barley

The hunt for high salt tolerant barley crops gets closer

Barley-(optimised-for-web)

Soil salinity severely impacts crop growth and yield. Within minutes of exposure to salt, cell expansion, leaf expansion, photosynthesis, transpiration and tillering are reduced. When salts accumulate to toxic concentrations in the shoot, especially in older leaves, a secondary inhibition of growth occurs through damage to the plant’s metabolism and ion imbalances. These effects occur weeks to months following salt application.

Plants have evolved numerous mechanisms to detect and respond to the effects of salt stress including a range of signal transduction mechanisms. However, investigating the maintenance of growth under salt stress has been limited by the lack of techniques that allow nondestructive measurements of plant growth through time. The resources and technologies now exist to phenotype many genotypes and identify those with high shoot ion-independent and shoot ion-dependent tolerance under greenhouse conditions.

Barley is one of the more salt-tolerant crops, able to grow in higher concentrations of salt than wheat, rice or maize. However, the growth of barley is still significantly affected by salinity. A better understanding of the genetic variation for salinity tolerance mechanisms within barley cultivars is required for future breeding improvement.

In a study by Stuart Roy and his international collaborators, nondestructive and destructive measurements are used to evaluate the responses of 24 predominately Australian barley (Hordeum vulgare L.) lines at 0, 150 and 250 mM NaCl. Considerable variation for shoot tolerance mechanisms not related to ion toxicity (shoot ion-independent tolerance) was found, with some lines being able to maintain substantial growth rates under salt stress, whereas others stopped growing. Hordeum vulgare spp. spontaneum accessions and barley landraces predominantly had the best shoot ion independent tolerance, although two commercial cultivars, Fathom and Skiff, also had high tolerance. The tolerance of cv. Fathom may be caused by a recent introgression from H. vulgare L. spp. spontaneum.

This study shows that the most salt-tolerant barley lines are those that contain both shoot ion-independent tolerance and the ability to exclude Na+ from the shoot (and thus maintain high K+:Na+ ratios).

Read the full paper, ‘Variation in shoot tolerance mechanisms not related to ion toxicity in barley’, here (Functional Plant Biologyhttps://doi.org/10.1071/FP17049).

To find out how the Australian Plant Phenomics Facility can help facilitate your plant science research visit our website.

International consortia tackle the global challenge to increase wheat yields at the APPF

Field of ripe wheat

Two international consortia of scientists from the United States, Great Britain, Mexico and Australia are currently carrying out research projects of global importance at the Australian Plant Phenomics Facility’s (APPF) Adelaide node for the International Wheat Yield Partnership (IWYP).

The first research project, Improving Yield by Optimising Energy Use Efficiency, is phenotyping an Excalibur x Kukri RIL population to determine genetics controlling energy use efficiency (EUE) in wheat. The aim is to identify genetic loci and markers to enable breeding of high-yielding germplasm with:

  • low rates of leaf respiratory CO2 released per unit growth,
  • optimised levels of sugars, organic and amino acids for growth, and
  • increased biomass at anthesis.

More than 85-90% of the energy captured by plants is used in high-cost cellular processes, such as transport of nutrients and respiration, meaning about only 10-15% is allocated to yield. Thus, any small gain in energy redistribution and use for a costly process can have a marked positive impact on biomass accumulation and yield.

Improvements in EUE can be achieved at the cell, tissue and whole-plant level, with respiration being a prime target.

“Our initial screening of 138 Australian commercial cultivars revealed a two-fold variation in rates of leaf respiration, three-fold variation in the ratio of respiration to growth rate during early development, and significant heritability of 35%. This demonstrates there is untapped genetic variation in EUE amenable to fine-tuning and optimisation of biomass accumulation in the lead-up to anthesis, with concomitant positive knock-on effects on yield”, said Australian National University’s Barry Pogson, Project Lead and Director of the ARC Centre of Excellence in Plant Energy Biology (AUS).

The project has partners at University of Western Australia (AUS), CIMMYT (MEX) and  the University of Adelaide (AUS).

The second research project, AVP1, PSTOL1 and NAS – Three High-Value Genes for Higher Wheat Yield, aims to enhance wheat yield by exploiting and building synergy of three high value genes (AVP1, PSTOL1 and NAS) and enabling molecular breeding by:

  • developing two-gene and three-gene pyramiding combinations of AVP1, PSTOL1 and NAS using available transgenic wheat lines and quantifying the additive effects on yield in multi-location field and greenhouse trials (as a proof of concept),
  • identifying wheat orthologs and allelic variants of TaAVP1, TaPSTOL1 and TaNAS, and designing molecular markers to the best alleles for marker-assisted breeding,
  • providing basic understanding of the physiological and molecular mechanisms behind improved yield and selecting wheat lines with the best allelic combination and field performance, and
  • assessing the necessity for using genome editing technologies to optimise gene function and enhance positive effect on wheat yield by modifying expression of the wheat alleles.

The genes Vacuolar Proton Pyrophosphatase 1 (AVP1), Phosphorus Starvation Tolerance 1 (PSTOL1) and Nicotianamine Synthase (NAS) have been shown to improve plant biomass production and grain yield. Over-expression of these genes results in improved biomass production and grain yield in a range of plant species, including cereals (rice, barley, wheat), in optimal growing conditions. The enhanced yield of the plants is believed to be due to improved sugar transport from source to sinks (AVP1), enhanced root growth and nutrient uptake (AVP1, PSTOL1) and increase in shoot biomass and tiller number (AVP1, PSTOL1, NAS2).

“Identifying and pyramiding the wheat orthologues of these high-value genes provides a real opportunity to produce wheat with significantly improved field performance and higher grain yield,” said Project Lead, Stuart Roy, from the University of Adelaide (AUS).

The project has partners at University of Melbourne (AUS), Arizona State University (USA), Cornell University (USA), University of California, Riverside (USA) and Rothamsted Research (GBR).

These extensive projects will continue throughout 2017 and into 2018.

 

Why is this research so important?

Wheat is the most widely grown of any crop globally, providing 20% of daily calories and protein. By 2050 wheat demand is expected to increase by 60%. To meet this demand, annual potential wheat yield increases must effectively double – an exceptional challenge.

In November 2012, funding agencies and organisations from the G20 countries agreed to work together and formed the global Wheat Initiative to develop a strategic approach to supporting research that would lead to dramatically increasing the genetic yield potential of wheat.

An essential pillar of this strategy is the International Wheat Yield Partnership (IWYP), a novel collaborative approach, enabling the best scientific teams from across the globe to work together in an integrated program to address the challenge of raising the genetic yield potential of wheat by up to 50% in the next two decades all over the world. IWYP builds on the initial research concepts of the Wheat Yield Consortium established by CIMMYT.

To deliver increased wheat yield, a combination of fundamental bioscience and applied research will be needed. IWYP will deliver this through a focused program of research to develop new knowledge, models and wheat lines suited to multiple environments ensuring global gains in wheat yields are achieved.

IWYP will target six key research scope areas:

  • uncovering genetic variation that creates the differences in carbon fixation and partitioning between wheat lines,
  • harnessing genes from wheat and other species through genetic modification to boost carbon capture and fixation to increase biomass production,
  • optimising wheat development and growth to improve grain yields and harvest index,
  • developing elite wheat lines for use in other breeding programs,
  • building on discoveries in wheat relatives and other species, and
  • fostering breakthrough technology development that can transform wheat breeding.

The “IWYP Science Program” provides a unique plan to generate new discoveries and provides for their rapid incorporation into wheat crops grown throughout the world. IWYP’s overarching aims are to stimulate new research, amplify the output from existing programs and make scientific discoveries available to farmers in developing and developed nations.

 

The Australian Plant Phenomics Facility

The APPF provides state-of-the-art phenotyping tools and expertise to help academic and commercial plant scientists from Australia and around the world understand and relate the performance of plants to their genetic make-up. Research facilitated at the APPF is leading to the development of new and improved crops, more sustainable agricultural practices, improved maintenance and regeneration of biodiversity in the face of declining arable land area and the challenges of climate change. Our services.

Do you need access to plant phenotyping capabilities? The PIEPS scheme can help!

Do you have an exceptional plant science research project destined to deliver high impact outcomes for agriculture? 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 applyAPPF Phenomics Infrastructure for Excellence in Plant Science (PIEPS).

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

Learn more about projects at the Australian Plant Phenomics Facility and keep in touch.

 

 

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™

 

 

Professor Mark Tester to talk plant science in Adelaide

Professor Mark Tester from King Abdullah University of Science & Technology (KAUST), Saudi Arabia, will present a talk in Adelaide this March:

“Into the field and into the genome – increasing salinity tolerance of crops”

Time:  Wednesday 8 March, 3.30pm – 4:30pm
Venue:  Hosted by The University of Adelaide, Plant Science Department, the talk will be held in the Plant Genomics Centre seminar room (Waite Campus, The University of Adelaide, South Australia) with drinks and nibbles afterwards. All are welcome.

About the speaker

Mark Tester is Professor of Bioscience at KAUST. After a PhD in Cambridge and lectureship there, he went to Adelaide, as a Research Professor in the Australian Centre for Plant Functional Genomics and Director of the Australian Plant Phenomics Facility. Mark was part of the team that led the establishment of this Facility, a $55m organisation that develops and delivers state-of-the-art phenotyping facilities, including The Plant Accelerator, an innovative plant growth and analysis facility. In his research group, forward and reverse genetic approaches are used to understand salinity tolerance and improve this in crops such as barley and tomatoes. His aspiration is to develop a new agricultural system where brackish water and seawater can be unlocked for food production.

Abstract

One-third of the world’s food is produced under irrigation, and this is directly threatened by over-exploitation of water resources and global environmental change. In this talk, the focus will be on the use of forward genetics to discover genes affecting salinity tolerance in barley, rice and tomatoes, along with some recent genomics in quinoa, a partially domesticated crop with high salinity tolerance. Rather than studying salinity tolerance as a trait in itself, we dissect salinity tolerance into a series of components that are hypothesised to contribute to overall salinity tolerance.

For barley, two consecutive years of field trials were conducted at the International Center for Biosaline Agriculture, a site with sandy soil and very low precipitation. Drip irrigation systems allowed the control of salinity by supplying plots with low (1 dS/m) and high salinity water (17 dS/m). A barley Nested Association Mapping (NAM) population developed by Klaus Pillen has been used to dissect physiologically and genetically complex traits in response to salt stress. Ten traits related to yield and yield components (e.g. days to flowering, harvest index, 100 seed mass) were recorded and five stress-indices were derived from each of these measurements. We have identified two significant loci located on the long arms of chromosomes 1H and 5H, which are both associated with several traits contributing to salinity tolerance, namely days to flowering, days to maturity, harvest index and yield.

For tomatoes, the focus is on genetics of tolerance in wild tomatoes, specifically Solanum galapagense, Solanum cheesmaniae and Solanum pimpinellifolium. An association genetic approach is being taken. High quality genome sequences have been made, and genotyping-by-sequencing undertaken. Tomatoes have been phenotyped in The Plant Accelerator and in the field, and analyses are currently in progress.

The application of this approach provides opportunities to significantly increase abiotic stress tolerance of crops, and thus contribute to increasing agricultural production in many regions.

Mark is in Adelaide between Mon 6th and Sun 12th March. If you would like to meet with Mark, please contact him directly: mark.tester@kaust.edu.sa

The Plant Accelerator

Plant phenotyping research projects facilitated by The Plant Accelerator vary from large scale screening of early growth, to salinity tolerance and water and nutrient use efficiency. Possible applications are diverse with respect to the measured traits and plant species studied. Please contact our experts to discuss how your research might benefit from the capabilities and services provided by The Plant Accelerator.

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The Plant Accelerator®,  Australian Plant Phenomics Facility, Adelaide, South Australia

The science and the craft: Barley-beer-whisky

The clever ABTS organising committee have announced the details of the 18th Australian Barley Technical Symposium. With a location like Hobart, offering world-class food and wine, stunning modern art and breathtaking natural attractions, coupled with the hot topics of barley, beer and whisky on the agenda, this symposium is sure to prove popular!

The program will cover:  Agronomy • Quarantine • Genomics • Marketing • Malting • Brewing • Breeding • Disease • Challenges.

Dates for your diary:  3 – 6 September 2017

Location:  Wrest Point Hotel Casino, Hobart, Tasmania

For more information and announcements go to:  www.abtsbarley.info

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.

field-canopy-temp-blog-image-1

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

 

 

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.

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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.

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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.