Strike a pose - bringing crop analysis into the 21st Century with automated field phenomics

20 June 2016

Scientists from the Earlham Institute (EI) and the John Innes Centre (JIC) have received a grant from Norwich Research Park Translational fund for CropQuant, a computerised infield crop monitoring workstation for precision agriculture.

‘CropQuant’ uses Raspberry Pi computers to control infield cameras to capture and process crop growth images. In-depth analysis is then conducted on EI’s high performance computers (HPC) to enable scientists across Norwich Research Park to link environmental data with crop growth and development to reduce farming costs.

Rising temperatures, drought, nitrogen uptake, plant disease and crop lodging are major threats to global crop production. While experienced breeders or farmers could identify some issues at early stages, human observations are expensive, time-consuming and sometimes subjective.

Advanced DNA sequencing technologies have made crop genome assembly a reality; however, these advances are restricted by the low-throughput and inaccurate field phenotyping. In order to enable agricultural practitioners (crop breeders and researchers, and farmers) to improve crop yields through field-based phenotyping methods1.

Automated phenomics is introduced to measure phenomes, physical and biochemical yield traits of organisms, as they change in response to genetic mutations and environmental influences.

As an infield phenomics solution – CropQuant – invented by Dr Ji Zhou (EI-JIC) and Dr Simon Griffiths (JIC), the device continuously monitors crop growth to quantify structural features. This compares the crop’s DNA for early identification of typical genetic traits - such as drought, heat tolerance, disease resistance and nutrition; reducing potential costs.

Currently being utilised in a wheat field trial project on the Norwich Research Park CropQuant can automate the capturing of crop growth and quantify drought adaptation and colour changes during the growing season by utilising the workstation’s imagery and statistical results.

“The Agri-Tech industry indicates that the emerging field phenomics market demands cost-effective and reliable phenotyping devices, which can automate crop growth measurements and extract key yield traits data in a realistic field environment,” said Dr Ji Zhou, Phenomics Project Leader at EI. “CropQuant will provide an affordable solution to prevent crop losses, contributing to food security, as well as industrial and academic purposes.”

CropQuant, together with a tailored high-throughput analysis pipeline, surpasses existing crop phenotyping solutions in cost2, mobility and maintenance. Environmentally, to aid precision agriculture, CropQuant could help farmers and breeders to control chemical applications to specific regions identified by workstations - protecting the quality of surrounding land and water.

To reliably quantify large crop phenotypic features, Dr Ji Zhou is developing new algorithms to conduct data analysis directly in the field using CropQuant. This function will be exceptionally beneficial for breeders or growers to speed-up their crop selection process. The EI/JIC team are currently working with industrial partners to test CropQuant and gauge interest from targeted beneficiaries.

CropQuant can also be used in large crop improvement programmes conducted by leading biotech companies, agricultural research institutes, crop insurance companies, and governments accountable for preventing crop losses.

Dr Zhou, added: “We have not identified a comparable commercialised device in both industry and academia to CropQuant. Some research groups have placed digital cameras in the field to perform continuous crop imaging. However, due to the design limit, those infield devices could only acquire images and do not have computation capabilities. Hence, they are limited in computer controlling and infield crop quantification, which cannot be easily improved for automated phenotyping and precision agriculture.

“The CropQuant device has a real potential to function as a service for agricultural practitioners and will benefit precision agriculture practices in the East Anglia region.”

EI is strategically funded by BBSRC and operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

Notes to editors

Notes to Editors

1)The crop yield monitoring devices and services market has rapidly expanded in recent years. MarketsandMarket expects it to reach $2.51 billion by 2020, with a compound annual growth rate of 7.17% between 2014 and 2020.

2) Following a thorough research and development phase, we anticipate being able to deliver a product at significantly cheaper than current market solutions - existing large-scale phenotyping solutions retail in the region of £300,000.

For more information, please contact:

Hayley London

Marketing & Communications Officer, Earlham Institute (EI)

  • +44 (0)1603 450107

hayley.london@earlham.ac.uk

The Earlham Institute (EI) is a world-leading research institute focusing on the development of genomics and computational biology. EI is based within the Norwich Research Park and is one of eight institutes that receive strategic funding from Biotechnology and Biological Science Research Council (BBSRC) - £6.45M in 2015/2016 - as well as support from other research funders. EI operates a National Capability to promote the application of genomics and bioinformatics to advance bioscience research and innovation.

EI offers a state of the art DNA sequencing facility, unique by its operation of multiple complementary technologies for data generation. The Institute is a UK hub for innovative bioinformatics through research, analysis and interpretation of multiple, complex data sets. It hosts one of the largest computing hardware facilities dedicated to life science research in Europe. It is also actively involved in developing novel platforms to provide access to computational tools and processing capacity for multiple academic and industrial users and promoting applications of computational Bioscience. Additionally, the Institute offers a training programme through courses and workshops, and an outreach programme targeting key stakeholders, and wider public audiences through dialogue and science communication activities.

www.earlham.ac.uk

The Biotechnology and Biological Sciences Research Council (BBSRC) invests in world-class bioscience research and training on behalf of the UK public. Our aim is to further scientific knowledge, to promote economic growth, wealth and job creation and to improve quality of life in the UK and beyond.

Funded by Government, BBSRC invested over £509M in world-class bioscience in 2014-15 and is the leading funder of wheat research in the UK (over £100M investment on UK wheat research in the last 10 years). We support research and training in universities and strategically funded institutes. BBSRC research and the people we fund are helping society to meet major challenges, including food security, green energy and healthier, longer lives. Our investments underpin important UK economic sectors, such as farming, food, industrial biotechnology and pharmaceuticals.

For more information about BBSRC, our science and our impact see: http://www.bbsrc.ac.uk For more information about BBSRC strategically funded institutes see: http://www.bbsrc.ac.uk/institutes