have been established with colleagues at La Trobe, including Monika Doblin (https://scholars.latrobe.edu.au/mdoblin), Tony Bacic (https://scholars.latrobe.edu.au/tbacic), Ricarda Jost (https://scholars.latrobe.edu.au/rjost), Oliver Berkowitz (https://scholars.latrobe.edu.au/oberkowitz) and Quentin Gouil (https://www.wehi.edu.au/people/matthew-ritchie/239/matthew-ritchie-lab-team) |
| Collaborator Contribution | Our team learned about the exciting single cell and cannabis work carried out at La Trobe. |
| Impact | Open invitation to visit and explore ways to develop spatial transcriptomics |
| Start Year | 2023 |
| Description | Collaboration with Mat Lewsey at University of La Trobe for snRNAseq |
| Organisation | La Trobe University |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Mt |
| Collaborator Contribution | Prof Lewsey is providing methodological advice/ support prior to a planned research visit in 2024 by my team to conduct experiments in Prof Lewsey's laboratory. This experiments are directly linked to a current BBSRC research grant. These experiments consumables and services will be provided at low cost. These were planned as part of the Partnering Award |
| Impact | We are benefitting from methodological support in our trial experiments in preparation for the research visit |
| Start Year | 2024 |
| Description | Collaboration with the Australian Commonwealth Scientific and Industrial Research Organization (CSIRO) |
| Organisation | Commonwealth Scientific and Industrial Research Organisation |
| Country | Australia |
| Sector | Public |
| PI Contribution | Our team of Runxuan Zhang and Wenbin Guo visited Commonwealth Scientific and Industrial Research Organization (CSIRO) Canberra on March 7th and 9th and met with data analysis group headed by Shannon Dillon. Runxuan Zhang delivered a presentation of our transcriptomics work. |
| Collaborator Contribution | Our team learned about work carried out at CSIRO including Phenomics, genome to phenomes, integrated analytics and crop breeding data science. |
| Impact | New connections with Australian researchers at CSIRO |
| Start Year | 2023 |
| Description | Regulation of transcript switching in response to temperature changes in barley and rice. |
| Organisation | Universidade de São Paulo |
| Country | Brazil |
| Sector | Academic/University |
| PI Contribution | My team has developed a long-read data analysis pipeline to construct accurate and comprehensive transcriptome annotation for accurate alternative splicing analysis. Rice needs a high-quality transcriptome, so my team is helping Dr. Cristiane Calixto create such resources using the tool we developed. |
| Collaborator Contribution | Dr Cristiane Calixo and her team will evaluate the methods we developed and provide data to improve the usability and advise the limitations of our process. The method is currently being filed for patent. The collaboration with her will help us improve the case for the patent to be granted. |
| Impact | A joint publication and proposal is currently underdevelopment. |
| Start Year | 2022 |
| Description | The regulatory role of alternative splicing in response to Zinc deficiency in rice |
| Organisation | Nanjing Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | My group focuses on the development of novel and cutting-edge computational methods for high throughput data, with a focus on accurate and fast transcript quantification for alternative splicing analysis using RNA-seq data. The cutting-edge computational tools developed in my lab are applied on a range of sequencing datasets developed in Prof Luqing Zheng's labs to improve the understanding of the function of Zinc in rice development. |
| Collaborator Contribution | Prof Luqing Zheng and his team are validating the results from our analysis and providing useful advice on the improvement of our methods and tools. The innovations are made based on these collaborations and we are also seeking funding to enlarge the scope and improve the depth of this collaboration |
| Impact | We have successfully obtained an exchange grant from Royal Society "International Exchanges 2023 Cost Share (NSFC), Royal Society, 2024-2026". There are also several collaborative publications in the making. |
| Start Year | 2023 |
| Company Name | Sharp Genomic Analysis Limited |
| Description | |
| Year Established | 2024 |
| Impact | the company yet to be officially spin-out |
| Description | 3D RNA-seq - A flexible and powerful tool for differential expression and alternative splicing analysis of RNA-seq data for biologists |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | 20 postgraduate students attended a training workshop I organized at the Nanjing Agricultural University , China, 10-11 August 2023 |
| Year(s) Of Engagement Activity | 2023 |
| Description | 3D RNA-seq Training at La Trobe University at Melbourne, Australia |
| 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 | 12 PhD students and postdocs at La Trobe University in Melbourne Australia have attend the 3D RNA-seq training workshop, which equipped them with analysis skill for RNA-seq data. An anonymous survey shows that 100% of participants would recommend the training course and the 3D RNA-seq tool to others. |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.eventbrite.com.au/e/3d-rna-seq-app-a-flexible-and-powerful-tool-for-analysis-of-rna-seq-... |
| Description | Deliver 3D RNA-seq training workshop at Australian National University |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Local |
| Primary Audience | Professional Practitioners |
| Results and Impact | Wenbin and I have undertaken a two-day workshop about their software 3D RNA-seq (https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/) for the analysis of transcriptomics data. Sessions are available to attend on the following dates and times: Wednesday 1 March 2023, 9:00am to 12:00 noon, Seminar Rooms 1 & 2 Thursday 2 March 2023, 9:00am to 12:00 noon, Seminar Rooms 1 & 2 |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.eventbrite.com.au/e/3d-rna-seq-workshop-tickets-556207510637 |
| Description | Introduction to Bioinformatics |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Postgraduate students |
| Results and Impact | I taught at courses for "Introduction to Bioinformatics" to an audience of 25 at University of Sao Paulo, Brazil, 14 August, 2024 |
| Year(s) Of Engagement Activity | 2024 |
| Description | Primer for Advanced 'Omics' Approaches |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Postgraduate students |
| Results and Impact | I taught one day workshop titled "Primer for Advanced 'Omics' Approaches", EastBio Doctoral Training Program master class in Dundee, UK, 31 Jan, 2025 |
| Year(s) Of Engagement Activity | 2025 |