Delivering low-cost, high-throughput root phenotyping screens for arable crops

Lead Research Organisation: The James Hutton Institute
Department Name: Ecological Sciences

Abstract

Plant roots are essential for the uptake of water and nutrients from soil. Consequently, root growth has significant effects on crop establishment and yield. Previous work by the project team, and others, has shown strong relationships between early root growth traits and the performance of arable crops in the field. However, measuring roots and selecting varieties with improved root systems in the field is time consuming, laborious and expensive. Using laboratory techniques, root growth can be measured quickly and cheaply - for 1000s of plants a year. Genotypes with better root growth and root architectures can be identified in the laboratory and assessments of selected plants can be made under field conditions to validate laboratory screens and assess field performance.

In this proposal we will use low cost, high-throughput methods to define the early root system of >1,600 different oilseed rape (OSR), barley and wheat genotypes in the laboratory. The roots of individual plants will be imaged at two time points. These images will then be analysed to determine the number of roots, root branching rates, root lengths, root growth rates and root angles. To validate and test the utility of measurements made in the laboratory, we will compare them with (1) measurements of root systems made in the field, and (2) data collected from new and legacy field trials assessing large numbers of new crop varieties for National and Recommended Lists to identify root traits correlated with establishment and yield for breeding.

Root growth and architecture are genetically controlled. We will identify genetic loci in large populations of OSR, barley and wheat affecting root growth and architecture traits that correlate with resource acquisition, establishment and yield in the field. An understanding of how best to combine beneficial alleles will be assessed through modelling approaches. To identify genetic targets for breeding we will develop mathematical models describing root growth and architecture in OSR that incorporate the effects of genetic variation. These mathematical models will be extended to predict the effects of root architecture on P acquisition and, thereby, identify potential genotypes with improved rooting and greater P acquisition for sustainable agriculture.

In summary, this proposal will deliver low cost, high-throughput platforms for root phenotyping. These will be of direct benefit to the breeding industry, allowing them to assess germplasm for root growth and architecture that correlate with improved establishment and yield. Genetic loci affecting root growth and architecture will be identified to accelerate the breeding of new varieties. Mathematical models will allow genotypes associated with improved root systems to be identified.

Technical Summary

We will develop low cost, high-throughput (HTP) phenotyping platforms to quantify root growth and architecture in oilseed rape (OSR), barley and wheat. We will phenotype >1,600 distinct genotypes, comprising >800 OSR, 580 barley and 250 wheat genotypes in the laboratory. Root systems will be imaged at two time points and root number, length, angle, branching and growth rates will be determined using ImageJ and bespoke image analysis software. Data from HTP phenotyping will be correlated with (1) field performance data, including establishment and yield from new field experiments and from industry/legacy data, and (2) 3D imaging of root systems using micro-computed tomography (micro-CT). These data will be integrated in two databases, one for root images and one for all other project data. We will identify genetic loci in large populations of OSR, barley and wheat affecting root growth and architecture traits that correlate with resource acquisition, establishment and yield in the field. In OSR, this will include the development of a new mapping population, the development of gene expression markers and expression QTL networks. It will also include fine mapping previously-identified candidate loci in an existing mapping population, through an ongoing UK-China collaboration. In barley, this will comprise genome-wide association mapping techniques. In wheat, this will comprise the use of new populations of step-wise alien introgressions from wild relatives. An understanding of how best to combine beneficial alleles will be assessed through modelling approaches. To identify genetic targets for breeding we will develop mathematical models describing root growth and architecture in OSR that incorporate the effects of genetic variation. These mathematical models will be extended to predict the effects of root architecture on P acquisition. Root data obtained from laboratory and field experiments will be used to parameterise and validate these models.

Planned Impact

Roots are an untapped breeding resource to facilitate crop establishment, increase crop yield potential and improve resource use efficiency. This project is designed to meet industry-driven demands for low-cost, high-throughput screening platforms for key root growth and architectural traits in a wide range of germplasm. The main outputs are: (1) simple, low-cost, high-throughput root phenotyping platforms for arable crops, (2) data on key root traits for oilseed rape (OSR), barley and wheat germplasm, (3) identification of root traits that are correlated with the breeding targets of establishment and commercial yield in the field, (4) a new dynamic model of the OSR root system incorporating the effects of genotype for predicting root architectures with improved capture of soil resources, and (5) identification of genetic loci associated with root development and architecture traits. The Pathways to Impact statement defines the activities that will expedite the utilisation of these outputs, primarily by industry but also by academic and public stakeholders.

The main impact, in the short term, will be achieved through interactions with industry groups, including companies involved in breeding new OSR, barley and wheat varieties. These groups will benefit immediately from the development of low cost, high-throughput root phenotyping during the project. Germplasm contributed by Industry Partners will be screened and the genetic potential for breeding new elite lines for root traits that improve resource acquisition, establishment or yield will be identified. This will bring competitive advantage through 'first mover' positioning and IP. In addition, genetic loci and markers associated with beneficial root traits will allow marker-assisted selection of genotypes with these traits and accelerate the breeding process in the medium and longer-terms. Results and outputs from the project will be disseminated to Industry Partners through CIRC meetings, and to the wider industry through joint industry-academic meetings, trade shows and the trade press, under the guidance of a Steering Committee.

Secondary impact will be achieved through academic routes. Thus, the academic research community will benefit from (1) improved knowledge of root development and architecture traits in crop plants, (2) the identification of genetic loci associated with root development and architecture traits in crop plants, and (3) new mathematical models describing the development of OSR root systems incorporating the effects of genotype.

Ultimately, impact will be felt by the wider society. To feed the world's burgeoning population, agricultural production must double in the next three decades within unpredictable environmental constraints. The development of crop varieties with improved resource use efficiency, establishment and yield through the selection of root traits, will serve to increase the food supplied from a given area. This will contribute to agricultural sustainability and greater food security.

Publications

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Adu M (2016) Effects of rooting media on root growth and morphology of Brassica rapa seedlings in South African Journal of Plant and Soil

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Adu MO (2015) Scanner-based Time-lapse Root Phenotyping in Bio-protocol

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Kalogiros DI (2016) Analysis of root growth from a phenotyping data set using a density-based model. in Journal of experimental botany

 
Title The Beauty of Roots at Dalhousie Building, University of Dundee 
Description Duncan J, Dupuy L, Pongrac P, Bengough G, Bingham I, Wishart J, Wright G, White P (2017) "The Beauty of Roots". We (a) assembled a collection of scientific images and (b) produced prints and etchings of plant roots. We (c) produced pictures of scientific images and framed the artist's prints and etchings. We (d) constructed a hydroponic system that was subsequently transferred to the gallery at the University of Dundee. We (e) wrote descriptions for all exhibits and (f) printed a booklet for the exhibition. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2017 
Impact Over 50 people attended the Opening Event. The Exhibition was subsequently viewed by students and visitors in the lobby of The Dalhousie Building, University of Dundee. The feedback was excellent. There was considerable interest in the Exhibition. It was featured in news items in The Courier (Dundee, 20/03/17) and on various websites. Tweets and other media showing the artworks and hydroponics have also appeared. We had several offers to host the exhibition at other venues. 
 
Title The Beauty of Roots at Dundee University Botanic Gardens 
Description Duncan J, Dupuy L, Pongrac P, Bengough G, Bingham I, Wishart J, Wright G, White P (2017) "The Beauty of Roots" Exhibition, Fascination of Plants Day, Dundee University Botanic Gardens, Sunday 21 May 2017. [>1,000 visitors]. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2017 
Impact Highlighted our work on roots to the general public. the exhibition was covered across various social media. 
 
Title The Beauty of Roots at Jean Duncan's Studio 
Description Duncan J, Dupuy L, Pongrac P, Bengough G, Bingham I, Wishart J, Wright G, White P (2017) Aspects of "The Beauty of Roots", Jean Duncan's Open Studio Event 29-30 April 2017. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2017 
Impact Publicised our work on roots to the general public. 
 
Title The Beauty of Roots at SNH-Batttleby 
Description Duncan J, Dupuy L, Pongrac P, Bengough G, Bingham I, Wishart J, Wright G, White P (2017) "The Beauty of Roots" Exhibition, Scottish Natural Heritage (SNH) Conference Centre at Battleby, August 2017. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2017 
Impact Highlighted our work on roots to visitors to Scottish Natural Heritage (SNH) Conference Centre at Battleby, August 2017. Some interest on social media. 
 
Title The Beauty of Roots at The Scottish Parliament 
Description Duncan J, Dupuy L, Pongrac P, Bengough G, Bingham I, Wishart J, Wright G, White P (2017) "The Beauty of Roots"An evening Exhibition at SEFARI-CKEI Showcase Event, The Garden Lobby, Scottish Parliament, Edinburgh, 18 April 2017. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2017 
Impact Highlighted our work to The Scotttish Parliament. 
 
Title The Beauty of Roots at the Lamb Gallery, University of Dundee 
Description Duncan J, Dupuy L, Pongrac P, Bengough G, Bingham I, Wishart J, Wright G, White P (2018) "The Beauty of Roots". Aspects of the original exhibition were shown in a larger Exhibition entitled "Botanical Conversations: The Science and Beauty of Plants" at the Lamb Gallery, University of Dundee, 21 January - 31 March 2018. 
Type Of Art Artistic/Creative Exhibition 
Year Produced 2018 
Impact Highlighted our work on roots to the general public. 
 
Description The project developed and deployed rapid, high throughput lab screens applicable to oilseed rape (OSR), barley and wheat at less than £1 /plant including growth, imaging and databasing. Over 40,000 images are in the combined database and these are available for further analysis. Field trials of OSR over three seasons identified correlations of root and seed parameters with establishment and yield. Mapping populations were screened to identify multiple genetic loci in OSR and barley affecting root growth and architectural traits that correlate with resource acquisition, crop establishment and yield in the field. Mathematical models were developed that describe root growth and architecture in OSR and incorporate the effects of genetic variation. These mathematical models will help to identify targets for breeding for improved root architecture and function. Putative loci affecting root traits under low and high phosphorus (P) supply have been identified in OSR using a new genetic map based on single nucleotide polymorphisms.

Data from high-throughput phenotyping were correlated with field performance data, including establishment and yield from new field experiments. Aside from the high throughput screening, a more detailed model was developed at the James Hutton Institute, integrating root system architecture, mineral acquisition and plant growth, which can be of value to other academic groups that conduct research on roots.
Exploitation Route Three types of low cost, high-throughput static phenotyping platforms for root phenotyping have been developed which are suited for a range of arable crops. These include (1) a method deploying flatbed scanners which can take dynamic images (Adu et al. 2014); (2) a static 'pouch and wick' system which is lower cost and easy to deploy for larger capacity screens (Thomas et al. 2016); (3) a smaller germination-paper screen which is faster and cheaper. The last two platforms are of direct benefit to the breeding industry. Discussion for offering an anonymous service for batch-testing are ongoing; mechanisms to allow industry to scale up this capability are under discussion. In addition, a field-based technique involving a new tractor mounted coring unit, and subsequent 'core breaks' and counting method has been developed. This method has been developed to image and count roots at high-resolution (e.g. 5 cm) intervals in the soil profile. This method is of particular relevance for commercial small-scale field trials. Mechanisms to deploy this technique and expertise to industry, in collaboration with ADAS, are under current discussion.

Genetic loci affecting root growth and architecture were identified to accelerate the breeding of new varieties. These are now being tested in larger, more diverse, populations in which smaller genetic regions can be identified, with a hope that markers can be taken forward by breeders. Mathematical models will help breeders to identify traits and genotypes are associated with improved root systems.

The robust correlations between seed size, seedling root traits, crop establishment and yield can be directly exploited by companies involved in supplying seeds to the OSR sector (breeders and seed producers). This is an area that can be developed in a follow-on project to convert these findings into practical breeding/selection and production protocols.

Through this CIRC project, the research team developed a reputation of a "trusted partner" for industry-led research and was approached by industry (United Oilseeds, KWS, Monsanto, Elsoms, DuPont, ADAS) with requests for root phenotyping analysis of their varieties. Several industry groups have visited to see the high-throughput phenotyping set-up, including Yara, Omya, Wolf Trax, Du Pont, ADAS.
Sectors Agriculture, Food and Drink

 
Description The high-throughput root phenotyping screens that we have developed at the University of Nottingham and at The James Hutton Institute have been used by various agricultural companies to assess the root traits of juvenile plants.
First Year Of Impact 2014
Sector Agriculture, Food and Drink
Impact Types Economic

 
Description BBSRC Strategic Workshop on Future Challenges in Crops for Improved Human Nutrition
Geographic Reach National 
Policy Influence Type Participation in a national consultation
 
Description The Beauty of Roots
Amount £2,400 (GBP)
Organisation Government of Scotland 
Department Scottish Government Rural and Environment Science and Analytical Services Division (RESAS)
Sector Public
Country United Kingdom
Start 01/2017 
End 04/2017
 
Title Scanner-based time-lapse root phenotyping 
Description Adu MO, ..Wiesel L; Bennett MR; Broadley MR; White PJ; Dupuy LX. (2015). Scanner-based Time-lapse Root Phenotyping. Bio-protocol, pp. e1424 
Type Of Material Technology assay or reagent 
Year Produced 2015 
Provided To Others? Yes  
Impact The protocol developed has been used by several Research Groups at The James Hutton Institute and elsewhere. It has inspired the development of phenotyping systems in other Institutes in the UK and elsewhere. 
URL http://www.bio-protocol.org/e1424
 
Description Strategic LoLa on Brassica (2014-2018) 
Organisation University of Nottingham
Country United Kingdom 
Sector Academic/University 
PI Contribution Philip J. White is a subcontractor to Martin Broadley in this project.
Collaborator Contribution The root phenotyping work from this CIRC project is providing novel trait data for analysis within the Association Transcriptomics analysis framework being developed by the PI (Ian Bancroft), and colleagues at Rothamsted, IFR and JIC. We hope this will help to identify novel markers for breeding.
Impact None to date.
Start Year 2013
 
Description Cereals 2014 Display 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Presentations and YouTube video generated much interest and various questions.

Several organisations showed interest in our techniques for high-throughput root phenotyping.
Year(s) Of Engagement Activity 2014
URL http://www.youtube.com/watch?v=0pwa-Ai6fa8
 
Description Cereals 2015 
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 Demonstration of root phenotyping activities at Cereals 2015 (e.g. root coring in the field).
Year(s) Of Engagement Activity 2015
 
Description High throughput root phenotyping and development of models to predict how crops utilise environmental resources to grow and produce yield. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Dupuy LX et al. (2016) High throughput root phenotyping and development of models to predict how crops utilise environmental resources to grow and produce yield. New Frontiers in Crop Research, a conference organised by SCI's AgriSciences Group and the BBSRC-KTN, 20 October 2016, London, UK. [Invited Talk]
Year(s) Of Engagement Activity 2016
 
Description Mineral nutrition of plants and people 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Presentation at University of Dundee's Art Science and Visual Thinking Course, 20th September 2018. This resulted in one student used "roots" as the subject of an art project and three other students creating art and design works on plants.
Year(s) Of Engagement Activity 2018
 
Description New ways to look at how roots interact with soils 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact Dupuy L [et al.] (2016) New ways to look at how roots interact with soils, 28 October 2016, University of Southampton. [Invited Seminar]
Year(s) Of Engagement Activity 2016
URL http://www.southampton.ac.uk/ifls/news/events/2016/10/28-crop-seminar.page
 
Description Plant, Soil, Water Interactions 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Policymakers/politicians
Results and Impact White PJ (2017) RD2.1.7: Plant, Soil, Water Interactions. Poster at Workshop on: From research to outcomes: Showcasing crop science research from the RESAS Science Research Programme and its benefit to Scotland and beyond, SASA Edinburgh, 7 December 2017.
Year(s) Of Engagement Activity 2017
 
Description Seeing underground for better crops 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Broadley M, White PJ, Thomas C, Whalley R (2016) Seeing underground for better crops. In: BBSRC-CIRC - Crop Improvement Research Club Impact Summary, Summer 2016, p. 5. Booklet distributed at Cereals2016.
Year(s) Of Engagement Activity 2016
URL http://www.bbsrc.ac.uk/circ
 
Description The Beauty of Roots - Exhibition Booklet 
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 A booklet produced for "The Beauty of Roots" exhibitions describing the artworks.
Year(s) Of Engagement Activity 2017,2018
 
Description The Beauty of Roots - sefariblog 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact White PJ (2017) The beauty of roots. Article published on sefariblog, 19 May 2017.
Year(s) Of Engagement Activity 2017
URL https://sefariblog.wordpress.com/2017/05/19/the-beauty-of-roots/
 
Description The Roots of Nutrition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact White PJ, Pongrac P, Wright G, Neugebauer K. (2016) The Roots of Nutrition. The Crunch, Science Centre, Dundee, 10th September 2016.
Year(s) Of Engagement Activity 2016
 
Description The beauty of rooting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Duncan J et al. (2017) The beauty of rooting. CECHR Annual Symposium, West Park Conference Centre, Dundee, 22nd February 2017. [Speed Talk]
Year(s) Of Engagement Activity 2017
 
Description The beauty of roots 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Postgraduate students
Results and Impact Pongrac P, Duncan J, Wishart J, Loades K, Dupuy L, Bengough G, Bingham I, Kelemen M, Vavpetic P, Pelicon P, Shelef O, White PJ (2017) The beauty of roots. CECHR Annual Symposium, West Park Conference Centre, Dundee, 22nd February 2017. [Poster]
Year(s) Of Engagement Activity 2017
 
Description White (2015) Open Lecture at Sao Paulo State University (Brazil) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact White PJ (2015) Mineral nutrition of plants and people. Sao Paulo State University, Tupa Campus, 29th September 2015.
Year(s) Of Engagement Activity 2015
 
Description White (2015) Seminar at University of Mato Grosso (Brazil) 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Undergraduate students
Results and Impact White PJ (2015) Recycling phosphorus for European agriculture. Seminar at University of Mato Grosso, Araguaia Campus, 10th October 2015.
Year(s) Of Engagement Activity 2015
 
Description White PJ (2016) Bread and potatoes and brassicas - Delivering mineral nutrients for human health. LEAF (Linking Environment and Farming) Technical Event, Balruddery Farm, The James Hutton Institute, 9th June 2016. [Poster, Presentation] 
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 Talk and poster at technical event
Year(s) Of Engagement Activity 2016
 
Description Wright et al. (2015) LEAF Open Farm Sunday 
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 Public/other audiences
Results and Impact Wright G, Thompson J, Dupuy L, White P et al. (2015) Know your roots - grow your roots: Computer analysis of root structure. LEAF Open Farm Sunday, The James Hutton Institute, Invergowrie, Dundee, 7th June 2015. [Considerable interest in the role of plant roots in food security]
Year(s) Of Engagement Activity 2015