Phenotyping root function in wheat

Lead Research Organisation: Rothamsted Research
Department Name: Sustainable Soils and Grassland Systems


In the UK, approximately 30% of the production of wheat is on soils where insufficient soil moisture decreases yields by (on average) 1-2 t/ha. This costs between £112M and £224M each year in lost production (Foulkes et al. 2001). Studies comprising a limited range of wheat cultivars have shown that genotypes with deep root systems have been associated with high yield in water limited environments, while those with shallow root systems have been associated with increased nutrient uptake when soil water is plentiful. However, there is no comprehensive understanding of what configuration of root system architecture leads to improved resilience of yields, water and nutrient use efficiency, or what the trade-offs, if any, there are with yield potential. This is because roots are hidden underground, and important traits are discovered only by laborious, destructive excavation of roots.

This project will develop a rapid, non-invasive technique using electromagnetic inductance (EMI) to measure the degree of soil drying at different depths in plots of different wheat varieties. Current EMI technology can be used to profile with changes in conductance with depth, but is not being used to study root activity. A key objective for the project will be to optimise the existing capabilities of EMI, so that they can be used to characterize water extraction profiles beneath different varieties of wheat. We will use electrical resistance tomography (ERT), which is labour intensive, invasive and slow, as a tool to provide high resolution images of soil drying to help with the optimisation of EMI which is rapid, non-contact and efficient.

Patterns of soil moisture extraction through the soil profile as the crop develops, which are related to growth and activity of the root system, will be measured with EMI. These data will be validated using conventional techniques such as root sampling via soil coring, buried soil moisture probes, changes in soil strength via penetrometer measurements, and root pulling strength. Initial field tests will comprise 20 UK élite wheat lines, some of which in preliminary data have shown differences in soil water extraction patterns. We will use our new root phenotyping tool kit in field trials with the Avalon x Cadenza mapping population, which has already shown significant genetic variation for nutrient uptake, yield and grain quality. We will determine the correspondence between QTLs identified with our new tool kit and wheat root QTLs already published. We will use soil drying data at various depths to test hypotheses that describe relationships between yield, deep water extraction, soil strength and root placement within drying superficial soil layers. This information is essential for the breeder: for instance, it is not enough to know which varieties can produce deeper roots; confirmation that such a root system translates to greater yield and yield stability across a range of environments is also required before any investment is made in selection for particular root traits.

At the start of the project we will establish a project advisory panel comprising breeders and other members of industry to help guide the selection of materials for investigation. This project will provide a completely new measurement possibility that can be applied to large field trials to give a spatial map of soil water at different depths over time. With the help of the project advisory panel we will identify existing field trials that can be used to test our new methods. There are numerous laboratory methods available for phenotyping roots in seedlings that have led to the discovery of QTLs linked to various root traits. However, it is rare that any of these QTLs are validated under field conditions because current methods of examining roots in the field are time-consuming and expensive. The proposed studies will fill this gap, and can possibly complement work on wheat roots in the BBSRC-LINK project based at NIAB.

Technical Summary

In this project we will develop an application protocol for electromagnetic conductance (EMI) so that it can be used to rapidly measure soil moisture patterns beneath wheat. We will use established methods of electrical resistance tomography (ERT) to "ground-truth" the new EMI protocol. The new method will be tested on and developed with approximately 20 UK wheat lines with known (based on our preliminary data) or perceived differences in rooting, drought tolerance, biomass, etc., selected in conjunction with the wheat breeders. The data from these initial tests will be used to optimise the depth profiling ability of EMI measurements so that they can be used to quantify genotypic differences in water extraction profiles, which we have shown to exist beneath different wheat lines. EMI and ERT data will be compared with data from buried soil moisture meters, soil sampling at various depths, root depth measurement with transparent rhizotrons and the emerging qPCR approach to measuring root DNA concentration in soil. Data from these invasive approaches will be used to validate and refine as necessary the EMI protocol.

We will use the optimised EMI protocol to phenotype root activity of individual lines of the Avalon x Cadenza mapping population for root function QTL discovery. Further phenotypic data will be collected using penetrometer measurements (which are rapid and statistically robust) and other field tests such as root pulling strength. We will adapt the successful maize "shovelomics" approach for wheat, which is based on simple, rapid measurements of excavated root systems.

Planned Impact

The project has the potential to make a significant impact on the academic community and the seeds industry. The project will develop a new tool to assess root function via the profile of soil drying beneath contrasting varieties of wheat, although in the longer term the approach we develop can be applied to all crops.

The initial impact on the seeds industry will be to provide a way to identify which wheats are the most effective at extracting water from the deep soil layers. In UK wheat lines Eric Ober has shown that varieties capable of doing this can produce higher yields when water is limited. However, with current methods identification of this trait is laborious and difficult. In the UK approximately 30% of the production of wheat is on soils where insufficient moisture decreases yields by (on average) 1-2 t/ha, costing between £112M and £224M each year in lost production. Thus, the benefit to the UK farming community is considerable and could lead to a more efficient use of water and nutrient resources.

This project has the potential to make international impact because in many parts of the world the yield of wheat is water limited. This is true for developed (e.g. Australia) and developing countries. Further, the approaches we will develop will have generic application, and could be applied to upland rice where the yield is water-limited and the crop is preferentially grown by poorer members of society. Although there have been yield improvements in rice and other crops by conventional selection for yield, greater progress can be achieved by understanding better why some varieties are more productive or stress resilient than others. In the absence of detailed information on plant traits such as root architecture, breeders rely on chance combinations of favourable alleles. However, with inexpensive, rapid tools to assess genotypic differences in trait expression in the field, such as the measurement of root activity proposed here, the identification and selection of superior genotypes can be accelerated.

The project is consistent with the idea of sustainable intensification: wheat crops that use the available soil water to best effect are more productive and N efficient, thus minimising environmental impact on agricultural land, and reducing the area of land that needs to be cultivated to produce a tonne of grain. Thus, the project is consistent with the food security goals of the BBSRC.

The project will pave the way to a deeper understanding of root function. It is a rule of thumb that with access to new measurement technologies, scientific advance will follow. It is anticipated that by combining existing techniques with the development of new methods in the proposed work, project outcomes will be readily taken up by the scientific community.


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Description There is an urgent need to develop new approaches to phenotype roots in the field which have a high throughput. Excavation of roots to make direct measurements is labour intensive. An alternative to excavation is to measure soil drying profiles and infer root activity. We grew 23 lines of wheat in 2013, 2014 and 2015. In each year we estimated soil water profiles with electrical resistance tomography (ERT), electromagnetic inductance (EMI) and penetrometer measurements as well as by measurements of soil water content. We determined the relationship between the measured variable and soil water content and matric potential. We found the measurements of soil water which were most closely related to matric potential (ERT and the penetrometer) gave the best discrimination between different wheat lines. We found differences between the wheat lines in soil water profiles with respect to both depth of water uptake and the extent of surface drying. We present evidence to support a stable root phenotype and that soil drying is related to root density as well as leaf area. Penetrometer measurements can provide a reliable approach to comparing soil drying profiles. They are sensitive to matric potential. In some circumstances EMI can also be used which is rapid and can be used to monitor large numbers of plots. EMI measurements are sensitive to water content.
Exploitation Route We met all the objectives of this project in full. We have identified that EMI has the potential to be used as a method to rapidly phenotype root function. We proposed to take this work forward jointly with Prof Binley at Lancaster with an application to the recent NERC Signals in Soil call. This was a joint submission between Rothamsted, Lancaster University, Nottingham University and the Open University, but unfortunately it was not funded.

The technology developed in this project is currently being used in the NERC/BBSRC ISPG ASSIST as well as in the BBSRC ISPG Designing Future Wheat.
Sectors Agriculture, Food and Drink,Environment

Description We investigated a panel of wheats selected by industry. The data was of direct interest to them. Updates on the project have been presented at the regular CIRC meetings. We successfully applied for a "path finder" project (BB/P004687/1) and we are now planning to submit a follow-on-proposal to the March 2017 deadline. With proof of concept data generated through a BBSRC Follow on Fund the team would then be in a position to progress discussions with plant breeding companies. These data would also provide evidence to justify work with an EMI manufacturing company to; (1) adapt existing hardware to be used on the back of a tractor and (2) implement the more robust analytical approach developed by the team to determine how electrical conductivity varies with depth. The first point would allow the data collection to be more automated rather than relying on a manual method. This would in turn reduce the cost to plant breeders in generating the data and/or allow them to use the technique on many more breeding plots per year. Adaption of the hardware is not considered a difficult technical challenge but would require investment, which could only be justified once the further proof of concept data for the underlying technique is generated. The proposed follow-on project will focus on demonstrating the utility of using EMI to monitor changes in soil water content with depth, in breeding trials, using the approach that has been developed in BB/J01950X/1 and described by Whalley et al. (2017). Update: the follow on project was not funded. However, the methods we developed are currently being used in Designing Future Wheat and ASSIST.
Sector Agriculture, Food and Drink,Environment
Impact Types Societal

Description Funding from industry
Amount £669,000 (GBP)
Funding ID 5325 
Organisation Syngenta International AG 
Sector Private
Country Switzerland
Start 03/2014 
End 12/2017