mark tester

The hunt for high salt tolerant barley crops gets closer

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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.

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™

 

 

A better way to tackle environmental variation in your greenhouse research

Statistics prove the smart way to deal with variation in your controlled environment greenhouse.

Plant phenomics allows the measurement of plant growth with unprecedented precision. As a result, the question of how to account for the influence of environmental variation across the greenhouse has gained attention.

Controlled environment greenhouses offer plant scientists the ability to better understand the genetic elements of specific plant traits by reducing the environmental variances in the interaction between genetics and environment.

But controlled environments aren’t as controlled as they seem – variation does exist. For example, some days are cloudy, some are not. The sun, as it crosses the sky, casts shadows differently on plants, depending on their position within the greenhouse. In fact, a recent study by colleagues at INRA in Montpellier showed significant light gradients within a greenhouse and provided sophisticated tools for understanding how much light each plant receives.

One practice for dealing with variation has been to rearrange the position of the plants around the greenhouse during the experiment, however, there is a better way.

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Rice plants growing in The Plant Accelerator® at the Australian Plant Phenomics Facility’s Adelaide node

The automated high-throughput phenotyping greenhouses at The Plant Accelerator® are controlled environment facilities which use sensor networks to identify and quantify environmental gradients (light, temperature, humidity) in the greenhouses. To further tackle environmental variation, Chris Brien, Senior Statistician at The Plant Accelerator®, led a study that showed good statistical design and analysis was key to accounting for the impact of environmental gradients on plant growth. It was argued that rearranging the plants during the experiment makes it impossible to adjust for the effect of gradients and should be avoided.

The study involved a two-phase wheat experiment involving four tactics in a conventional greenhouse and a controlled environment greenhouse at The Plant Accelerator® to investigate these issues by measuring the effect of the variation on plant growth.

To learn more about Chris’s study read the full paper here.

To discuss the benefits of good statistical design contact Chris Brien.

To access The Plant Accelerator® for your research:  The Plant Accelerator® at the Australian Plant Phenomics Facility (APPF) is available to all publicly or commercially funded researchers. We have a full team of specialists including statisticians, horticulturalists and plant scientists who can provide expert advice to you when preparing your research plans.

 

 

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

Delicious potential: The genome of quinoa decoded

Scientists have successfully decoded the genome of quinoa, one of the world’s most nutritious and resilient crops.

The study, published online this week in Nature, was an international collaboration led by Professor Mark Tester at the King Abdullah University of Science and Technology (KAUST), Saudi Arabia.

The enormously popular “super-food” is gluten-free, has a low glycaemic index and contains an excellent balance of essential amino acids, fibre, lipids, carbohydrates, vitamins, and minerals, causing international demand for the grain to soar and prices to skyrocket as demand exceeds supply.

“Apart from its nutritional benefits, the ability of quinoa to grow on marginal land is possibly most exciting”, said Prof Mark Tester. “It can grow in poor soils, salty soils and at high altitudes. It really is a very tough plant. Quinoa could provide a healthy, nutritious food source for the world using land and water that currently cannot be used, and our new genome takes us one step closer to that goal.”

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Quinoa pilot trials in the Australian Plant Phenomics Facility’s high-throughput phenotyping Smarthouse at The Plant Accelerator®

Future research projects will focus on identifying the genes that make quinoa so tolerant to poor soils. In pilot experiments carried out at the Australian Plant Phenomics Facility‘s Adelaide node, The Plant Accelerator®, different growth conditions and salt applications were tested in preparation for larger-scale studies. The first studies showed that quinoa still grows well when watered with half-strength sea water, when many other crops would die. Since performing these initial experiments, Professor Tester and his team have secured further research funding to work towards establishing quinoa as a broadacre crop.

“We are extremely excited to support this important research”, said Dr Bettina Berger, Scientific Director at The Plant Accelerator®. “As part of this collaborative project, The Plant Accelerator® will perform two screening runs of a diversity panel in the second half of 2017 to identify the genetic basis of salt tolerance in quinoa”.

Further reading:

The full published study in Nature. doi:10.1038/nature21370

KAUST An Integrated Repository for Population Genomics in genus Chenopodium

BBC News online article

Nature Middle East online article

 

Salt tolerant genetic loci in rice exposed

Rice is a staple food for over half of the world’s population. It is also the most salt-sensitive cereal crop, with losses in yield reaching up to 69%.

In a new study published in Nature Communications collaborators from King Abdullah University of Science and Technology (KAUST) and The Plant Accelerator®, Australian Plant Phenomics Facility investigated the early responses of rice plants to moderately-saline conditions and pinpointed new salt-tolerant genetic loci.

Project lead, Professor Mark Tester (KAUST), supervised PhD student Nadia Al-Tamini’s project which grew 297 indica and 256 aus rice varieties under low and high salinity. Using a technique called ‘high-throughput non-invasive phenotyping’ plants are moved on conveyor belts, imaged daily using digital cameras to monitor biomass and shoot development, and weighed to carefully measure transpiration levels (water use).

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Dr Bettina Berger (left) and Nadia Al-Tamimi (right) in The Plant Accelerator®

“The Plant Accelerator® allowed us to analyse numerous aspects of the growth of multiple plants simultaneously,” says Professor Tester.

Using the facility’s cutting-edge technology, the researchers were able to show some genes, for example those connected with signaling processes, were important to plant growth in the first two to six days after salt application, while other genes became prominent later.

“This is perhaps the most astonishing aspect of this work – we can now obtain genetic details daily, pinpointing exactly when each locus comes into play in response to salinity,” says Professor Tester.

The results of this study could prove useful for breeding programs seeking to address yield and stress resistance to meet the demand of our increasing global population and climate challenges.

Congratulations to everyone involved in this study!!

Find the full articlewww.nature.com/articles/ncomms13342

More on Nadia Al-Tamini’s story:  https://blog.plantphenomics.org.au/2015/02/24/saudi-arabian-students-joins-plant-accelerator-team-to-investigate-salinity-tolerance-in-rice/

Professor Mark Tester, Plant Science Associate Director of the Center for Desert Agriculture Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Saudi Arabia, mark.tester@kaust.edu.sa, www.kaust.edu.sa/en/study/faculty/mark-tester

Dr Bettina Berger, Scientific Director, The Plant Accelerator, Australian Plant Phenomics Facility, University of Adelaide, www.plantphenomics.org.au, bettina.berger@adelaide.edu.au