FACCE ERA-NET+MODCARBOSTRESS

Lead Research Organisation: Aberystwyth University
Department Name: IBERS

Abstract

Climate change accelerates the need for a smarter, more efficient, more secure agriculture. Because climate change is predicted to increase spatial and temporal variability, crop models able to predict the best local allele/phene combinations within a species, in addition to the best management systems (such as, for instance, species choice, rotations, sowing dates...) will be of great value for farmers and breeders worldwide. Aware of these issues and avenues, breeding companies now massively invest in crop and climate modelling.However, current crop models have large uncertainties, in particular under drought and high temperatures that often occur in combination and while their occurrences are likely to increase in several regions of the world. Whereas major environmental drivers of growth such as temperature, light and evaporative demand are now well captured in experiments, in particular following a concerted effort of the community, the availability of these information under various [CO2] is the exception. Our project will aim at delivering to simple, low cost, principles and solutions for manipulating combined stresses, including elevated CO2, in experimental set-ups. We will start to apply these principles to the different platforms that are part of the current project.

Technical Summary

The project aims to harmonize tools / protocols for climate measurement and control, with sufficient spatial and temporal resolution to allow parameters evaluation and design cost-effective CO2 control devices for the controlled application of high CO2 treatments. We aim to challenge modelling hypotheses by performing experiments under combined stresses (Water deficit / High Temp. / CO2) in greenhouses and climate chambers, under constant or fluctuating conditions. Key variables/parameters (biomass, leaf area, architecture and carbon allocation) and physiological parameters (photosynthesis, stomatal conductance, chlorophyll fluorescence parameters and specific metabolites) will be used to parameterize models. We will compare available state-of-the art models/modelling approaches to climatic variability and combined stresses to identify specific model deficiencies; further develop modelling approaches to improve the capacity of crop models to integrate climatic variability and combined stresses and evaluate the value of traits (and trait combinations) measured in phenotyping platforms with the ultimate aim of developing climate change-ready wheat and oilseed rape genotypes.

Planned Impact

The global human population will climb to a projected peak of c9 billion over the next 40 years. During this timeframe, changes in climate may have a significant negative impact on crop performance. Two trends have been identified with high confidence: that CO2 levels will rise globally and that, within Europe, the weather will become increasingly variable both within and between years and extreme weather events will become more frequent. Up to now, breeding programs have essentially depended on selecting plants suited to a particular locale (and its climate), but breeding companies often test the new varieties on multiple locations to ensure broad adaptability. However in the expectation of climate instability and change, this strategy needs further modification. One approach is to undertake large-scale multisite trials gathering target populations of environment (TPE). The use of diverse geographical locations for such trials allows the selection of genotypes that are productive under a variety of climatic conditions and, therefore, are more likely to be resilient to multiple and fluctuating climatic variables. However, this strategy will face a limitation because of climate uncertainty and the unlimited combinations of climatic conditions that should require also an unlimited combination of experimental situations. A second limitation is that such strategy requires having now the allelic combination in hands, which is obviously not the case. Modelling is increasingly acknowledged as a powerful solution to overcome these limitations. In principle, it should allow any combination of traits/alleles to be tested against any climatic scenario, either present or future, thus allowing for customization of crops for specific climate scenarios.
Apart from an expected impact of global food security the project will have future economic impact on farming communities by extending the growth range and increasing both the security and the productivity of temperate arable crops in more marginal environments in Europe and elsewhere, increasing land values. An ability to produce increased yields of a high quality raw food material will not only minimize the need for food imports and keep food prices down but should also have a positive effect on the nutritional status of the population.
The report (http://royalsociety.org/policy/publications/2009/reaping-benefits/) "Reaping the Benefit' stressed the need for scientists who could link practical applications related to crops with recent developments in biotech, modeling and systems informatics. The current project offers opportunities for capacity building of young scientists having skills in disciplines such as ecophysiology, bioclimatology, modelling and statistics in addition to traditional plant physiology. The multidisciplinary combination of skills required to undertake the present programme of work will produce a series of researchers who are comfortable communicating as part of a team using modelling and micro-climate evaluation together with high throughput techniques, (robotics, imaging, biochemistry). This project thus makes strong links between the 'pipeline' of discovery and translational research leading directly to delivery of impact from new crop varieties

Publications

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Egea-Cortines M (2018) Editorial: Phenomics. in Frontiers in plant science

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Faralli M (2019) article in Water-saving traits can protect wheat grain number under progressive soil drying at the meiotic stage: a phenotyping approach

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Lobos GA (2017) Editorial: Plant Phenotyping and Phenomics for Plant Breeding. in Frontiers in plant science

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Zhou J (2018) Plant phenomics: history, present status and challenges in Journal of Nanjing Agricultural University

 
Description New data pertaining to the combined effects of heat and drought on grain set in wheat suggest that mild drought can protect against severe thermal shock at meiosis.

Allelic variation for photosynthetic effeciency have been discovered by examining progeny of a cross between European and Afghani wheats. Phenotypic characteristation of progeny with know alleles at this locus reveal that the favourable allele (from the Afghani parent) confers a growth advantage that is maintained under stress conditions, leading to enahnced yeild

Data from these experiments are being used to refine mathematical models that predict how wheat responds to high ambient temperature stress. This is currently a challenge for modeling as there is little agreement between different models for crop behaviour when the ambient temperature exceeds 25C
Exploitation Route Other consortium members are using the data produced to improve modelling. The markers used for mapping the locus may have application in breeeding heat tolerant wheat lines.
Sectors Agriculture, Food and Drink,Environment

 
Description A China-UK joint phenomics consortium to dissect the basis of crop stress resistance in the face of climate change
Amount £30,612 (GBP)
Funding ID BB/R02118X/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 06/2018 
End 06/2022
 
Description NRC-UKRI Pilot Programme. Prototyping Root System Architecture in Avena: Technologies for Environmental Sustainability and Food Security
Amount £55,323 (GBP)
Funding ID BB/S020926/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 03/2019 
End 10/2019
 
Title Analysis of cereal grain colour 
Description Software in Matlab has been developed to analyse dimensional data and colour from scanned images of cereal grains. It automatically separates seed from background, omits seeds and labels which touch the edge of the image, and touching seeds from the analysis, then provides a table of individual seed dimensions (length, width and area) and mean colour (taking acount of the scale of RGB colour) and provides summary data for each image. It has facilities to adjust scaling appropriately if smaller objects, e.g. groats are being scanned and after calibration can automatically correct for scanner resolution settings and specific scanner characteristics. Once a wide range of colour data has been collected classifiers will be developed for the varios colour classes found. 
Type Of Material Data analysis technique 
Year Produced 2019 
Provided To Others? Yes  
Impact This tool is now being used routinely by the IBERS oat breeding team 
 
Title Analysis of cereal grain traits using X-ray micro computed tomography 
Description This dataset is from an experiment ran at the National Plant Phenomics Centre, Wales. Using a new and novel CT analysis method which is linked on this record 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact not yet 
 
Title Analysis of cereal grain traits using X-ray micro computed tomography 
Description software for trait extraction 
Type Of Material Computer model/algorithm 
Year Produced 2018 
Provided To Others? Yes  
Impact not yet 
URL https://github.com/NPPC-UK/microCT_grain_analyser
 
Title µCT imaging raw data and data analysis of small grain cereals and their wild relatives 
Description micro CT raw data files (pre-processed tiffs) and image analysis files of grain and spike morphological traits (.csv). From an NPPC project and available via a University DOI 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact not yet 
 
Description BioLumic 
Organisation Massey University
Department Institute of Food, Nutrition and Human Health
Country New Zealand 
Sector Academic/University 
PI Contribution We have developed dynamic phenotyping protocols and data analysis routines that are being evaluated for use in NZ, on research topics that overlap with core IBERS/NPPC research areas in grassland research, seed biology and photophysiology.
Collaborator Contribution Treatments for plants/seeds that exploit a deep knowledge of photophysiology but have a long term effect on plant production
Impact Invited visit and seminars at Massey University, NZ, with exchanges of ESRs planned
Start Year 2019
 
Description Data and model parameterisation 
Organisation Wageningen University & Research
Country Netherlands 
Sector Academic/University 
PI Contribution Collaboration on data collected within the remit of MODCARBOSTRESS project to optimise the research outcomes. We are providing data and analytical expertise to this.
Collaborator Contribution WUR are providing their data for further analysis, which is a collaborative enterprise. WUR are also providing expertise on expt design in the context of spatially constrained conveyor phenotyping systems
Impact This collaboration will enhance the accuracy of predictive models of photosynthesis in wheat and genetic models in various species.
Start Year 2016
 
Description John Innes Centre 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution Led a joint responsive mode grant on control of chromosome pairing in model and crop plants
Collaborator Contribution wheat genetics and molecular probes
Impact n/a
Start Year 2015
 
Description John Innes Centre 
Organisation John Innes Centre
Country United Kingdom 
Sector Academic/University 
PI Contribution We provide phenotyping expertise for a funded BBSRC LoLa project on Brassicas
Collaborator Contribution They provide a variety of other expertises and germ plasm
Impact Funded BBSRC sLoLa; links to stakeholders in industry and policy
Start Year 2017
 
Description Maricopa 
Organisation Arizona State University
Country United States 
Sector Academic/University 
PI Contribution Contribution to an international workshop and to a grant application aimed at understanding the effect of intermittent shade stress on growth and yield
Collaborator Contribution Possibility to host experiments related to MODCARBOSTRESS at the outdoor facilities at Marocopia.
Impact Expression of Interest submitted to the IWYP, which was accepted for a full grant application
Start Year 2017
 
Description Research collaboration with Aarhus University 
Organisation Aarhus University
Department Department of Food Science
Country Denmark 
Sector Academic/University 
PI Contribution The purpose of the visit was to investigate photorespiration and the quantum yield of photosynthesis in varieties of wheat in relation to abiotic stresses. This includes setting up the capability to make these measurements and providing training of these techniques and analysis to their current staff and students. The purpose of this research is to investigate variation in photorespiration, and also to provide new in-vivo constants to more accurately parameterise the fundamental model of photosynthesis. We supplied the experienced personnel and gas analysis equipment to make the measurements.
Collaborator Contribution Aarhus University provided technical support, glasshouse and controlled environment facilities to the collaboration.
Impact No outputs as yet. However there are two manuscripts in preparation. Outcomes from this research will be used to parameterise models for further work.
Start Year 2016
 
Title OpenCV Auto White Balancer 
Description An simple function to automatically adjust the white balance of an image, optimised for plant images. 
Type Of Technology Software 
Year Produced 2017 
Open Source License? Yes  
Impact n/a 
URL https://github.com/NPPC-UK/OpenCV_Auto_White_Balance
 
Title microCT_grain_analyser 
Description The pipeline provides a simple method to segment and extract grain traits from 3D models 
Type Of Technology Software 
Year Produced 2018 
Open Source License? Yes  
Impact at least 2 other papers, one published and one accepted subject to modifications, will result from this software, in addition to on going collaborative grants 
 
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 Invited talk at meeting on Resilient Crops, Aarhus University, Dec 2019 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact This meeting brought together breeders from across North Western Europe with academics (mainly Nordic) to discuss approaches to current and future climatic challenges
Year(s) Of Engagement Activity 2019
 
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 RWS, provided centre piece of IBERS marquee 
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 provided rhizatrons and other phenotyping equipment as the centre piece in the IBERS marqee, with staff to explain the role of new computer assisted technologies in plant improvement and food security
Year(s) Of Engagement Activity 2018
 
Description Valagro, Italy 
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 Industry/Business
Results and Impact Visit by personnel from small biotech company producing bio-stimulants that affect crop response to stresses
Year(s) Of Engagement Activity 2018
 
Description Ystwyth Valley Farmers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact This was one of many farming groups, including Young Farmers groups from across the UK, that have visited NPPC/IBERS over the past several years. The visitors are shown the breeding and phenotyping technologies and other science related topics such as climate change, GM, food science and environmental issues are often discussed.
Year(s) Of Engagement Activity 2019
 
Description visit Lord Bourne Parliamentary Under Secretary of State at the Wales Office 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact Tour and discussion of the role of the NPPC as a National Facility, and its role in training
Year(s) Of Engagement Activity 2018