Laser Ablation Tomography: delivering high-throughput anatomical-scale phenotyping

Lead Research Organisation: University of Nottingham
Department Name: Sch of Biosciences

Abstract

Food security represents a major global issue. Crop production needs to double by 2050 to keep pace with a global population increasing to 9 billion. This target is even more challenging given the impact of climate change and the need for agriculture to become more environmentally sustainable. Developing crops better adapted to climate change is essential. Advances in DNA technologies (termed genomics) are helping revolutionise our ability to develop crops better able to adapt to different environments. However, our ability to image the shape of (parts of) plants (termed phenotyping) represents a major bottleneck. For example, the shape and size of the cells that make up a root or leaf have a major effect on how efficiently a plant functions. However, it has not been possible for plant scientists to screen thousands of plants to detect differences in plant cell shape and size needed to select new improved plant varieties, to date.

This project proposes to employ a revolutionary new type of imaging approach (called Laser Ablation Tomography or LAT) which has recently been developed in the USA that, for the first time, allows scientists to rapidly screen thousands of plant samples for variation in cell size and shape. LAT has many advantages over existing physical or optical sectioning methods. For example, it is much faster, easier and more precise than traditional hand sectioning methods and also provides 3D (rather than 2D) information. Hence, LAT provides unique opportunities to select crops with increased yield and/or resilience to environmental stresses employing entirely new cell shape-based reasoning. For example, we will use LAT to look at many biological questions of relevance to food security including screening new varieties of wheat for variation in the shapes and sizes of cells in roots, stems, leaves, flowers and seeds: and understanding how plant cells respond to water logging or bacterial infection.

In order to maximise access and train researchers we will base the new LAT equipment in a specialised research building termed the Hounsfield Facility. This facility has an expert team of staff with an excellent track record of service supporting UK and European scientists using a related form of X-ray based tomography (termed CT) to image crops and other biomaterials. The expert staff will also explore other applications of LAT to study, for example, soil, food and biomedical samples. The availability of the LAT equipment will also be critical to early career researchers and establishing new collaborations between project partners with both industry and academia, thereby enhancing UK capabilities.

Technical Summary

Advances in genomics and selection are revolutionizing our ability to develop crops resilient to different environments. However, phenotyping remains a major bottleneck to fully exploit germplasm diversity. To date, high-throughput phenotyping has focused on whole organ(ism) shape or quality traits. However, anatomical traits in crops have recently been shown to deliver major improvements in yield and climate resilience. Nevertheless, it has not been possible for plant scientists to screen thousands of plants to detect differences in plant cell shape and size needed to select new improved plant varieties, to date.

Our project proposes to employ a revolutionary new type of imaging approach called Laser Ablation Tomography (LAT) which has recently been developed in the USA that, for the first time, allows scientists to rapidly screen thousands of plant samples for variation in cell size and shape. LAT has many advantages over existing physical or optical sectioning methods. For example, it is much faster, easier and more precise than traditional hand sectioning methods, plus (unlike optical sectioning) the high-power laser can image samples irrespective of their thickness. LAT image datasets will then be analysed using image analysis software to quantify 2D and 3D anatomical parameters. Hence, the LAT phenotyping platform is ideal for crop research, permitting rapid, precise, quantitative evaluation of the thousands of samples required for genetic analysis and plant breeding.

The creation of LAT facility at the Hounsfield Facility provides unique research and training opportunities to select novel crop varieties employing entirely new (anatomical based) criteria. In the longer term, we will explore applications of LAT to study other biomaterials, for example, soil, food and biomedical areas, and develop new opportunities with other groups in both industry and academia, thereby enhancing UK capabilities and direct relevance to BBSRC strategy.

Planned Impact

To maximise the impact of the BBSRC ALERT17 investment, the LAT instrument would be based in the Hounsfield Facility, which currently provides a national capability in X-ray Computed Tomography (CT) imaging for crops. The LAT equipment will be housed in dedicated laboratory space within a new £100K University funded extension to the Hounsfield Facility specifically designed for this purpose. We have previously received multimillion pound investment for plant phenotyping at the whole organ level from the ERC and the University of Nottingham. The LAT would extend this, to allow the incorporation of phenotyping at the cell-scale. Provision of a LAT will also support development of new bio-image analysis methods and associated software tools.

To ensure expert technical support, members of the Hounsfield staff including Dr Andrew Mathers will be dedicated to its operation, whilst Dr Darren Wells will oversee management, maintenance and user training in LAT-related activities. The Hounsfield Team are ideally qualified to support the LAT equipment, given their successful 4 year track record providing tomography services to UK and EU researchers (e.g. as a platform for the European Plant Phenotyping Network; EPPN and EPPN2020 projects). Contact and booking details for the facility will be provided on the Hounsfield Facility website (and Craig Sturrock and Darren Wells will be the main points of contact managing access and training).

The main beneficiaries of the ALERT17 investment in a LAT facility will be UK plant scientists as it will provide a unique high throughput 3D anatomical scale phenotyping facility. Currently, this centres around plant groups from several Universities and Institutions within the UK, but we also anticipate users from the commercial sector and other European countries. The research preformed with LAT will not be limited to plants and we have groups working with soil microbes and food, for example, that have all expressed interest in using thisequipment.

The applicants and collaborators in this proposal have numerous links with industrial partners some of which have already provided letters of support who will also access the facilities either directly or via Nottingham collaborators. Plant Breeding Companies will be specifically interested in the plant phenotyping capabilities of LAT, especially related to analysis of complex 3D structures such as roots and anthers. The LAT facility would be ideally placed to meet the growing needs of the UK and wider European plant science community for innovative crop phenotyping platforms (coordinated by the BBSRC via the new ESFRI roadmap H2020 project EMPHASIS-PREP). New companies in biomedical area for example will also be interested in the 3D imaging capabilities of the LAT based on our experience at the Hounsfield Facility providing CT services to UK researchers.

The wider scientific community will also benefit from both the research performed on this machine, image datasets made available and the image analysis tools developed. We will engage with scientists through publications, conference presentations and website presence to inform them of the opportunities that LAT provides for imaging and the facilities in Nottingham. In order to make LAT visible to the widest spectrum of potential users we will add it to the resource lists on the websites that includes the Hounsfield Facility, GARNet and UK Plant Science Federation, the UK Plant Phenomics Network (UKPPN) as well as the equipment listed on the International Plant Phenotyping Network (of which Nottingham is a founding member).

In the longer term, we will explore applications of LAT to study other biomaterials, for example, soil, food and biomedical areas, and develop new opportunities with other groups in both industry and academia, thereby enhancing UK capabilities and direct relevance to BBSRC strategy.

Publications

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Description Over the last 10 months there has been close liaison between the Manufacturer and Nottingham team with regards delivery of equipment in March 2019.

We have designed and delivered a building extension for the LAT equipment.
Exploitation Route Once in place the LAT equipment will be used by others
Sectors Agriculture, Food and Drink,Education

 
Description Penn State University / University of Nottingham 
Organisation Penn State University
Department Department of Plant Science
Country United States 
Sector Academic/University 
PI Contribution The University of Nottingham team have pioneered research on root development and non-invasive imaging of root architecture using X-ray microCT. The team have recently built a state-of-the-art root phenotyping platform (called the Hounsfield Facility after the Nottingham born Nobel prize winning inventor of CT, Sir Godfrey Hounsfield). The UK team provide expertise in molecular genetics, developmental biology and imaging of crop roots.
Collaborator Contribution The Penn State University (PSU) team have pioneered research on field phenotyping of crop root architecture and anatomy. The PSU team have recently developed a state-of-the-art root phenotyping approach termed Laser Ablation Tomography (LAT). The PSU partner contribute expertise in crop root architecture and anatomical traits using their 'shovelomics' and 'anatomics' phenotyping pipelines and facilities.
Impact The international partnering award between University of Nottingham (UoN) and US collaborators at Penn State University (PSU) has proved extremely productive. Highlights arising as a result our partnering award during the past 4 years include: 1. >20 student-staff exchanges between the UK & US teams* 2. 3 research workshops and scientific meetings relating to root phenotyping* 3. Major US and UK research awards include A. A joint $7 million ARPA-E research grant entitled DEEPER* B. An International Newton Award to UK, US & Asian partners* C. Joint equipment development (resulting in a BBSRC ALERT17 equipment award Grant Ref: BB/R013748/1)* 4. >10 co-authored papers/manuscripts published, in press, submitted or in preparation to high impact journals* (including Current Biology, New Phytologist and Nature Communications) 5. Staff secondments (Professor Jonathan Lynch has a 20% appointment at UoN) 6. Visit to UoN by PSU Senior Management (Feb 2018) to discuss strategic research opportunities between our Institutions. *Denotes interdisciplinary outputs involving maths, plant, crop, soil and computer sciences.
Start Year 2014