NRC-UKRI Pilot Programme. Prototyping Root System Architecture in Avena: Technologies for Environmental Sustainability and Food Security
Lead Research Organisation:
Aberystwyth University
Department Name: IBERS
Abstract
This pilot study brings together unique, complementary expertise in the UK and Canada for the optimization of root phenotyping platforms in germplasm development. The project will assess root phenotyping pipelines with the ultimate aim of relating differences in root architecture to field agronomic performance. The implementation of new high throughput phenotyping methods will enable the development of varieties with root architectures that provide yield resilience under a range of climates - benefiting the farming industry and global food security. Crop improvement has until recently focussed on above-ground biomass accumulation and partitioning. Improving the resilience of crop yields through the more efficient allocation of resources to root system architecture has not been explored in as much detail and is fundamental for efficient uptake and utilization of water and nutrients. Renewed interest in diversifying our crop resources has developed as the world focuses on food security and the environment. Oats are an alternative cereal for intensive arable rotations increasing crop diversity. Oats are a high-protein cereal crop with significant health benefits including a source of dietary fiber, antioxidants, and micronutrients. In Canada, the Protein Industries Canada (PIC) supercluster has formed to address the need for crop protein innovation and value-added processing technologies and PIC has targeted growth in oats. In the UK, demand for oats for food use has risen by over 30% in the past 10 years due to its proven health benefits. This has driven research into developing an improved understanding of yield formation in oats and in developing superior germplasm using advanced phenotyping and genotyping techniques. Root system architecture (RSA) defines the shape and spatial arrangement of the root system. The intent of the project is to optimize and utilize precision root phenotyping technologies to identify diversity in important root and RSA traits in oat species. These will be related to field performance in trials in both the U.K. and Canada. In addition, we will apply appropriate genomic technologies to begin to understand the genetics of RSA.
Technical Summary
This pilot study brings together complementary expertise in the UK and Canada for the optimization of root phenotyping platforms in germplasm development. The project will assess root phenotyping pipelines with the ultimate aim of relating differences in root architecture to field agronomic performance. The implementation of new high throughput phenotyping methods will enable the development of varieties with root architectures that provide yield resilience under a range of climates - benefiting the farming industry and global food security. Crop improvement has until recently focussed on above-ground biomass accumulation and partitioning. Improving the resilience of crop yields through the more efficient allocation of resources to root system architecture has not been explored in as much detail and is fundamental for efficient uptake and utilization of water and nutrients. Renewed interest in diversifying our crop resources has developed as the world focuses on food security and the environment. Oats are an alternative cereal for intensive arable rotations increasing crop diversity. Oats are a high-protein cereal crop with significant health benefits including a source of dietary fibre, antioxidants, and micronutrients. Demand for oats for food use has risen by over 30% in the past 10 years due to its proven health benefits. This has driven research into developing an improved understanding of yield formation in oats and in developing superior germplasm using advanced phenotyping and genotyping techniques. Root system architecture (RSA) defines the shape and spatial arrangement of the root system. The intent of the project is to optimize and utilize precision root phenotyping technologies to identify diversity in important root and RSA traits in oat species. In addition, we will apply appropriate genomic technologies to begin to understand the genetics of RSA.
Planned Impact
The pilot study will assess root phenotyping pipelines with the ultimate aim of relating differences in root architecture to field agronomic performance. The implementation of new high throughput phenotyping methods will enable the development of varieties with root architectures that provide yield resilience under a range of climates - benefiting the farming industry and global food security. Precision, high-throughput non-destructive technologies are also paramount for breeding efficiencies and defining trait variability, for example, of plant water use efficiency, seed nutritional content, or even the shape and spatial arrangement of root systems for increased stress tolerance and nutrient uptake. The project will develop required knowledge and technologies for future follow-up projects and project outputs
Publications
Esvelt Klos K
(2021)
The Genetic Architecture of Milling Quality in Spring Oat Lines of the Collaborative Oat Research Enterprise.
in Foods (Basel, Switzerland)
Faralli M
(2019)
Water-Saving Traits Can Protect Wheat Grain Number Under Progressive Soil Drying at the Meiotic Stage: A Phenotyping Approach
in Journal of Plant Growth Regulation
Feurtado JA
(2020)
The Hidden Half: Platform Development for Probing Crop Root Systems
Ghahremani M
(2021)
Direct and accurate feature extraction from 3D point clouds of plants using RANSAC
in Computers and Electronics in Agriculture
Isidro-Sánchez J
(2020)
Genomic Designing of Climate-Smart Cereal Crops
Jin X
(2022)
Crop phenotyping studies with application to crop monitoring
in The Crop Journal
Maughan PJ
(2019)
Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species.
in BMC biology
Mendanha T
(2020)
Drought priming effects on alleviating the photosynthetic limitations of wheat cultivars ( Triticum aestivum L.) with contrasting tolerance to abiotic stresses
in Journal of Agronomy and Crop Science
Robb C
(2020)
Semi-Automated Field Plot Segmentation From UAS Imagery for Experimental Agriculture.
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
| Description | This project has everaged unique expertise in Canada & the UK for better phenomics facilitating crop root improvement. Oats have been developed as an emerging crop for dissection of cereal root architecture (trait-to-gene). This advanced pilot study has built excellent partnerships between unique, complementary expertise in the UK and Canada for the optimization of root phenotyping platforms in germplasm development. The project has assessed and developed a wide range of root phenotyping pipelines with the ultimate aim of relating differences in root architecture to field agronomic performance. Through detailed phenotyping of near-isogenic lines (QTL-NILs) where contrasting haplotypes for specific major QTL have been fixed in a common oat genetic background, we have identified the interaction of traits such as height, flowering time, yield components and grain quality with seedling root system architecture. Gene expression analyses of contrasting genotypes (e.g. of Vrn1 alleles) have identified potential regulators of root architecture and function. |
| Exploitation Route | The implementation of new high throughput phenotyping methods will enable the development of varieties with root architectures that provide yield resilience under a range of climates - benefiting the farming industry and global food security. Precision, high-throughput non-destructive technologies are also paramount for breeding efficiencies and defining trait variability, for example, of plant water use efficiency, seed nutritional content, or even the shape and spatial arrangement of root systems for increased stress tolerance and nutrient uptake. The project will develop required knowledge and technologies for future follow-up projects and project outputs. Results will form the basis for longer-term oat improvement projects: for example, mineral uptake and utilization studies - important for improving nutrient use efficiency as well as for understanding reslience to stresses such as drought and water logging.Functional gene identification through genetics and genomic technologies, will allow us to achieve higher outputs and make greater research gains. The next phase would be to utilize established phenomic pipelines to get to the genetics and define gene networks controlling root architecture and nutrient-water foraging efficiencies. |
| Sectors | Agriculture, Food and Drink,Education,Environment,Manufacturing, including Industrial Biotechology |
| Description | Development of novel phenotyping methods are being used to measure plant performance that allows us to ascertain how events or treatments early in the life of the plant are translated into effects on yield, resilience under stress and of grain quality. Precision, high-throughput non-destructive technologies are also paramount for breeding efficiencies and defining trait variability, for example, of plant water use efficiency, seed nutritional content, or even the shape and spatial arrangement of root systems for increased stress tolerance and nutrient uptake. Results have been used in funding applications to further collaboration bewteen the research groups concerned in Canada and in the UK. |
| Sector | Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology |
| Description | (CROPDIVA) - Climate Resilient Orphan croPs for increased DIVersity in Agriculture |
| Amount | € 5,998,258 (EUR) |
| Funding ID | 101000847 |
| Organisation | European Commission |
| Sector | Public |
| Country | European Union (EU) |
| Start | 09/2021 |
| End | 08/2025 |
| 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 | 04/2021 |
| End | 09/2024 |
| Description | Farming Connect Innovation Project Grant: Demonstration of oat production in diverse environments and management conditions Howarth, Cowan, Griffiths, Moorby |
| Amount | £14,000 (GBP) |
| Organisation | Government of Wales |
| Sector | Public |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 09/2019 |
| Description | Healthy Oats |
| Amount | € 2,186,398 (EUR) |
| Funding ID | 82128 |
| Organisation | Government of Wales |
| Department | Welsh European Funding Office |
| Sector | Public |
| Country | United Kingdom |
| Start | 01/2021 |
| End | 09/2023 |
| Title | Exome capture design for hexaploid oats |
| Description | A Nimblegen bait design was made targetting 140Mb of coding sequence as annotated from the IBERS Avena byzantina genome assembly. The A. byzantina sequences were supplemented with the most divergent coding sequences identified in transcriptome and preliminary exome capture databases for the IBERS NAM population parents and a small number of additional hexaploid accessions (including A. fatua and A. sterilis). |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Validation underway, March 2020. |
| Title | Renseq capture for hexaploid oats |
| Description | A Resistance gene ENrichment SEQence (Renseq) capture design has been made by Nimblegen based on sequences derived from the IBERS Avena byzantina genome assembly. These sequences include NB-ARC and RLCK gene families. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2020 |
| Provided To Others? | No |
| Impact | Validation to be carried out in summer 2020. |
| Title | Hexaploid oat transcriptomes |
| Description | RNAseq (Illumina) for six Avena byzantina tissues to support annotation of the A. byzantina reference genome. Additional data from two A. sterilis, two A. fatua and seventeen A. sativa accessions has been generated. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | No |
| Impact | Annotation of the A. byzantina genome is of a very high quality (BUSCO completeness of 99.7%) |
| Description | Root Phenotyping |
| Organisation | NRC Canada |
| Country | Canada |
| Sector | Public |
| PI Contribution | the aim of this project is to compare root phenotyping approaches being used in Canada and UK, with a focus on oat germplasm. NPPC will utilise cost effective high throughput methods |
| Collaborator Contribution | The Canadian side brings additional germplasm and high resolution 3D root imaging approaches |
| Impact | not yet |
| 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 | Climate change interview BBC Wales |
| 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 | Public/other audiences |
| Results and Impact | An interview focused on projects associated with climate change. Brassicas are a good illustration of winter temperature effects. Other aspects of climate change we work on are water use efficiency, together with abiotic stresses eg drought and flooding, nutritients, high temperature, salinity. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Collaborators visiting from Saskatoon, Canada as part of BBSRC-NRC project |
| 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 | The collaborative project is on rooting of oats, but there was considerable interest in our work on vernalsation effects on flowering time and plant architecture of canola as this is an important Canadian crop |
| Year(s) Of Engagement Activity | 2019 |
| Description | IBERS participation in crop diversity meeting, Brussels, 27/3/19 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | IBERS (CH) participation in crop diversity meeting, Brussels, 27/3/19 |
| Year(s) Of Engagement Activity | 2019 |
| Description | IBERS presentation at BIC Innovation event, Anglesey, on green protein and oat products 16/7/19 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | IBERS presentation at BIC Innovation event, Anglesey, on green protein and oat products 16/7/19 |
| Year(s) Of Engagement Activity | 2019 |
| 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 | Oat genomics consortium building workshop |
| 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 | Meeting between UK, US, Canadian amongst others developing research approaches for oat genomics, disease resistance and root studies. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Oat genomics workshop 2019 |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A meeting was held in Toronto to discuss the current state of oat genomics projects and related collaborations. Seven groups from UK, US, Canada, Germany and Sweden took part. Plans were confirmed for the recently funded UK programme, and preparations made for a significant Canadian funding application. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Pan-oat consortium meeting |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | A meeting was held in San Diego following the Oat Workshop at the 2020 PAG conference in January 2020 to establish a pan-genome sequencing consortium for oat. Several dozen conference attendees were present. Dr Martin Mascher outlined the existing consortium and invited additional participation. Discussions of strategy and funding followed. |
| Year(s) Of Engagement Activity | 2020 |
| Description | Presentation at Conference |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation entitled Assessing crop root system architecture for improved lodging resistance, nutrient efficiencies, and soil-borne disease resistance - opportunities and results to the Saskatchewan Cattlemen's Association Beef and Forage Research Forum |
| Year(s) Of Engagement Activity | 2021 |
| Description | Presentation at PAG 2023 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presntation at Plant and Animal Genome conference, San Diego January 2023 |
| Year(s) Of Engagement Activity | 2023 |
| Description | Presentation for Cereals Live |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation produced for Cereals Live to replace the usual in-person event. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.youtube.com/watch?v=KVv-b9g7OwI |
| Description | Presentation for on-line conference: TEAGASC National Tillage Conference |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Presentation of results of research to conference- several media articles have resulted from the talk along with detailed discussions with industry, both farmers and oat millers |
| Year(s) Of Engagement Activity | 2021 |
| URL | https://www.youtube.com/watch?v=g7wZ41fQdqE&t=1044s |
| Description | Presentation to Conference ( Wales Real Food and Farming Conference) |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | The Wales Real Food and Farming Conference is arranged by a team from a range of organizations in the food, farming and other sectors. All are passionate about developing and supporting sustainable, equitable and resilient farming and food systems. We believe that farming and food can be good for people, communities and the environment. This talk was part of a debate on the seed production and trialling systems and involved people from a wide range of sectors. Considerable discussion has resulted from this meeting along with further engagement activities with individual participants |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.youtube.com/watch?v=LiI2Ryc8EEk |
| Description | Presetation for Cereals Live |
| Form Of Engagement Activity | A broadcast e.g. TV/radio/film/podcast (other than news/press) |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Presentation produced for Cereals Live to replace the usual in-person event. |
| Year(s) Of Engagement Activity | 2020 |
| URL | https://www.youtube.com/watch?v=fpwqpmlF-AY&t=4s |
| Description | Project involvement in IBERS BioBank Seed Store launch activities 25/10/19 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Project involvement in IBERS BioBank Seed Store launch activities 25/10/19 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Project involvement in IBERS Centenary of Plant Breeding event 2/7/19 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Public/other audiences |
| Results and Impact | Project involvement in IBERS Centenary of Plant Breeding event 2/7/19 |
| Year(s) Of Engagement Activity | 2019 |
| Description | Project team presence at Cereals Event 2019 |
| Form Of Engagement Activity | Participation in an activity, workshop or similar |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Project team presence at Cereals Event 2019 - Senova, IBERS, AHDB - 12th-13th June 2019, Boothby Graffoe, Lincs |
| Year(s) Of Engagement Activity | 2019 |
| Description | Speaker, PAG Oat workshop |
| 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 | Invited speaker at PAG, Oat workshop. PAG is the largest international agri-genomics conference and the workshop in 2020 was a focal point to attract participants in a pan-genome sequencing consortium for oat (grant holder organsised a follow-on breakfast meeting for subsequent detailed discussion). |
| Year(s) Of Engagement Activity | 2020 |
| Description | Tour of IBERS oat fields 1/8/19 |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Tour of IBERS oat fields 1/8/19 including visits to site at Gogerddan, Trawscoed and Pwllpeiran to show variety of oat growing environments and demonstrate the performance of different oat varieties. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Undergraduate visit from Edge Hill University |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Undergraduate students |
| Results and Impact | 8 Plant Science students (+ 2 staff) visited and we discussed the various projects currently running in the Phenomics Centre, which include the effect of altered vernalisation on flowering time and plant architecture. They also visited the new Seed Biobank and BEACON biorefining centre. |
| Year(s) Of Engagement Activity | 2019 |
| Description | Visit by YFC Cymru rural affairs group, tour of Phenomics glasshouse facility |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Other audiences |
| Results and Impact | I was able to discuss the work we are undertaking to understand the responce of brassicas to changing winter temperatures and its implications for crop production/fodd security |
| Year(s) Of Engagement Activity | 2020 |
| Description | Workshop |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Root phenotyping workshop as part of UK-Canada collaboration |
| Year(s) Of Engagement Activity | 2019 |