New wheat root ideotypes for improved resource use efficiency and yield performance in reduced input agriculture

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

Abstract

This proposal for LINK funded project will build on a solid base of work currently underway, funded through existing LINK programmes, BBSRC, directly by industry, the Scottish Government and the NIAB Trust fund. The proposed study will seek to initiate a better understanding of wheat root growth, morphology and functional relationships with nutrient and water uptake. Methods to describe roots in a diverse range of winter wheat types will be implemented in controlled glasshouse conditions and in the field. The project will form the foundation for improving nutrient sequestration and conversion in this important UK crop through initiation of pre-breeding and development of ideal root ideotypes suitable for use in current and future wheat production. The consortium will concentrate on efficient or enhanced use of resources, especially nitrogen and phosphate and will consider interactions with water availability. In addition, the importance of interactions with beneficial mycorrhizal fungi on nutrient sequestration and the negative impact of soil-borne pathogenic fungi on susceptible genotypes will be considered under field conditions. Finally, the potential impact of agrochemical seed coats on root performance will be assessed. Overall, research in root biology leading to increases in nutrient uptake efficiency will contribute to reductions in diffuse pollution and will substantially reduce green house gas emission due a reduction in the use of nitrogen fertilisers in wheat cultivation

Technical Summary

The main objective of this study is to determine the impact of wheat root growth and morphology on the efficiency of nutrient uptake and hence yield and to explore how this interacts with selected environmental and agronomic parameters. We will assess the level of genetic variation for root development in a range of genotypes in controlled environments and assess the performance of a sub-set of lines with contrasting root characters under field conditions. Interactions with mycorrhizal and pathogenic fungi and the effect of seed coat agrochemical applications will also be assessed. Pre-breeding of improved lines using elite and more diverse germplasm sources will be initiated. The key technical aspects of this work are to identify and develop methods to study root systems in controlled environments and in field experiments for a set of 95-100 wheat lines comprised of genotypes for which there is extensive existing phenotypic information for adaptive traits and which represent a range of diverse types. These methods will be deployed to characterise the root system of the set of wheat lines, and assess nutrient uptake and yield performance in field plots at defined levels of macronutrient inputs, concentrating on nitrogen and phosphorus and selected crop protection chemicals applied as seed coat treatments. We shall also collect samples from the field experiments to assess the potential of wheat genotypes to form mutualistic associations with mycorrhizal and pathogenic fungi. In addition the impact of agrochemical seed treatments on both mutualistic and pathogenic interactions will be assessed. Finally, to underpin future research we shall develop a new bi-parental mapping population using genotypes that demonstrate markedly different root growth and morphologyand initiate pre-breeding work with the intention of developing lines in which ideal wheat root ideotypes are combined with ideal above-ground characters typical of high yielding varieties.

Planned Impact

This LINK Consortium brings together leading academic experts in crop science, genetics, plant physiology and soil ecology (NIAB, SCRI, ADAS and York University) with first rate industry scientists from four major UK plant breeding companies, two crop protection companies (BASF and Monsanto) and a major player in UK agricultural marketing and services (Frontier Agriculture Ltd). The problems we address are highly topical; Adding information where there has been little prior research on the wheat root system which interfaces the soil environment will add value to the demanding target of security of food production in a changing and increasingly variable climate where water availability is compromised and regulation dictates reduced fertilizer inputs. The potential of this work will resonate with many in the scientific community, in government, governmental organizations and with the general public. Effective exploitation of the results of this research is therefore critical and is specifically what the LINK programme and the industry Consortium is set up for. The breeding companies have the potential to directly exploit the results in their commercial programmes. The crop protection companies marketing seed treatments will benefit from understanding how their compounds interact with root systems. Breeders and crop protection specialists will benefit from a better understanding of the dynamic interactions between roots, beneficial mycorrhizal fungi, soil pathogens and seed coat chemicals. Growers and organizations supplying growers will benefit from new varieties that are high yielding under changing climatic conditions. Each of the academic Centres in this collaborative project have strong track records in delivering research in LINK projects and ensuring that outputs are disseminated and exploited by the industry consortium. NIAB will be the leading Institute and Andy Greenland will co-ordinate the activities described in this programme.
 
Description Quantification of cereal root systems during plant development to maturity raises several challenges. Root systems are relatively large compared with more commonly explored species in research, and vary with plant genotype, but are also highly dynamic during the cereal growth season and in response to environmental factors such as nutrient availability. This research aimed to quantify root phenotype in UK wheat varieties at four growth stages, using one of two methods: i) a flat bed filter paper based system to characterise roots at seedling stage; and ii) a metre-length rhizotube system to characterise roots at stem elongation, anthesis and maturity. Root responses to nitrogen supply were also assessed using the rhizotube system. We found significant differences between varieties in root size and in rooting depth / shape. The maximum rooting volume occurred at anthesis, with the majority of the root expansion being found between xx cm and xxcm deep in the rhizotubes. The overall increase in root size with development and depth depended on wheat variety but was significantly affected by the length of the growing season to anthesis. Changes in both root size and shape were found into response to nitrogen treatment, and in addition there was evidence of differences in the type of responses between varieties.
We have developed a method to extract wheat DNA from soil and quantify the amount of roots present at depths down to 1m. We show that our qPCR detection system is specific to wheat and barley but will not detect other common agricultural crops. When evaluated alongside the results of root washing from soil cores taken from winter wheat plots in field experiments, our novel method produces comparable results with high correlations between data produced by either method (r = 0.88-0.99 on a plot by plot basis). The relatively high throughput of our assay allowed us to determine the root biomass in samples taken at four depth intervals from a twenty two variety field trail over two seasons. Analysis of our results showed both variety and depth as significant factors in the distribution of root biomass. These results suggest that our assay is a useful tool for investigating the genetic basis of wheat root biomass distribution in field grown crops.
Plant roots interact with a complex microbial community in the soil, including microbes that enter into the root tissue. Prominent among these are the arbuscular mycorrhizal fungi (AMF), which can provide demonstrated benefits for plant growth. Here, we develop an improved tool to describe the diversity of AMF within roots and in the surrounding soil, and test this in a number of different wheat trials, looking at contrasts in treatments and varieties. The approach is to amplify a variable region of the 18S ribosomal RNA gene using AMF-specific primers, and then to pool samples and sequence using the Ion Torrent PGM platform. Reads are clustered into sets at approximately the level of species so that relative species abundance can be determined. The method revealed high species diversity of AMF in both roots and soil, and high spatial variation in communities from one plot to another. Studies will need to be carefully designed to take this variation into account in order to detect the effects of variables such as depth in the soil, agronomic treatments, or crop varieties.
Exploitation Route This LINK Consortium brings together leading academic experts in crop science, genetics, plant physiology and soil ecology (NIAB, SCRI, ADAS and York University) with first rate industry scientists from four major UK plant breeding companies, two crop protection companies (BASF and Monsanto) and a major player in UK agricultural marketing and services (Frontier Agriculture Ltd). The problems we address are highly topical; Adding information where there has been little prior research on the wheat root system which interfaces the soil environment will add value to the demanding target of security of food production in a changing and increasingly variable climate where water availability is compromised and regulation dictates reduced fertilizer inputs. The potential of this work will resonate with many in the scientific community, in government, governmental organizations and with the general public. Effective exploitation of the results of this research is therefore critical and is specifically what the LINK programme and the industry Consortium is set up for. The breeding companies have the potential to directly exploit the results in their commercial programmes. The crop protection companies marketing seed treatments will benefit from understanding how their compounds interact with root systems. Breeders and crop protection specialists will benefit from a better understanding of the dynamic interactions between roots, beneficial mycorrhizal fungi, soil pathogens and seed coat chemicals. Growers and organizations supplying growers will benefit from new varieties that are high yielding under changing climatic conditions. Each of the academic Centres in this collaborative project have strong track records in delivering research in LINK projects and ensuring that outputs are disseminated and exploited by the industry consortium. NIAB will be the leading Institute and Andy Greenland will co-ordinate the activities described in this programme.
Sectors Agriculture, Food and Drink

 
Description During the project we regularly updated the agricultural and scientific community through a range of industry events and papers. Following final verification our current findings suggest that the tools we have developed should be very useful in further root research activity.
First Year Of Impact 2016
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal,Economic,Policy & public services

 
Title An analytical method for estimating root mass in soil samples 
Description DNA is extracted from root samples and assayed for for species specific sequences e.g wheat. Estimates of of root mass are obtained from a calibration curve. 
Type Of Material Technology assay or reagent 
Provided To Others? No  
Impact In wheat it has provided valuable information about root mass differences between varieties 
 
Title NWRI Doubled haploid (DH) populations 
Description DH populations are useful in dissecting the genetic loci contributing to traits - in this project this will be root traits in wheat 
Type Of Material Biological samples 
Year Produced 2016 
Provided To Others? Yes  
Impact The DH populations will be made available to all the partners in the LINK consortium 
 
Title NWRI method for quantifying wheat DNA in soil samples as a proxy for root biomass in field plots 
Description DNA is extracted from soil core using a PowerSoil kit (MO BIO Laboratories, Inc., Carlsbad, USA.) in accordance with the manufacturer's protocols. Wheat DNA in the soil extracts was quantified by real time PCR. Root biomass was estimated against a calibration curve deriverd from pure wheat DNA 
Type Of Material Technology assay or reagent 
Year Produced 2015 
Provided To Others? Yes  
Impact Estimation of different root biomass between wheat varieties and nitrogen fertilizer inputs 
 
Description "HGCA Research in Focus" article in Crops Magazine, Dec 7th 2013. 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact none
Year(s) Of Engagement Activity 2013
 
Description "Root phenotype and plant resource use in winter wheat" at a JHI meeting for cereal researchers on the 12th Nov 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Questions and discussion

none
Year(s) Of Engagement Activity 2014
 
Description "Wheat Breeding 2014" Tools, targets and progress, conference at Rothamsted on the 29-30th Jan 2014. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact There was discussion at the conference

none
Year(s) Of Engagement Activity 2014
 
Description AAB meeting on Crop Resource Use Efficiency and Field Phenotyping on March 25th & 26th 2013. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Questions and Discussion

none
Year(s) Of Engagement Activity 2014
 
Description Arable Farm Event meeting in March 2013. 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Questions and Discussion

None
Year(s) Of Engagement Activity 2014
 
Description Article in Farmers Guardian 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Interview for an article published in Farmers Guardian "Genetic techniques will change varieties available by 2027" offering insights into the way in which research will shape the future of UK farming.
Year(s) Of Engagement Activity 2017
URL https://www.fginsight.com/news/news/genetic-techniques-will-change-varieties-available-by-2027-21106
 
Description Cambridge Botanic gardens festival of plants, May 2014 
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 Schools
Results and Impact Demonstrated the value of science as a career choice

Increased interest in science
Year(s) Of Engagement Activity 2014
 
Description Cambridge Festival of Science 
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 Within the annual Cambridge Festival of Science, NIAB plays a prominent role in a public exhibition organised by the Cambridge Partnership for Plant Science. The exhibition takes place as part of Science Saturday which attracts members of the public from East of England,the Midlands, London and the South-East of England. Our theme for 2014 was 'Roots' and the work and scope of the project "New Wheat Root Ideotypes for Improved Resource use Efficiency and Yield Performance in Reduced Input Agriculture" (BB/H014381/1) was presented in a poster and discussed with visitors to the exhibit.
Year(s) Of Engagement Activity 2014
URL http://www.sciencefestival.cam.ac.uk
 
Description Cambridge Science festival, March 2014 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Schools
Results and Impact Encoraged young acedemics to consider agriculture and plant science research

Interest in science
Year(s) Of Engagement Activity 2014
 
Description Cereals 2012 and 2013 
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 Professional Practitioners
Results and Impact There was a lot of farmer interest and questions.

We have established small TAG farmer groups for discussion about soil and root work
Year(s) Of Engagement Activity 2012,2013
 
Description Cereals 2013 event 
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 Arable farming event attended by approx 20,000 visitors Display plots and information boards explaining wheat resynthesis, the importance of genetic diversity, and pre-breeding

no actual impacts realised to date
Year(s) Of Engagement Activity 2013
 
Description Cereals Event 2014 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Participants in your research and patient groups
Results and Impact The demonstration at the evenent dissemenated information about the project, its progress and outputs

It gave rise to several email enquiries
Year(s) Of Engagement Activity 2013,2014
 
Description Conference poster (2015) Root phenotyping systems: contrasting controlled environment ex situ and in the field systems. MonoGram, Rothamsted Research 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster (NWRI) presentation intended to update and inform researchers, industry and others involved in ag technology (eg suppliers of research items)
Year(s) Of Engagement Activity 2015
 
Description European Plant Phenotyping Network Winter Phenotyping Seminar 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Presented outline of NIAB's work to develop a DNA based assay to measure root biomass in soil, carried out within "New Wheat Root Ideotypes for Improved Resource use Efficiency and Yield Performance in Reduced Input Agriculture" (BB/H014381/1). I created a short powerpoint presentation and participated in discussions.
Year(s) Of Engagement Activity 2015
URL http://www.plant-phenotyping.org/winterschool2015
 
Description Getting to the root of the matter with DNA technology 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Industry/Business
Results and Impact Journalistic article in our in-house 'Landmark' publication. The article was a full and detailed description (complete with photographs) of NIAB's work to develop a DNA based assay to measure root biomass in soil, carried out within "New Wheat Root Ideotypes for Improved Resource use Efficiency and Yield Performance in Reduced Input Agriculture" (BB/H014381/1). The article was written in a style that was accessible to lay readers.
Year(s) Of Engagement Activity 2015
URL https://members.niab.com/page/landmark-bulletin-preview
 
Description NIAB Open Day 2017 
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 NIAB Open Day (27/6/17) including formal presentation of a seminar on the future of plant breeding innovation plus Q&A, tours of breeding material in the field and poster displays.
Year(s) Of Engagement Activity 2017
 
Description NWRI Speaker Presentation Tools and techniques for phenotyping plant:soil interactions, International Plant and Algal Phenomics Meeting. Prague, Czech Republic. Invited Keynote speaker - 27th-30th June 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact (NWRI) Keynote Speaker presentation intended to update and inform researchers, industry and others involved in ag technology (eg suppliers of research items)
Year(s) Of Engagement Activity 2015
 
Description NWRI poster presentation Recent developments in root phenotyping pipelines of cereal crops: Transparent soil and Rhizotubes. Roots down under, Canberra, Australia. Oral presentation - 5th-9th October 2015 
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 Poster (NWRI) presentation intended to update and inform researchers, industry and others involved in ag technology (eg suppliers of research items)
Year(s) Of Engagement Activity 2015
 
Description Professional Development Training for Farmers programme 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact I participated in two regional seminars for farmers, one at NIAB, Cambridge, the other at Otley Campus, Easton & Otley College, Suffolk. I described the scope for the project "New Wheat Root Ideotypes for Improved Resource use Efficiency and Yield Performance in Reduced Input Agriculture" (BB/H014381/1) and presented results from our variety trials. The presentation engendered a lively discussion among a group of progressive farmers, agronomists and growers. Approximately twenty professional farmers and agronomists attended each seminar. The NIAB TAG Professional Development Training for Farmers programme attracts growers likely to be early adopters of novel technologies.
Year(s) Of Engagement Activity 2014
 
Description Professional Development Training for Farmers programme NIAB?TAG 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact This has resulted in new interest in variety differences. Many of the farmers were interested in matching specially adapted wheat varieties to their different soil types.

There was an interest in having field trials on specific farms and for us to look at other crops.
Year(s) Of Engagement Activity 2014
 
Description UK-Brazil Workshop - ESALQ, Piracicaba, Brazil - 6-8 June 2016 Managing the Rhizosphere to Alleviate Food Poverty 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact This is an international meeting themed on root - soil interactions and the flux of nutrients within the rhizosphere. An abstract has been submitted for a presentation of NIAB's work to develop a DNA based assay to measure root biomass in soil, caried out within "New Wheat Root Ideotypes for Improved Resource use Efficiency and Yield Performance in Reduced Input Agriculture" (BB/H014381/1).
Session themes include:
Session 1 - Roots, carbon and the rhizosphere
Session 2 - The rhizosphere and soil nutrient acquisition
Session 3 - Microorganisms in the rhizosphere
Session 4 - Managing the rhizosphere
Session 5 - Synchroton analysis of plant-soil interactions
Year(s) Of Engagement Activity 2016
 
Description UKPPN Root Phenotyping Workshop, 7-8 April 2016 
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 This is an international meeting themed on root phenotyping. An abstract has been submitted for a presentation of NIAB's work to develop a DNA based assay to measure root biomass in soil, caried out within "New Wheat Root Ideotypes for Improved Resource use Efficiency and Yield Performance in Reduced Input Agriculture" (BB/H014381/1). If the abstract is not accepted for presentation a poster will be taken instead.

Session themes include:
Field Phenotyping
CE-based Techniques
Root Anatomical Traits
Root Modelling
Year(s) Of Engagement Activity 2016
URL http://www.ukppn.org.uk/2016-agm-roots/