plant biology

This is your chance! An invaluable opportunity to access phenotyping capabilities to further your plant science research

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 was announced in May and 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.

Don’t miss this 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)

To find out how we can support your research, contact us.

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%.

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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.

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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)

 

 

Canberra, Camille and the Cropatron…

As the sun rises over another crisp autumn morning in Canberra, you will find French intern, Camille Mounier, keenly watching over her rice lines in the Cropatron at the Australian Plant Phenomics Facility’s node at CSIRO Agriculture and Food.

Her project, ‘A complex system biology approach to understand the factors affecting canopy photosynthesis’, is being led by Dr Xavier Sirault, Director of the node, in partnership with the Chinese Academy of Sciences.

The project team aim to develop system models of canopy photosynthesis for both rice and wheat, in particular, developing novel methods to combine these system models with phenomics data. This approach will help in the identification of the critical factors controlling photosynthetic energy conversion efficiency in C3 species with the view to improving canopy photosynthetic efficiency, and subsequently, crop yields in small grain cereals.

Using the Cropatron platform, Camille will acquire data on canopy growth, gas and energy exchange in order to validate the biophysical photosynthetic model developed by Prof Xinguang Zhu, Head of Plant Systems Biology Group at the CAS-MPG Partner Institute for Computational Biology.

The Cropatron is a PC2 compliant, fully environmentally controlled (temperature, CO2 and humidity) greenhouse equipped with an automated gantry system (operating at 3.5m above the floor) for proxy-sensing imaging of plants grown in mini canopies. The sensing head is composed of an hyperspectral camera (400-1000nm) for measuring chlorophyll pigments, Far IR imaging for proxy sensing of canopy conductance, LiDAR for quantifying canopy architecture and monitoring growth over time, lysimeters for measuring water use at plot level and a gas exchange chamber at canopy level for measuring canopy assimilation.

Academic and commercial plant scientists are welcome to access the Cropatron platform – find out about pricing, availability and bookings here.

 

Taking the kinks out of curves

In a recent paper, researchers have developed a methodology suitable for analyzing the growth curves of a large number of plants from multiple families. The corrected curves accurately account for the spatial and temporal variations among plants that are inherent to high-throughput experiments.

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An example of curve registration.  a The salinity sensitivity (SS) curves of the 16 functions from an arbitrary family, b SS curves after the curve registration, and c the corresponding time-warping functions. The salinity sensitivity on the y-axis of a and b refers to the derivative of the relative decrease in plant biomass

 

Advanced high-throughput technologies and equipment allow the collection of large and reliable data sets related to plant growth. These data sets allow us to explore salt tolerance in plants with sophisticated statistical tools.

As agricultural soils become more saline, analysis of salinity tolerance in plants is necessary for our understanding of plant growth and crop productivity under saline conditions. Generally, high salinity has a negative effect on plant growth, causing decreases in productivity.  The response of plants to soil salinity is dynamic, therefore requiring the analysis of growth over time to identify lines with beneficial traits.

In this paper the researchers, led by KAUST and including Dr Bettina Berger and Dr Chris Brien from the Australian Plant Phenomics Facility (APPF), use a functional data analysis approach to study the effects of salinity on growth patterns of barley grown in the high-throughput phenotyping platform at the APPF. The method presented is suitable to reduce the noise in large-scale data sets and thereby increases the precision with which salinity tolerance can be measured.

Read the full paper, “Growth curve registration for evaluating salinity tolerance in barley” (DOI: 10.1186/s13007-017-0165-7) here.

Find out how the Australian Plant Phenomics Facility can support your plant science research here.

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High-throughput phenotyping in the Smarthouse™ at the Adelaide node of the APPF

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Barley plants growing in the Smarthouse™

 

 

Travel grant opportunity to attend the 34th Annual Root Biology Symposium

IPPN Root Phenotyping Working Group
Travel Grant for Researchers Using Phenotyping
IPG 2017, 34th Annual Root Biology Symposium
Columbia, Missouri, USA
7-9 June 2017

The IPPN Root Phenotyping Working Group (RPWG) encourages mobility among researchers and enhances international contacts between research groups. With this sponsorship grant RPWG  supports participation of Early Career Researchers at the IPG 2017, 34th Annual Root Biology Symposium.

  • Up to four grants of 500 EUR per researcher can be awarded.
  • 1 May 2017

Conditions:

  • You are affiliated with a university or a research institution and you are an early career scientist, PhD student, or postdoc who finished his PhD no later than ten years ago.
  • Please fill in the travel grant application and submit it to Saoirse Tracy.
  • The applications will be evaluated by the RPWG Board.

Getting to the root of plant zinc health

Sunlight and water are two obvious requirements essential for healthy growth of plants, but did you know that zinc is also a vital ingredient? Zinc is a critical nutrient in hundreds of enzyme systems which are necessary for normal plant function. Zinc is also critical for human health – in fact, zinc is involved in more body functions than any other mineral.

Plants get zinc from the soil via their root systems. This uptake of nutrients is enhanced in many plants by mycorrhizal fungi which colonise the roots, creating a vast connection between the plant roots and the soil around them. Mycorrhizal fungi effectively increase the surface area of the roots, collecting nutrients from the soil beyond the reach of plant roots alone, and transfer these nutrients back to the plant.

Scientist, Dr Stephanie Watts-Williams, wants to find out how such mycorrhizal fungi can improve the zinc nutrition of plants, and subsequently impact on human health – particularly in countries where zinc malnutrition is a serious issue.

Read on here about Stephanie and her research at The Plant Accelerator®, Australian Plant Phenomics Facility, and other Waite Research Precinct partners.

Discover more about Stephanie’s research here or find her on Twitter:  @myco_research

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Dr Stephanie Watts-Williams at The Plant Accelerator®, Australian Plant Phenomics Facility