high resolution plant phenomics centre

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”.

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(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.

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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.

Taking five with… Michael Schaefer

The three national nodes of the Australian Plant Phenomics Facility (APPF) are home to a highly talented team of plant science researchers and specialists. This passionate, cross-disciplinary team is skilled in areas such as agriculture, plant physiology, biotechnology, genetics, horticulture, image and data analysis, mechatronic engineering, computer science, software engineering, mathematics and statistics. But who are they?

Today we take five minutes to get to know…

Michael Schaefer, PhD

Tell us a little about where you work within the APPF.

I am based at the CSIRO node of the APPF in Canberra. This centre focuses on “deep phenotyping” (delving into metabolism and physiological processes within the plant) and “reverse phenomics” (dissecting traits to discover their mechanistic basis). Here, next generation research tools are being developed and applied to probe plant function and performance, under controlled conditions and in the field.

What do you do there?

I’m a Research Scientist and Team Leader of the Translational Phenomics and Services team. My team looks after all of the new projects that come into our node of the APPF, from dealing with clients directly, to designing experiments based on the client’s needs, right through to providing the final data products and support with analysis.

What is the best part of your job?

As one of the newest team members, the best part of my job has been meeting and working with new people and dealing with new projects in different plants and crops. Every case is different, so designing and running each project is unique which provides a lot of variety.

Where do you see plant phenomics research in 5-10 years time?

I think in 5-10 years’ time plant phenomics research will be very different. We can already see that sensors and technology are getting smaller, faster and cheaper. I think much of what we do with large sensors (lidar for example) will be replaced by much smaller handheld devices or drones that will process data on the fly and give you a result straight away. This will affect all areas of science, not just plant science, so I think it will just be something that we have to adjust to.

“The moment I realised I loved plant science was…”

Somewhere during my undergraduate degree. I was doing straight science, biology, chemistry and physics – very broad – and then I started making links with how physics could be related to the environment (i.e. plants etc.). This seemed to make more sense to me, as I could see the application and how it could directly affect people now, rather than working on something theoretical that may or may not ever be used.

If you could solve one plant science question, what would it be?

For me, I’m really interested in pastures, so it would be the holy grail to be able to accurately, remotely measure above-ground biomass and split it into the green and senesced fractions.

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Michael Schaefer at the western entry of Angkor Wat, Cambodia

“When I am not working I am…”

At home spending time with my wife Ali and daughter Emilia, or outdoors playing cricket, golf or fishing.

If you could have one super power, what would it be?

Good question…. being able to bend time and space like Dr. Strange. That would be pretty cool!

“If I wasn’t a plant scientist I would be a…”

Fishing guide!

What is your most treasured possession?

They’re not a possession but my family are the most important to me.

If you could have dinner with two famous people who would they be?

Barack Obama and Tiger Woods.

What’s the one thing about you that would surprise people?

I have my private aeroplane pilot licence. I did my pilot training while I was doing my PhD – not that I get to fly much these days.

The APPF provides academic and commercial researchers with expert advice and access to high quality plant growth facilities and state-of-the-art automated phenotyping capabilities in controlled environments and in the field. We provide a suite of analytical tools to support high-throughput phenotyping and deep phenotyping in either controlled environments or in the field. Our dedicated team of experts provide consultation on project design and high quality customer support. If you would like to know more about our services and how we can support your plant science research, please contact us!

Last chance to secure an internship – apps close tomorrow!

This is your chance to investigate your plant science questions with the support of the highly skilled Australian Plant Phenomics Facility (APPF) team and the incredible technology and infrastructure we have available.

Internships are offered at the APPF in Adelaide and Canberra for enthusiastic, highly motivated postgraduate students with a real interest in our research and technology. Current postgraduate students in the following areas are encouraged to apply:

  • Agriculture
  • Bioinformatics
  • Biology
  • Biotechnology
  • Computer Science
  • Genetics
  • Mathematics
  • Plant physiology
  • Science
  • Software engineering
  • Statistics

Interstate students are strongly encouraged to apply!

We offer postgraduate internship grants which, in general, comprise:

  • $1,500 maximum towards accommodation in Adelaide or Canberra, if required
  • $500 maximum towards travel / airfare, if required
  • $10,000 maximum toward infrastructure use

The APPF has identified a number of priority research areas, each reflecting a global challenge and the role that advances in plant biology can play in providing a solution:

  • Tolerance to abiotic stress
  • Improving resource use efficiency in plants
  • Statistics and biometry
  • Application of mechatronic engineering to plant phenotyping
  • Application of image analysis techniques to understanding plant form and function

Students proposing other topics will also be considered.

APPF postgraduate internship grants involve access to the facility’s phenotyping capabilities to undertake collaborative projects and to work as an intern with the APPF team to learn about experimental design, image and data analysis in plant phenomics.

Selection is based on merit. Applications are assessed on the basis of academic record, research experience and appropriateness of the proposed research topic. Interviews may be conducted.

Postgraduate students are encouraged to contact APPF staff prior to submitting their application to discuss possible projects.

APPLICATIONS CLOSE:  31 March 2017. For further information click here.

 

Why apply for an internship with the APPF?

Well, aside from the fact we are a pretty nice bunch…

PhD student Rohan Riley, from Western Sydney University, undertook his research at APPF’s Adelaide node (The Plant Accelerator®) after being awarded a Postgraduate Student Internship Grant with us in 2015.

His research attempted to explain the unpredictability of plant growth responses in terms of resource limitation by introducing fungal communities to plants which are isolated from soils containing high or low levels of salinity and analysing the effects on plant stress at the phenotypic level.

This is what he had to say about his experience:

”Using daily phenotyping following the application of salt stress and controlled watering-to-weight in The Plant Accelerator® allowed for an unprecedented resolution and range of plant genetic changes in response to combinations of nutrient level, salinity and two different fungal communities that would not otherwise be achievable in a regular greenhouse,” said Rohan.

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”As a PhD student with limited experience in greenhouse experiments, the highly controlled growth conditions, large-scale automation, digital imaging and software technology (high-throughput phenotyping) at The Plant Accelerator® provided me with the work-space, expertise and technical support to make a complicated experiment possible.”

“It has been an amazing experience to conduct this experiment at The Plant Accelerator®. I am walking away from the facility with a big smile on my face, an incredible dataset for my PhD research and invaluable experience in greenhouse based plant research.”

To find out more about Rohan’s research:  https://www.researchgate.net/profile/Rohan_Riley

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)

 

 

Missed out on the 4th International Plant Phenotyping Symposium?

Presentations from the 4th International Plant Phenotyping Symposium, organised by CIMMYT, are now available to view online.

The presentations include José Jiménez-Berni from the Australian Plant Phenomics Facility (APPF) team. You can watch his keynote presentation, “Next generation high-throughput plant phenomic tools”, here.

You can also download a pdf of the abstract book or find more news in the future on Twitter.

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José Jiménez-Berni presenting at the 4th International Plant Phenotyping Symposium

 

 

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