crop improvement

Supporting the agricultural industry through R&D to deliver successful new products to market

Developing and bringing new agricultural products to market can be costly and time consuming for industry. Nufarm Limited recently sought the technology and expertise of the Australian Plant Phenomics Facility (APPF) to provide independent testing on potential new foliar sprays under development.

“The full service approach at the APPF, from the technology to the specialist staff, really appealed to us”, said Chad Sayer from Nufarm’s Product Strategy Group.

“The non-destructive, high-throughput phenotyping technology at the APPF gave us the ability to gain insights into our products under development that we could not achieve anywhere else. Their highly skilled, specialist team helped us design our experiments and provided invaluable advice throughout the project, right through to the data analysis.

“This has been exciting for us. Our pilot project delivered such promising results, we already have a large project underway”.

Nufarm wheat 000335

(L) Plants undergoing spray treatment.  (R) Daily observation and analysis by the horticultural team

“We have a bespoke approach, working closely with our customers to design their experiments to deliver the best results”, said Dr Bettina Berger, Scientific Director at the Adelaide node of the APPF.

Dr Berger and her colleagues provide consultation on all projects carried out at the Adelaide node, supporting the development of the initial design and execution of the research. The specialist horticultural team set up the experiments and manage them through to completion. Customers can make use of online monitoring and access of projects throughout the experiment stage via Zegami (‘live processing’ which allows result checking on a day-to-day basis). On completion of experiments image analysis and data analysis are handled by our skilled engineering, software and statistics team. The research team then provide consultation on results and further follow-up as required.

0382 on 5-5-17 (6)

Plants in a Smarthouse at the Adelaide node of the APPF undergo daily image analysis throughout the experiment

The APPF is available to all publicly or commercially funded researchers. For further information or to discuss how we can support your research, please visit the APPF website for contact details. For more information about this project, contact Dr Berger.

Nufarm Limited is an Australian company. It is one of the world’s leading crop protection and specialist seeds companies, producing products to help farmers protect their crops against damage caused by weeds, pests and disease. With operations based in Australia, New Zealand, Asia, Europe and the Americas, Nufarm sells products in more than 100 countries around the world. Find out more about Nufarm here.

Zegami is a web application which allows users to filter, sort and chart data from experiments undertaken in the Smarthouses at the APPF Adelaide node, with the unique feature of being able to group that data with the corresponding images. To get a real feel for the application, we highly recommend you watch the video. Further reading here.

A step closer to salt tolerant chickpea crops

A recent study has collected phenotypic data of chickpea (Cicer arietinum L.) which can now be linked with the genotypic data of these lines. This will enable genome-wide association mapping with the aim of identifying loci that underlie salinity tolerance – an important step in developing salt tolerant chickpeas.

In this study, Judith Atieno and co-authors utilised image-based phenotyping at the Australian Plant Phenomics Facility to study genetic variation in chickpea for salinity tolerance in 245 diverse accessions (a diversity collection, known as the Chickpea Reference Set).

Chickpea is an important legume crop, used as a highly nutritious food source and grown in rotation with cereal crops to fix nitrogen in the soil or to act as a disease break. However, despite its sensitivity to salt, chickpea is generally grown in semi-arid regions which can be prone to soil salinity. This results in an estimated global annual chickpea yield loss of between 8–10%.

Screen Shot 2017-05-19 at 9.53.17 am

Salinity tolerance phenotyping in a Smarthouse at the Australian Plant Phenomics Facility’s Adelaide node at the Waite Research Precinct – Plants were imaged at 28 DAS for 3 consecutive days prior to 40 mM NaCl application in two increments over 2 days. Plants were daily imaged until 56 DAS. Right pane shows 6-week-old chickpeas on conveyor belts leaving the imaging hall proceeding to an automatic weighing and watering station.

 

The study found, on average, salinity reduced plant growth rate (obtained from tracking leaf expansion through time) by 20%, plant height by 15% and shoot biomass by 28%. Additionally, salinity induced pod abortion and inhibited pod filling, which consequently reduced seed number and seed yield by 16% and 32%, respectively. Importantly, moderate to strong correlation was observed for different traits measured between glasshouse and two field sites indicating that the glasshouse assays are relevant to field performance. Using image-based phenotyping, we measured plant growth rate under salinity and subsequently elucidated the role of shoot ion independent stress (resulting from hydraulic resistance and osmotic stress) in chickpea. Broad genetic variation for salinity tolerance was observed in the diversity panel with seed number being the major determinant for salinity tolerance measured as yield. The study proposes seed number as a selection trait in breeding salt tolerant chickpea cultivars.

Screen Shot 2017-05-19 at 9.54.30 am

Genotypic variation for salinity tolerance in the Chickpea Reference Set. Varying levels of salinity tolerance exhibited by different chickpea genotypes. Exposure of sensitive genotypes to 40 mM NaCl caused severe stunted growth, leaf damage, and led to less number of reproductive sites (flowers and pods) compared to moderately tolerant and tolerant genotypes.

 

The rapid development of new, high-resolution and high-throughput phenotyping technologies in plant science has provided the opportunity to more deeply explore genetic variation for salinity tolerance in crop species and identify traits that are potentially novel and relevant to yield improvement. The Australian Plant Phenomics Facility provides state-of-the-art phenotyping and analytical tools and expertise in controlled environments and in the field to help academic and commercial plant scientists understand and relate the performance of plants to their genetic make-up. A dedicated cross-disciplinary team of experts provides consultation on project design and high quality support.

To read the full paper in Scientific Reports, “Exploring genetic variation for salinity tolerance in chickpea using image-based phenotyping” (doi:10.1038/s41598-017-01211-7), click here.

To find out more about the Australian Plant Phenomics Facility and how we can support your research click here.

 

 

 

An exciting offer of help for significant plant science research projects

Do you have an exceptional plant science research project destined to deliver high impact outcomes for Australian agriculture? Do you need access to plant phenotyping capabilities?

The Phenomics Infrastructure for Excellence in Plant Science (PIEPS) scheme is open to all publicly funded researchers. Emphasis is placed on novel collaborations that bring together scientists preferably from different disciplines (e.g. plant physiology, computer science, engineering, biometry, quantitative genetics, molecular biology, chemistry, physics) and from different organisations, within Australia or internationally, to focus on problems in plant science.

The PIEPS scheme involves access to phenotyping capabilities at the Australian Plant Phenomics Facility (APPF) at a reduced cost to facilitate exceptional research projects. Researchers will work in partnership with the APPF to determine experimental design and optimal use of the equipment. Our team includes experts in agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics.

Applications are assessed in consultation with the APPF’s independent Scientific Advisory Board. Selection is based on merit.

This is an outstanding opportunity to gain access to invaluable expertise and cutting edge technology to accelerate your research project and make a real impact in plant science discovery.

Applications close:  30 September 2017

For more information and to apply:  APPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS)

 

 

Drought knows no borders

The Australian Plant Phenomics Facility (APPF) was delighted to welcome His Excellency Mr Mohamed Khairat, Ambassador of The Arab Republic of Egypt, to its Adelaide node recently.

Egyptians share our love of wheat, however, they are heavily reliant on wheat imports which are struggling to keep up with demand. As a remedy, 1.5 million hectares of Egyptian land has been set aside for local wheat production, but there are challenges ahead. Egyptian wheat growers suffer from the same yield limiting issues of heat and drought as we do here in southern Australia.

While touring the facility, His Excellency shared his enthusiasm for future collaboration with the APPF’s Dr Trevor Garnett.

“There is a wealth of knowledge and experience at the APPF and the Waite Campus of the University of Adelaide in plant phenotyping and wheat production. His Excellency sees exciting opportunities for Egyptian scientists and PhD students to collaborate on research and share ideas on how to improve this essential crop”, said Dr Garnett.

abassador-of-egypt-250117-pic1

His Excellency Mr Mohamed Khairat, Ambassador of The Arab Republic of Egypt (pictured right) talks with Dr Trevor Garnett in the DroughtSpotter greenhouse at The Plant Accelerator®, Australian Plant Phenomics Facility (Adelaide node)

 

Major investment in plant root phenotyping to answer key questions

screen-shot-2017-01-24-at-11-16-27-am

3-D image of root architecture – Lynch Laboratory, The Pennsylvania State University, USA

It all starts in the roots

Australian agriculture operates in a largely harsh, resource limited (nutrients, water) environment so the role of plant roots is even more vital to crop performance.

While advances in technology have resulted in a tenfold increase in crop productivity over the past century, soil quality has declined. Advanced root systems that increase soil organic matter can improve soil structure, fertiliser efficiency, water productivity, crop yield and climate resilience, while mitigating topsoil erosion — all of which provide near-term and sustained economic value.

It is acknowledged within the international plant science and phenotyping community that root phenotyping is a critical component for crop improvement, but no ideal hardware solution has been developed yet. There is always a compromise between destructive and non-destructive measurement, throughput and resolution, and ultimately, cost.

Recognition of these challenges and increased research investment to find the answers is now coming to the fore in international plant science.

USD $7 million for plant root research granted

Researchers in Penn State’s College of Agricultural Sciences have just received a USD $7 million grant from the U.S. Department of Energy’s Advanced Research Projects Agency-Energy, or ARPA-E, to design a low-cost, integrated system that can identify and screen for high-yielding, deeper-rooted crops.

The interdisciplinary team, led by Jonathan Lynch, distinguished Professor of Plant Nutrition, will combine a suite of technologies designed to identify phenotypes and genes related to desirable root traits, with the goal of enhancing the breeding of crop varieties better adapted for nitrogen and water acquisition and carbon sequestration.

“With ARPA-E’s support, we plan to create DEEPER, a revolutionary phenotyping platform for deeper-rooted crops, which will integrate breakthroughs in non-destructive field phenotyping of rooting depth, root modeling, robotics, high-throughput 3D imaging of root architecture and anatomy, gene discovery, and genomic selection modeling,” Lynch said.

“ARPA-E invests in programs that draw on a broad set of disciplines and require the bold thinking we need to build a better energy future,” said ARPA-E Director, Ellen D. Williams.

The project is part of ARPA-E’s Rhizosphere Observations Optimizing Terrestrial Sequestration, or ROOTS, program, which is aimed at developing crops that enable a 50 percent increase in carbon deposition depth and accumulation, while also reducing nitrous oxide emissions (a contributor to greenhouse gas) by 50 percent and increasing water productivity by 25 percent.

Read the full article, by Charles Gill from The Pennsylvania State University, here.

UDC Plant Science Centre

Through a € 1.3m investment from Science Foundation Ireland, the Integrated Plant Phenomics and Future Experimental Climate Platform has been established at University College Dublin (UCD) in Ireland. The combination of infrastructure and facilities available to researchers will represent the first of its kind globally.

The platform will be housed in the same building at UCD allowing seamless transition from experiment to scanner. It will consist of a large capacity 3D X-ray CT scanner which uses X-rays taken from multiple angles to non-destructively build-up a 3D image of whole plants and their internal structures, both above and below ground with fast (minutes) scan times and six reach-in, high-spec plant climate chambers with full (de)humidification capabilities. Novel custom additions will include full-spectrum variable LEDs, enabling more accurate representation of sunlight conditions experienced by crops under field conditions. The chambers will integrate thermal imaging to continuously capture leaf temperature and inferred ecophysiological processes (gas exchange).

Breakthroughs in crop/plant/soil/food science will be possible, particularly below ground and at night, because the consequences of climate change or new crop breeds on below-ground /night-time processes have not been readily accessible before the advance of X-ray CT, thermal imaging and integration of these components into an infrastructure platform.

The Centre unites a large number of UCD plant scientists that investigate fundamental and applied aspects of plant science and work alongside industry in exploiting research breakthroughs.

Read more here.

Danforth Plant Science Center

A new industrial-scale X-ray Computed Tomography (X-ray CT) system at the Danforth Plant Science Center in Missouri, USA, is the first of its kind in the U.S. academic research sector dedicated to plant science and can provide accelerated insight into how root systems affect plant growth. The technology was established in late July 2016 under a collaborative multi-year Master Cooperation Agreement with Valent BioSciences Corporation (VBC) and is also supported with funds from a recent National Science Foundation grant.

“X-ray imaging has been a mainstay in medical and industrial research and diagnostics for many decades, yet it is rarely used in plant science,” said Chris Topp, Ph.D., assistant member of the Danforth Center and principal investigator for the project. “The X-ray CT system will allow us to ‘see’ roots in soil and study plants as a connected system of roots and shoots growing in diverse environments.”

“This system is unlike any other in the United States,” said said Keith Duncan, research scientist in the Topp Lab and manager of the new system. “It gives us a great deal of control over the X-ray conditions and will allow us to gather structural data on any object we put into the machine. It provides us with an internal look at not only the root systems, but what’s going on inside the stem and other parts of the plant without taking invasive measures such as removing the plant from the ground or cutting into it.”

In addition to grain crops, this project will also advance research in root and tuber crops such as cassava, potato, groundnut and others that are important for food security in many regions around the globe, but are especially hard to study.

The project combines state-of-the-art technology with computational analysis, quantitative genetics and molecular biology to understand root growth and physiology to assist researchers in understanding roots as they grow in real time in real soil. Both Topp and Duncan agree, this collaboration is just the tip of the iceberg.

“I expect that in a short time, the X-ray imager will catalyze numerous research projects among Danforth Center, St. Louis, national and international researchers that were previously not possible,” said Chris Topp, Ph.D., assistant member of the Danforth Center and principal investigator for the project.

Read more here. Learn more about the partnership and X-ray system here.

Hounsfield Facility for Rhizosphere Research

The Hounsfield Facility for Rhizosphere Research is a unique platform established with €3.5 million in funding from the European Research Council, the Wolfson Foundation, BBSRC, and the University of Nottingham. It accommodates ERC funded postdoctoral researchers and PhD students, X-ray imaging research equipment and automated growth facilities in one state-of-the-art building and fully automated greenhouse complex.

A key impediment to genetic analysis of root architecture in crops has been the ability to image live roots in soil non-invasively. Recent advances in microscale X-ray Computed Tomography (μCT) now permit root phenotyping. However, major technical and scientific challenges remain before μCT can become a high throughput phenotyping approach.

This unique high throughput root phenotyping facility exploits recent advances in μCT imaging, biological image analysis, wheat genetics and mathematical modelling to pinpoint the key genes that control root architecture and develop molecular markers and new crop varieties with improved nutrient and water uptake efficiency.

The facility’s ambitious multi-disciplinary research program will be achieved through six integrated work packages. The first 3 work packages were designed create high-throughput μCT (WP1) and image analysis (WP2) tools that will be used to probe variation in root systems architecture within wheat germplasm collections (WP3). Work packages 4-6 will identify root architectures that improve water (WP4) and nitrate uptake efficiencies (WP5) and pinpoint the genes that regulate these traits. In parallel, innovative mathematical models simulating the impact of root architecture and soil properties will be developed as tools to assess the impact of architectural changes on uptake of other nutrients in order to optimise crop performance (WP6).

screen-shot-2017-01-24-at-11-14-23-am

The Hounsfield Facility for Rhizosphere Research, University of Nottingham, UK

 

Phenomics Workshop at Purdue – be quick!

Purdue University’s Agronomy and Agricultural and Biological Engineering departments are offering a field-based Phenomics Workshop for crop research professionals involved in predicting yield and characterising biotic and abiotic stress, as well as engineers involved in developing and using sensors and sensor platforms for application.

Space is limited!

Date:  13 – 14 March 2017

Topics:  Prediction and Exploration of Agronomic Performance Using Integrated Data Sets • Effective Ground Truthing • Phenomics for Crop Improvement • Implementation of UAS Experiments • Image Analysis • Advanced Phenomic Analytical Techniques (i.e. reducing dimensionality, spatial statistics)

Cost:  $500 for professionals

Register here

For more information

Or contact Chad Martin – P: (765) 496­-3964   E: martin95@purdue.edu

screen-shot-2017-01-20-at-8-59-06-am

What the experts are saying about plant phenotyping and food security

‘It takes a village to raise a child’ states the age-old saying, but now it will take a village to feed the child as well – if we’re smart.

“Agriculture’s critical challenges of providing food security and better nutrition in the face of climate change can only be met through global communities that share knowledge and outputs; looking inward will not lead to results,” said Ulrich Schurr, Director of the Institute of Bio- and Geosciences of the Forschungszentrum Jülich and Chair of the International Plant Phenotyping Network (IPPN), speaking at the 4th International Plant Phenotyping Symposium in Mexico recently.

4th-ippn-conf-photo-2-group

Dr Jose Jimenez-Berni (keynote speaker), Dr Xavier Sirault (Co-Chair IPPN), Dr Trevor Garnett and Dr Bettina Berger from the Australian Plant Phenomics Facility at the symposium

200 world-class scientists from over 20 countries gathered from 13 to 15 December 2016 to share knowledge and technology at the symposium, co-hosted by IPPN and the Mexico-based International Maize and Wheat Improvement Center, known by its Spanish acronym, CIMMYT.

The symposium was attended by Dr Bettina Berger, Dr Trevor Garnett, Dr Xavier Sirault and Dr Jose Jimenez-Berni from the Australian Plant Phenomics Facility (APPF). Dr Sirault is also Co-Chair of the IPPN and Dr Jimenez-Berni gave a keynote lecture on field phenotyping techniques developed at the High Resolution Plant Phenomics Facility (HRPPC) node of the APPF and how they can be applied to screen for plant development including biomass and canopy architecture in the field.

4th-ippn-conf-photo-1-berni-talking

Dr Jimenez-Berni (APPF) delivering his keynote lecture at the symposium

The symposium focused on three themes:

  • Advances in Plant Phenotyping Technologies to explore the frontiers of what can be sensed remotely and other technological breakthroughs.
  • Phenotyping for Crop Improvement to consider the application of phenotyping technologies for crop improvement (breeding, crop husbandry, and estimating the productivity of agro-ecosystems).
  • Adding Value to Phenotypic Data to review how phenomics and genomics can combine to improve crop simulation models and breeding methodologies (e.g., genomic selection).

Read the full article ‘Harnessing medical technology and global partnerships to drive gains in food crop productivity’ written by Mike Listman on CIMMYT’s website.

Read more excellent plant science articles by Mike Listman here.