PhenomUK - Crop Phenotyping: from Sensors to Knowledge

Lead Research Organisation: University of Nottingham
Department Name: School of Computer Science

Abstract

Major improvements in crop performance are needed to keep pace with population growth, which is driving up global food demand, and climate change, which is increasing the vulnerability of cropping systems to extreme weather events in the UK and internationally. Whilst plant breeding efforts have greatly benefited from advances in genomics, profiling the crop phenome (i.e. the structure and function of plants) associated with their genetic structure and environment remains a major bottleneck.

Solutions will be multidisciplinary, requiring engineering and computer science as well as plant biology. Sensors are required that can measure of a diverse range of properties of complex, deformable, living and growing objects - plants - often in quite hostile environments. Structural and functional plant traits capturing key properties of roots, shoots, flowers, seeds, etc. must be recovered from those measures effectively and efficiently. Most data capture is image-based, requiring advanced computer vision techniques. Trait data are then used to provide understanding of e.g. plants' growth rates, flowering times, seed production and yield, using advanced data analysis and machine learning methods.

PhenomUK's vision is of an integrated, mutually-informed community of computer scientists, engineers and biologists, working together across discipline boundaries to shape the technologies needed to address one of the global challenges of the 21st century - the provision of a secure food supply to a growing population against a background of resource depletion and climate change. Through series of Annual Conferences, workshops, networking visits, online training events and pump-priming research projects, this multidisciplinary network project will:

1. ensure that UK scientists have access to the innovative technological capabilities needed to drive world-leading basic discovery research in the plant, crop and agricultural sciences
2. provide the deeper understanding of national plant phenotyping capabilities, needs and opportunities required to allow the UK to participate fully in and gain maximum benefit from international initiatives such as the pan-European infrastructure being created by the ESFRI EMPHASIS project (https://emphasis.plant-phenotyping.eu).

Technical Summary

PhenomUK is a Technology Touching Life network proposal centred on plant phenotypic technologies. Its primary aim is to foster interdisciplinary research into innovative, and potentially disruptive, technological capabilities that will drive world-leading discovery research in plant and agricultural science. It will do this by bringing together the engineering and physical and life science communities to consider novel technologies and their integration to a degree not achieved by previous projects driven by specific biological hypotheses and objectives.

Attention will centre on the combination and integration of existing and emerging phenotyping technologies in three directions:
1. Across phenotyping contexts, to maximise the benefit obtained from the different types of knowledge created by phenotyping
2. Across biological and temporal scales, to produce much richer data streams than are currently available
3. Over time, creating robust phenotyping systems incorporating sensor selection and placement, data acquisition, fusion, analysis and management.

This will position the UK to play a leading role in the rapidly developing international phenotyping community and obtain maximum benefit from emerging technologies and the many stand-alone phenotyping tools and data sets developed to date.

Planned Impact

This network will coordinate UK activities around plant phenotyping. Beneficiaries will include the UK plant phenotyping community as well as a broad range of teams working on various specialist aspects of sensor design and deployment, data extraction tools and data analysis in the context of plant phenotyping. In addition, tools and resources, as well as the accumulated knowledge, will be of direct benefit to breeding and agrochemical and agro-biotechnology companies, farmers and agronomists, and all sectors with a stake in food security and sustainability. Finally, the environmental monitoring sector will have benefit from access to many of the tools.

The major impacts will be the coordination of all the above sectors in the UK community, facilitating identification of synergies and helping place the UK at the forefront of this rapidly moving field. The network will be a point of contact with international activities in the phenotyping field including IPPN, the Wheat Initiative EWG on phenotyping and specific activities ongoing in the US, Canada, Australia, India, China, Spain, France and Germany as well as CGIAR centres such as CIMMYT.

Importantly the network will link the academic community with industry, not only the technology providers but also the users such as breeders, farmers and environmentalists. This will ensure a direct pipeline from basic research through to application. This will all be achieved through the range of planned activities, aimed at bringing together diverse skills, resources and problems to seek best solutions.

Finally, the ultimate output of these improved tools generated as result of coordination by the network will be improved germplasm and agronomy to produce crops more efficiently, sustainably and critical aid food security. This will be critical to feed forecast population increases whilst coping with land use pressures and negative consequences of climate change.

Publications

10 25 50
 
Description PhenomUK Network Launch 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Study participants or study members
Results and Impact Te PhennonUK Launch meeting was held at Rothamsted Research on Feb 12th 2019. Some 45 representatives of academic and industrial bodies engaged in plant phenotyping attended. The purpose of the meeting was to present the funding and other instruments available to PhenomUK members and encourage preparations for the first call for proposals. Formal talks were given by the PI and Co-I, a BBSRC representative (Richard Traini() and 3 selected network members, This was followed by round table discussions. The talks were professionally recorded, as were short interviews with delegates, providing material to be used in network promotion.
Year(s) Of Engagement Activity 2019
URL https://www.phenomuk.net
 
Description PhenomUK Web Presence 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Study participants or study members
Results and Impact A PhenomUK website and twitter feed (https://www.phenomuk.net, @PhenomUK) have been created and are managed by the network coordinator, The Twitter currently has 258 followers. The website contains public and members only sections, news and events. Following the launch event a dedicated page hosting employment opportunities in phenotyping is being created, along with a directory of network members and a forum for technical discussions.
Year(s) Of Engagement Activity 2018
URL https://www.phenomuk.net