food security

Sun protection and diversity could be key to more productive rice crops

With a rapidly growing population, improving the yield of global food staples such as rice has become an urgent focus for plant scientists.

In a recent study published on Plant Physiology, scientists have discovered they can improve rice productivity by selecting rice varieties that are better at capturing sunlight to produce grains instead of reflecting it as heat.

The team, which included Dr Xavier Sirault from the Australian Plant Phenomics Facility’s High Resolution Plant Phenomics Centre (APPF – HRPPC), focused on rice’s natural diversity by using traditional breeding techniques to select cultivated varieties – or cultivars – that are better at converting sunlight into food.

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“We studied hundreds of plants from five rice cultivars and found that there is variation between these varieties in relation to the quantity of light they use for growth or dissipate as heat. Some of them are capable of converting more sunlight into chemical energy, producing greater leaf area over time,” said lead researcher, Dr Katherine Meacham.

When leaves intercept sunlight, this sunlight is either; 1) absorbed by the leaf and converted via the process of photosynthesis into the plants own components; leaves, grains, roots, etc. 2) dissipated as heat as an strategy to protect the proteins of the plant from sun damage (photo-protection) or, 3) re-emitted as fluorescent light. In this study, the researchers measured fluorescence to infer the quantity of energy that is either converted into food or dissipated as heat.

“Recently scientists in the US found that they can produce transgenic plants that are better at catching sunlight without getting sun damage. Our work shows that this is also achievable by taking advantage of the natural variation of rice plants,” says Professor Robert Furbank, Director of the ARC Centre of Excellence for Translational Photosynthesis and one of the authors of this study.

“What is new about our research is that scientists had previously thought there was not much variation in how efficiently leaves could absorb and use light, and the reason for this is that they were not considering the full picture and measuring the plants throughout the entire day under natural illumination. We revealed that there are considerable differences between the five rice cultivars under moderate light and that means that there is room for selecting the most efficient plants,” said Professor Furbank.

“We found that there is room for improvement in some cultivars that can result in more photosynthesis without risking the plant’s protection strategies against sunlight damage.

The scientists measured fluorescence by clipping light receptors on leaves throughout a whole day to get a full picture of how the plant uses sunlight.

Traditional breeding for photosynthetic traits has not been a common strategy in any major cereal crop, in part due to the difficulty in measuring photosynthesis in thousands of plants. However, rapid screening tools are now available to study the interaction between the genes and the way they interact with the environment.

“Using unique facilities at the Australian Plant Phenomics Facility’s High Resolution Plant Phenomics Centre we were able to follow chlorophyll fluorescence in rice canopies throughout the entire day under natural illumination. This gave us completely different results when compared to the usual 30 min measurement of leaf level light use efficiency. By combining this with digital biomass analysis using PlantScan, we could link light use efficiency with growth, revealing genetic variation in rice varieties not previously detected,” said Professor Furbank.

“Our next step is to find varieties with superior photo-protection. We can directly use these for breeding and find the genes responsible. We have the capacity to screen many thousands of rice varieties for which we have gene sequence through the International Rice Research Institute,” said Dr Meacham.

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Measuring photosynthesis.  Photo credit:  International Rice Research Institute (IRRI)

 

 

Major investment in plant root phenotyping to answer key questions

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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).

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

 

Planting a seed with STEM students

During January 2017 the Australian Plant Phenomics Facility’s (APPF) Canberra-based High Resolution Plant Phenomics Centre (HRPPC) is welcoming science, technology, engineering and maths (STEM) students from across Australia to participate in laboratory visits as part of the annual National Youth Science Forum.

STEM education is key to enabling our next generation to tackle the challenges of a fast growing population, globalisation and climate change, underpinning innovation towards future solutions.

One of the challenges is feeding the world. The United Nations Food and Agriculture Organisation estimates that about 795 million of the 7.3 billion people in the world, or one in nine, were suffering from chronic undernourishment in 2014-2016.

Research facilitated at the APPF is leading to the development of new and improved crops, healthier food, more sustainable agricultural practices, improved biodiversity care, and the use of crops to develop pharmaceuticals. By exposing students to this important area of research and encouraging cross-disciplinary approaches through STEM, the APPF hopes to plant the seeds of ideas that may unlock new solutions in the minds of the next generation of leading agriculture scientists and engineers.

This year the program for students visiting the APPF-HRPPC will emphasise the engineering aspects of our work, covering laboratory as well as field aerial data capture and analysis, and our aim of supporting a sustainable food future for our nation. The students will have the opportunity to interact with scientists, software engineers and mechatronic engineers, learn about the direct applications of the research conducted at the APPF, possible career paths they can follow and what the future offers in these fields.

The National Youth Science Forum is an immersive, 12 day residential science program aimed at students entering Year 12 who are passionate about STEM and wish to pursue careers in these fields. The residential program attracts over 400 students each year and connects students with researchers and visits to world class laboratories.

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Images:  Dr Xavier Sirault presenting to visiting National Youth Science Forum students at the Australian Plant Phenomics Facility’s High Resolution Plant Phenomics Centre in Canberra

 

 

 

 

More salad please!

With indoor-vertical farming on the rise, lettuce production can be customised more than ever, by choosing the right varieties, temperature, lighting and nutrient supply to produce the leaves consumers want. Achieving this goal requires optimisation of numerous components and a recent collaborative study between the USA and Australia, published in Frontiers in Plant Science, has proven optical sensors can be used to evaluate lettuce growth, color and health non-destructively.

The research team, Ivan Simko and Ryan Hayes from the US Department of Agriculture and Robert Furbank from the ARC Centre of Excellence for Translational Photosynthesis and formerly Australian Plant Phenomics Facility – High Resolution Plant Phenomics Centre, designed the study to test the feasibility of using optical sensors for physiological evaluation of lettuce plants in early stages of their development. The method developed can help in breeding programs and optimising farming practices to meet the requirements of an increasingly demanding market.

Read the full study, Non-destructive phenotyping of lettuce plants in early stages of development with optical sensors, published in Frontiers in Plant Science, here.

Or read the abstract here:

Abstract

Rapid development of plants is important for the production of ‘baby-leaf’ lettuce that is harvested when plants reach the four- to eight-leaf stage of growth. However, environmental factors, such as high or low temperature, or elevated concentrations of salt, inhibit lettuce growth. Therefore, non-destructive evaluations of plants can provide valuable information to breeders and growers. The objective of the present study was to test the feasibility of using non-destructive phenotyping with optical sensors for the evaluations of lettuce plants in early stages of development. We performed the series of experiments to determine if hyperspectral imaging and chlorophyll fluorescence imaging can determine phenotypic changes manifested on lettuce plants subjected to the extreme temperature and salinity stress treatments. Our results indicate that top view optical sensors alone can accurately determine plant size to approximately 7 g fresh weight.

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Comparison of the size and the colour of plants cultivated at optimal (OPT), low (COLD) and high (HOT) temperatures (experiment 3). Plants were initially grown at OPT for 10 days and the either continuously kept in OPT or transferred to COLD or HOT for 8 days. Sides of the square pots are 68mm long.

Hyperspectral imaging analysis was able to detect changes in the total chlorophyll (RCC) and anthocyanin (RAC) content, while chlorophyll fluorescence imaging revealed photoinhibition and reduction of plant growth caused by the extreme growing temperatures (3 and 39°C) and salinity (100 mM NaCl). Though no significant correlation was found between Fv/Fm and decrease in plant growth due to stress when comparisons were made across multiple accessions, our results indicate that lettuce plants have a high adaptability to both low (3°C) and high (39°C) temperatures, with no permanent damage to photosynthetic apparatus and fast recovery of plants after moving them to the optimal (21°C) temperature. We have also detected a strong relationship between visual rating of the green- and red-leaf color intensity and RCC and RAC, respectively. Differences in RAC among accessions suggest that the selection for intense red color may be easier to perform at somewhat lower than the optimal temperature.

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Genomic position of the quantitative trail locus (QTL) for light green colour (qLG4) on linkage group 4. Visual rating of the green colour intensity was performed on adult plants in field, while the relative chlorophyll content (RCC) was determined from hyperspectral reflectance measured on cotyledons of seedlings cultivated in plastic boxes (experiment 7). The orange line parallel with the linkage map shows the significance threshold (a = 0.05). The allele for light green colour and low RCC originates from cv. La Brilliante. Detailed description of the linkage map for this population and its construction was published previously (Hayes et al., 2014; Simko et al., 2015b). Distance in cM is shown on the right site of the linkage map. LOD, logarithm of odds.

This study serves as a proof of concept that optical sensors can be successfully used as tools for breeders when evaluating young lettuce plants. Moreover, we were able to identify the locus for light green leaf color (qLG4), and position this locus on the molecular linkage map of lettuce, which shows that these techniques have sufficient resolution to be used in a genetic context in lettuce.

Citation

Simko I, Hayes RJ and Furbank RT (2016) Non-destructive Phenotyping of Lettuce Plants in Early Stages of Development with Optical Sensors. Front. Plant Sci. 7:1985. doi: 10.3389/fpls.2016.01985

 

 

Accurate field canopy temperature measured in seconds

A method for cost-effective, reliable and scalable airborne thermography has been developed, resolving a number of challenges surrounding accurate high-throughput phenotyping of canopy temperature (CT) in the field, such as weather changes and their influence on more time consuming measurement methods. Utilising a manned helicopter carrying a radiometrically-calibrated thermal camera, thermal image data is captured in seconds and processed within minutes using custom-developed software; an invaluable advantage for large forward genetic studies or plant breeding programs.

The method and research results, by a collaboration between CSIRO Agriculture and Food, the Australian Plant Phenomics Facility – High Resolution Plant Phenomics Centre, CSIRO Information Management and Technology, and the ARC Centre of Excellence for Translational Photosynthesis were published recently in Frontiers in Plant Science.

Read the full study“Methodology for high-throughput field phenotyping of canopy temperature using airborne thermography”, here or the abstract below.

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Airborne thermography image acquisition and processing pipeline. Total time to acquire and process images for an experiment comprising 1,000 plots of size 2 x 6 m is ca. 25 min. (A) Image acquisition with helicopter. The images are recorded on a laptop and the passenger, left, provides real time assessment of the images and feedback to the pilot. This step takes < 10 s for an experiment comprising 1,000 plots of size 2 x 6 m. (B) Screenshot of custom-developed software called ChopIt. ChopIt is used for plot segmentation and extraction of CT from each individual plot for statistical analysis. This step takes ca. 20 min for an experiment comprising 1,000 plots of size 2 x 6 m.

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Airborne thermography image acquisition system comprising a helicopter cargo pod with thermal camera and acquisition kit mounted on the skid of a Robinson R44 Ravel helicopter. Photo insert shows the inside of the helicopter cargo pod with arrow denoting FLR® SC645 thermal camera: ±2°C or ±2% of reading; < 0.05°C pixel sensitivity; 640×480 pixels; 0.7 kg without lens.

Abstract

Lower canopy temperature (CT), resulting from increased stomatal conductance, has been associated with increased yield in wheat. Historically, CT has been measured with hand-held infrared thermometers. Using the hand-held CT method on large field trials is problematic, mostly because measurements are confounded by temporal weather changes during the time required to measure all plots. The hand-held CT method is laborious and yet the resulting heritability low, thereby reducing confidence in selection in large scale breeding endeavors. We have developed a reliable and scalable crop phenotyping method for assessing CT in large field experiments. The method involves airborne thermography from a manned helicopter using a radiometrically-calibrated thermal camera. Thermal image data is acquired from large experiments in the order of seconds, thereby enabling simultaneous measurement of CT on potentially 1000s of plots. Effects of temporal weather variation when phenotyping large experiments using hand-held infrared thermometers are therefore reduced. The method is designed for cost-effective and large-scale use by the non-technical user and includes custom-developed software for data processing to obtain CT data on a single-plot basis for analysis. Broad-sense heritability was routinely >0.50, and as high as 0.79, for airborne thermography CT measured near anthesis on a wheat experiment comprising 768 plots of size 2 × 6 m. Image analysis based on the frequency distribution of temperature pixels to remove the possible influence of background soil did not improve broad-sense heritability. Total image acquisition and processing time was ca. 25 min and required only one person (excluding the helicopter pilot). The results indicate the potential to phenotype CT on large populations in genetics studies or for selection within a plant breeding program.

Citation:  Deery DM, Rebetzke GJ, Jimenez-Berni JA, James RA, Condon AG, Bovill WD, Hutchinson P, Scarrow J, Davy R and Furbank RT (2016) Methodology for High-Throughput Field Phenotyping of Canopy Temperature Using Airborne Thermography. Front. Plant Sci. 7:1808. doi: 10.3389/fpls.2016.01808

 

 

Adelaide to host 5th International Plant Phenotyping Symposium

The Australian Plant Phenomics Facility is thrilled to announce the city of Adelaide, South Australia will host the 5th International Plant Phenotyping Symposium in October 2018!

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2018 Host City, Adelaide, South Australia   (Image source: South Australian Tourism Commission)

The International Plant Phenotyping Network (IPPN) voted during its general assembly, held alongside the 4th International Plant Phenotyping Symposium in Mexico recently.

We look forward to welcoming the international plant phenotyping community to Adelaide in 2018!

 

 

Hello, ni hau, hola, guten tag, marhaba, bonjour… knowledge sharing the key to plant science success

The Australian Plant Phenomics Facility (APPF) is a national facility, available to all plant scientists, offering access to infrastructure that is not available at this scale or breadth in the public sectors anywhere else in the world.

Our three nodes in Adelaide and Canberra frequently welcome international research, industry and government guests to tour facilities and share knowledge in plant phenomics. Encouraging and supporting a global community focused on providing better nutrition and food security is key to the APPF vision we uphold.

Recently the CSIRO based HRPPC node of the APPF hosted a VIP visit by the Secretary of the Department of Industry, Innovation and Science, Glenys Beauchamp, CSIRO CEO, Larry Marshall, and the Canadian High Commissioner, His Excellency Paul Maddison.

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Larry Marshall (CEO, CSIRO), Glenys Beauchamp (Secretary, Department of Industry, Innovation and Science) and His Excellency Paul Maddison (Canadian High Commissioner) in front of a Phenomobile Lite at the APPF HRPPC           (Image courtesy of the CSIRO)

Hosted by Drs Xavier Sirault and Jose Jimenez-Berni, the visitors observed aspects of the work done by the APPF’s HRPPC in the controlled environment and had the opportunity to see first-hand one of the centre’s purpose built and designed Phenomobile Lite buggies which are used in the field for capturing plant traits.

The group discussed an overview of the range of research and development activities and issues facing Australia in science and technology and the Canadian High Commissioner shared his interested in areas of existing and potential collaboration between Australia and Canada.

We welcome and encourage engagement with the international plant science community. If you would like to visit one of our sites, discuss your plant phenomics research or book one of our facilities, please contact us – we love plant science!