NU Smart Farms

Crop and Soil Sciences

Crop and Soil Sciences

Diagnostics and crop health

Our work in diagnostics focuses on improved use and sustainable management crop protection products.

Precision agriculture is founded on the premise that 'you can’t manage what you can’t measure'. We need to detect and categorise pathogens, pests and weeds within timescales that allow us to make active management decisions.

We now use detection technologies that allow diagnostic testing in the field to return results within 5 to 20 minutes, focusing on the following areas which enable increased precision in terms of what products to spray and when to spray them:

  • for the presence of pathogens or pests
  • for the management of their resistance to chemical control agents

Mechanisms of Resistance

Resistance to crop protection products usually falls into two distinct mechanisms called target site resistance (TSR) and non-target site resistance (NTSR). TSR is caused by mutations (often Single Nucleotide Polymorphisms (SNPs) which alter the shape of the target site protein for the active ingredients (AI) in herbicides. The mutations make the herbicide target protein less sensitive to inhibition, resulting in resistance of the weed to specific herbicide chemistries.

NTSR on the other hand is a collective term referring to mechanisms other than TSR. NTSR is linked to enhanced detoxification of herbicides in which associated weed populations are difficult to control. They are resistant to many classes of post-emergence herbicides, irrespective of their mode of action. These classes include phenylurea (PU), sulphonylurea (SU), aryloxyphenoxypropionates (FOP) and cyclohexanedione (DIM) classes.

We have been working to understand the fundamentals of the molecular mechanisms of herbicide resistance in grass weeds which enable us to identify the reliable biomarkers for herbicide resistances

Rapid in-field tests for identifying herbicide resistances in grass weeds:

Non-Target Site Resistance

Newcastle University researchers have identified a protein (glutathione transferaseAmGSTF1’) that is presented in a high level in all NTSR populations of black-grass so far identified. As a result we can use the levels of AmGSTF1 in black-grass to assess the level of herbicide resistance.

In collaboration with Mologic Ltd, our researchers have developed a rapid diagnostic test to detect the AmGSTF1 protein level in black-grass leaves. Using the same principle as a pregnancy test, the test can detect the levels of AmGSTF1 protein in black-grass within 10 minutes. The world-first Black-grass Resistance Diagnostic device (BReD) was launched at the industry trade show ‘Cereals 2018’.

As an on-farm diagnostic test, BReD gives growers and agronomists real-time information of the degree of NTSR in black-grass populations. This enables them to alter control strategies to counteract herbicide resistance.‌


Target site resistance in black-grass

Single Nucleotide Polymorphisms (SNPs) are sometimes found in the target site for the active ingredients in herbicides. They cause mutations in the proteins, resulting in resistance of the weed to specific chemicals.

Testing is usually performed by sending seeds to a laboratory for herbicide challenge assays. These can take weeks to perform, and the results of the analysis become detached from sampling and decision making.

Detection of SNPs in the laboratory is straightforward. Detection in the field is more challenging. But it would allow agronomists or farmers to make more immediate decisions about spraying.

Working with industry partners Genesys Biotech Ltd and Velcourt, we have developed tests to enable rapid decision-making about weed management. The tests are based on:

  • DNA amplification chemistry using LAMP (Loop mediated AMPlification), and
  • novel probe chemistry

The tests enable resolution of target site mutations within 20 minutes.

 Figure 1. The example results show the discrimination of Single Nucleotide Polymorphisms (SNPs) at amino-acid position 197 of the acetolactate synthase (ALS) gene. The results show the discrimination of wild type genotypes (green) from mutation carrying resistant plants (in blue) and heterozygote plants (green) using the assay.

Phenotyping and breeding

High throughput precision phenotyping is vital to study crop plant responses to stress.

Phenotyping is a major limiting factor for genetic and physiological analysis in the plant sciences.

We are developing high throughput phenotyping platforms using remote sensing and imaging technology. The technology includes visual, thermal, multispectral and hyperspectral sensing and imaging. We are building systems which integrate automated image analysis. These systems aid the phenotyping and monitoring of large number of crop plants under field conditions.

We compare different spectral data sets at different spatial resolutions, using unmanned aerial vehicles (UAVs) and tractor mounted systems. This allows us to assess the capacity to measure crop growth, development and stress responses. Our measurements include canopy size, senescence, stomatal closure, and nutrient stress response.

Improving efficiency and increasing understanding

These innovative tools and techniques help us to integrate high throughput phenotyping with genotypic information. This allows us to identify genetic regions associated with physiological and phenological traits. In turn, this helps us to improve the efficiency of crop breeding programmes and in-season crop monitoring. Improving efficiency in this way is vital for managing commercial production systems.

Our approach provides accurate, precise, large scale phenotypic data under field conditions. It helps to bridge the gap between high throughput phenotyping and genotyping. It increases understanding of phenomics to increase yield gains for future food security.

Precision crop production

New technological approaches are being developed to change our approach to food production.

The global population is predicted to reach 9.5 billion by 2050. Along with climate change, this has led to a need to adapt our farming methods. We refer to this new approach as precision agriculture. It enables optimisation of inputs to maximise production and minimise environmental damage.

At Newcastle, we are using precision tools such as crop and soil sensing. We use these tools alongside spatial and temporal modelling techniques to improve site-specific crop management.

This approach enables real-time monitoring of inter- and intra-field variability and the development of decision support systems. We start with specific problem solving, such as pathogen control. Scaling and integration of data leads to whole farm systems management.

Precision agriculture

For crops 

  • an ability to operate field and plot trials on a wide range of crops
  • 1,400 acre commercial arable unit to scale up trials or provide a systems approach
  • laboratory facilities available on both farms, enabling more detailed agronomic and analytical measurements
  • mobile laboratories, enabling experiments to be performed within crops
  • pest and disease monitoring equipment including links into national and international surveillance networks
  • sensors on combines, providing high resolution information on grain yield and protein content during harvest so that yield and proteins can be mapped and measured
  • canopy sensing (vehicle mounted):
    • CropCircle 430 fixed wavelength multispectral sensor
    • CropCircle 470 adjustable multispectral sensor
  • an N-sensor (passive and ALS systems)
  • Greenseeker NDVI sensor
  • a Pasturemeter+ which provides rapid on-the-go measurement of pasture height and prediction of dry matter content for silage.

Explore further capabilities in phenotyping and breeding

For soil

  • gamma radiometer, the only known instrument in the UK to measure emissions of naturally-occurring gamma radiation
  • a DualEM-21s electromagnetic induction sensor, giving high resolution maps of the soil's electrical conductivity at four different depths, relating to soil texture
  • digital GPS-enabled penetrometer, for measuring compaction
  • a TDR soil moisture probe, for measuring topsoil moisture (0-20cm)
  • COSMOS-UK site on-farm, a stationary wide-area soil moisture sensor
  • nine field drainage plots, to capture surface water and field losses from the soil

Soil health

Healthy soils support healthy crops and healthy animals.

Healthy soils:

  • cycle nutrients and water efficiently
  • suppress pathogens
  • sequester carbon
  • enhance soil biodiversity

Soil health optimisation is necessary to increase crop yields with minimal environmental impact. This is the aim of the sustainable intensification of agriculture.

On our Smart Farms, we use state-of-the-art sensors to monitor indicators of soil health. We validate these against standard measures of soil function. We map soil health using GIS technologies.

This approach allows us to understand how soil health varies at the field and farm scale. We are better able to:

  • recognise the factors that influence the health of our soils
  • design targeted interventions to improve soil health

Target Site Resistance

Detection of Single Nucleotide Polymorphisms (SNPs) leading to target site resistance in the laboratory is straightforward, however, detection in the field is more challenging. Working with collaborators Genesys Biotech Ltd and Velcourt, researchers have developed tests based on DNA amplification using a technique called LAMP combined with a novel probe chemistry. The tests enable resolution of target site mutations within 20 minutes (as show in the results below), enabling modifications to the management practice to occur in real-time in the field.