A China-UK joint phenomics consortium to dissect the basis of crop stress resistance in the face of climate change
Lead Research Organisation:
Aberystwyth University
Department Name: IBERS
Abstract
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Publications
Zhou J
(2018)
Plant phenomics: history, present status and challenges
in Journal of Nanjing Agricultural University
Zhao B
(2021)
Multi-omic dissection of the drought resistance traits of soybean landrace LX
in Plant, Cell & Environment
Yang W
(2020)
Crop Phenomics and High-Throughput Phenotyping: Past Decades, Current Challenges, and Future Perspectives.
in Molecular plant
Yang W
(2021)
Editorial: State-of-the-Art Technology and Applications in Crop Phenomics.
in Frontiers in plant science
Wu D
(2021)
A deep learning-integrated micro-CT image analysis pipeline for quantifying rice lodging resistance-related traits
in Plant Communications
Wu D
(2019)
Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice.
in Journal of experimental botany
Wang X
(2021)
The different root apex zones contribute to drought priming induced tolerance to a reoccurring drought stress in wheat
in The Crop Journal
| Description | A number of publications involving data sharing and re-use are in progress. This includes the transfer of rice data to the UK and Miscanthus, wheat and forages data to China. A number of exchanges have taken place but planned ones were delayed during covid. We plan to request a no-cost project extension |
| Exploitation Route | Further grant applications are planned, especially in the machine learning area. 2 studentships have been obtained in UK Reciprocal Exchanges of germplasm have been agreed, including wheat and soybean. |
| Sectors | Agriculture Food and Drink Environment |
| URL | https://www.plant-phenomics.ac.uk/ |
| Description | They have led to media interactions. |
| First Year Of Impact | 2024 |
| Sector | Agriculture, Food and Drink,Culture, Heritage, Museums and Collections,Other |
| Impact Types | Cultural |
| Description | Applying remote sensing to improve nitrogen use efficiency for potato breeding and commercial production: Agri-tech in China: Newton Network + (ATCNN) |
| Amount | £7,000 (GBP) |
| Organisation | Newton Fund |
| Sector | Public |
| Country | United Kingdom |
| Start | 06/2018 |
| End | 02/2019 |
| Description | Dissecting climate robustness for sustain-able wheat production (SUSWHEAT) |
| Amount | 11,045,079 kr. (DKK) |
| Organisation | Independent Research Fund Denmark |
| Sector | Public |
| Country | Denmark |
| Start | 03/2021 |
| End | 09/2024 |
| Title | Data from: Combining high-throughput micro-CT-RGB phenotyping and genome-wide association study to dissect the genetic architecture of tiller growth in rice |
| Description | Manual phenotyping of rice tillers is time consuming and labor intensive and lags behind the rapid development of rice functional genomics. Thus, automated, non-destructive phenotyping of rice tiller traits at a high spatial resolution and high-throughput for large-scale assessment of rice accessions is urgently needed. In this study, we developed a high-throughput micro-CT-RGB (HCR) imaging system to non-destructively extract 730 traits from 234 rice accessions at 9 time points. We could explain 30% of the grain yield variance from 2 tiller traits assessed in the early growth stages. A total of 402 significantly associated loci were identified by GWAS, and dynamic and static genetic components were found across the nine time points. A major locus associated with tiller angle was detected at nine time points, which contained a major gene TAC1. Significant variants associated with tiller angle were enriched in the 3'-UTR of TAC1. Three haplotypes for the gene were found and rice accessions containing haplotype H3 displayed much smaller tiller angles. Further, we found two loci contained associations with both vigor-related HCR traits and yield. The superior alleles would be beneficial for breeding of high yield and dense planting. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| URL | https://datadryad.org/stash/dataset/doi:10.5061/dryad.gm18v5f |
| Description | UK- China Phenomics- Metabolomics Network |
| Organisation | Huazhong Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | We have established wide ranging collaborations focusing on plant phenomics, plant metabolomics and the role of nitrogen in plant stress responses |
| Collaborator Contribution | We are designing new research programmes together and joint publications. The Chinese collaborators cover all of my internal travel and subsistence costs when in China. |
| Impact | This is a multi-disciplinary collaboration involving computer imaging and omic (particularly metabolomic analyses) 1. Sun Y, Wang M, Mur LAJ, Shen Q, Guo S. Unravelling the Roles of Nitrogen Nutrition in Plant Disease Defences. Int J Mol Sci. 2020;21(2). 2. Sun Y, Hou M, Mur LAJ, Yang Y, Zhang T, Xu X, et al. Nitrogen drives plant growth to the detriment of leaf sugar and steviol glycosides metabolisms in Stevia (Stevia rebaudiana Bertoni). Plant Physiol Biochem. 2019;141:240-9. 3. Sun Y, Li Y, Wang M, Wang C, Ling N, Mur LAJ, et al. Redox imbalance contributed differently to membrane damage of cucumber leaves under water stress and Fusarium infection. Plant science. 2018;274:171-80. |
| Start Year | 2018 |
| Description | UK- China Phenomics- Metabolomics Network |
| Organisation | Nanjing Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | We have established wide ranging collaborations focusing on plant phenomics, plant metabolomics and the role of nitrogen in plant stress responses |
| Collaborator Contribution | We are designing new research programmes together and joint publications. The Chinese collaborators cover all of my internal travel and subsistence costs when in China. |
| Impact | This is a multi-disciplinary collaboration involving computer imaging and omic (particularly metabolomic analyses) 1. Sun Y, Wang M, Mur LAJ, Shen Q, Guo S. Unravelling the Roles of Nitrogen Nutrition in Plant Disease Defences. Int J Mol Sci. 2020;21(2). 2. Sun Y, Hou M, Mur LAJ, Yang Y, Zhang T, Xu X, et al. Nitrogen drives plant growth to the detriment of leaf sugar and steviol glycosides metabolisms in Stevia (Stevia rebaudiana Bertoni). Plant Physiol Biochem. 2019;141:240-9. 3. Sun Y, Li Y, Wang M, Wang C, Ling N, Mur LAJ, et al. Redox imbalance contributed differently to membrane damage of cucumber leaves under water stress and Fusarium infection. Plant science. 2018;274:171-80. |
| Start Year | 2018 |
| Description | UK- China Phenomics- Metabolomics Network |
| Organisation | Shanxi Agricultural University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | We have established wide ranging collaborations focusing on plant phenomics, plant metabolomics and the role of nitrogen in plant stress responses |
| Collaborator Contribution | We are designing new research programmes together and joint publications. The Chinese collaborators cover all of my internal travel and subsistence costs when in China. |
| Impact | This is a multi-disciplinary collaboration involving computer imaging and omic (particularly metabolomic analyses) 1. Sun Y, Wang M, Mur LAJ, Shen Q, Guo S. Unravelling the Roles of Nitrogen Nutrition in Plant Disease Defences. Int J Mol Sci. 2020;21(2). 2. Sun Y, Hou M, Mur LAJ, Yang Y, Zhang T, Xu X, et al. Nitrogen drives plant growth to the detriment of leaf sugar and steviol glycosides metabolisms in Stevia (Stevia rebaudiana Bertoni). Plant Physiol Biochem. 2019;141:240-9. 3. Sun Y, Li Y, Wang M, Wang C, Ling N, Mur LAJ, et al. Redox imbalance contributed differently to membrane damage of cucumber leaves under water stress and Fusarium infection. Plant science. 2018;274:171-80. |
| Start Year | 2018 |
| Description | Wanneng Yang |
| Organisation | Huazhong Agricultural University |
| Department | College of Veterinary Medicine |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Collaboration has involved exchanges and application for partenering award |
| Collaborator Contribution | They have provided expertise in computer vision and phenotyping, Nanjing and HZAU have contributed travel and accommodation costs. HZAU have seconded senior staff to AU for one year and more likely to follow during the duration of the collaboration. HZAU spin-out company provided specialised equipment and software at cost to facilitate the project |
| Impact | Frontiers in Plant Science and J Ex Bot papers; BBSRC partnering award, 2018; novel machine learning software developed for feature recognition and quantification |
| Start Year | 2017 |
| Description | Ying Wang Anhui Normal University |
| Organisation | Anhui Normal University |
| Country | China |
| Sector | Academic/University |
| PI Contribution | Training in genetics and phenotyping technologies |
| Collaborator Contribution | Experience in water stress tolerance |
| Impact | ongoing |
| Start Year | 2019 |
| Description | BBC Radio Wales interview for What if ... series on climate change |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | The series is a chance to highlight ongoing projects with a link to various aspects of climate change. The effect of milder winters was discussed in regard to vernalisation requirement of brassicas (both oilseed rape and vegetables). I was also asked to speculate on how Welsh Agriculture might look in 50 years time. |
| Year(s) Of Engagement Activity | 2020 |
| Description | CEUG workshop |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | The UK Controlled Environment Association held its annual meeting in Aberystwyth . Tours were provided for the NPPC and a lecture provided to the meeting |
| Year(s) Of Engagement Activity | 2023 |
| URL | https://www.ceug.ac.uk/event/2023-uk-ceug-meeting-at-aberystwyth-university/ |
| Description | Dr Kun visit |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | From the Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing 100081, on a fact finding mission |
| Year(s) Of Engagement Activity | 2023 |
| Description | Fascination of plants, Aberaeron |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Public/other audiences |
| Results and Impact | NPPC staff ran a stall, aimed at introducing plant biology and crop breeding to the general public. The exhibits were "hands on" and illustrated bio-diversity, adaptation as well as the use of tachnology to study and improve plants/crops |
| Year(s) Of Engagement Activity | 2017 |
| Description | ITV-wales interview for "Wales This Week" current affairs programme |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Interview & filming footage for ITV-wales: 30 minute programme on the use of AI in Wales |
| Year(s) Of Engagement Activity | 2024 |
| Description | NPPC website and data portal |
| Form Of Engagement Activity | Engagement focused website, blog or social media channel |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A general website including information on activities at NPPC, platforms available, resources generated in terms of data and software. A secure access portal is provided for transfer of unpublished data between the Centre and users. |
| Year(s) Of Engagement Activity | 2015,2016,2017,2018,2019 |
| URL | https://www.plant-phenomics.ac.uk/ |
| Description | Sept 2023 delegation from China |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A group of Chinese Researchers from Nanjing, Wuhan and Shanghai visited for 2 days, gave and listened to seminars |
| Year(s) Of Engagement Activity | 2023 |