Mapping the barley genome – good news for farmers

December 9, 2013

Filed under: Research — acpfg @ 1:20 pm

Did you know that ACPFG researchers were part of the international consortium, comprising 22 different institutes, that this year mapped the barley genome?
This is really good news, especially if you are a barley farmer because the outcomes of this project could potentially lead to higher yields, improved tolerance to biotic and abiotic stresses and more nutritious foods. Researchers involved in the project consider this a major step forward in barley research!

Scientists have mapped the barley genome providing breeders with knowledge to pinpoint functional genes. Image by Dag Endreson sourced on Flickr

Scientists have mapped the barley genome providing breeders with knowledge to pinpoint functional genes. Image by Dag Endreson sourced on Flickr

The project
As part of the project, all of the 32,000 genes in barley were reviewed. One of the most important discoveries for the agricultural industry was the identification of differing recombination rates in the different regions of barley’s chromosomes. Researchers identified areas of chromosomes where recombination rate was low but functional genes’ locations were high.
This means that there are parts of the barley chromosome that don’t readily form new combinations of genes during sexual reproduction. Unfortunately many of the desirable genes for environmental tolerance were also located in these regions of the chromosomes.
Breeders can now use this important finding to identify strategies to force recombination in those areas, potentially resulting in higher variation in progeny.
The mapping of the barley genome was so significant that it was published in Nature, an esteemed scientific journal. If you’re interested you can read the article here.
The Australian interest was led by scientists from the Australian Centre for Plant Functional Genomics (ACPFG) along with researchers from the University of Adelaide and the ARC Centre for Excellence in Plant Cell Walls.

Barley – the facts
Barley belongs to the same family as wheat and rye and together they provide about 30% of all calories consumed worldwide. Because barley is very closely related to wheat, the results can be used to help wheat research also.
Wheat and barley are two of Australia’s most economically important crops with exports totalling $6 billion (wheat) and $1.3 billion (barley) in 2011 according to The Department of Foreign Affairs and Trade

Australia exported $1.3 billion worth of barley in 2011. Image by Epicbeer sourced on Flickr

Australia exported $1.3 billion worth of barley in 2011. Image by Epicbeer sourced on Flickr

Link to Nature article:

Nitrogen Use efficiency ARC Linkage Grant

July 3, 2013

Filed under: Research — acpfg @ 11:41 am

ACPFG was successful in securing an Australian Research Council linkage grant in the latest rounds, released this week. The project aims to improve the nitrogen use efficiency of cereal plants, therefore reducing the reliance on fertilisers which in turn causes outbreaks of toxic algal blooms like the ones seen in China this week.

The team, led by Dr Trevor Garnett and Dr Sigrid Heuer at ACPFG, will identify and investigate nitrogen uptake pathways to identify what it is that is limiting plants’ nitrogen uptake. Improving the nitrogen uptake process in plants will increase the plant’s ability to use nitrogen more efficiently, leading to reduced and more sustainable nitrogen fertiliser usage.

‘Nitrogen is one of the most expensive and problematic inputs for cereal farming. Current farming practices lead to the inefficient use of nitrogen fertiliser. The excess fertiliser travels via the water system to river deltas resulting in algal blooms and is a major contributor to greenhouse gas outputs,’ said lead researcher on the project, Dr Trevor Garnett. ‘Improving nitrogen use efficiency in cereals will decrease fertiliser usage, providing a basis for greater economic and environmental sustainability of cereal growing.’


Image: Example of a toxic algal bloom off Washington, US. Left is the natural colour, right has been enhanced to reveal chlorophyll concentrations (Image: SeaWiFS Project, NASA/Goddard Space Flight Center/ORBIMAGE)

Drs Garnett and Heuer are working with Dr Ute Roessner from the University of Melbourne and Professor Michael Small from the University of Western Australia. Partner organisations on the project include DuPont Pioneer in the US and Australian Grains Technology (AGT) in Australia.

Making membrane proteins: curdlan synthase

December 8, 2012

Filed under: Research — Tags: , — acpfg @ 8:43 am

Curdlan is a polysaccharide which is used in Chinese medicine to stimulate the immune system to prevent skin infections. Researchers at the Australian Centre for Plant Functional Genomics have managed to make curdlan synthase, the enzyme that synthesises curdlan, in the laboratory.

The techniques they used to produce the enzyme should be very useful to finding out about some of nature’s most secretive proteins – membrane proteins.

Scientists have solved only around 350 membrane protein structures compared to more than 84 000 structures of soluble proteins. And membrane proteins are some of the most important proteins in biology – for example about half of all medications achieve their effects through membrane protein receptors. In humans, membrane proteins detect signals from hormones like adrenaline, and in plants they produce cellulose and other polysaccharides that build cell walls or protect plant cells.

Diagram showing membrane proteins of different types embedded in the cell membrane

There are several types of membrane proteins. They are hard to produce in the laboratory because they’re not stable unless they’re bound to lipids. Maria Hrmova’s group uses surfactants during protein synthesis to stabilise the proteins.
Image: modified from a public image.

Despite their importance, membrane proteins are notoriously difficult to produce in the laboratory. Most protein structural biologists produce proteins by getting bacteria like E. coli to do the job. They give the bacteria the relevant gene, and use a series of chemical tricks to get them to make protein. But bacteria aren’t quite like plants or animals, and that means they can’t always make plant and animal proteins successfully.

When Maria Hrmova and her team at ACPFG used E. coli bacteria to make the membrane protein curdlan synthase, the bacteria didn’t do the job properly. The bacteria produced parts of the protein, but never its full length. Bacteria often have trouble making membrane proteins because they need to be produced in a special way so they’re protected by membranes as they’re made.

So Maria and her team turned away from bacteria, and used an extract from plant cells combined with lipids and surfactants to produce the protein. And the method worked. The curdlan synthase they made was full length and it was correctly synthesised in artificial membranes made of lipid bilayers. They could also reconstitute the protein in lipid nano-discs. Most importantly, the protein was happy to produce curdlan.

Next Maria and her team will be trying to crystallise the protein so they can find out its three-dimensional molecular structure and get the details of how the enzyme joins individual sugars together to make curdlan. The scientists hope this will contribute to research into curdlan’s medical uses. It will also add to our knowledge of how plants create their cell walls.

The research was published in BBA-Biomembranes.

The scientists who worked on the project were Agalya Periasamy, Nadim Shadiac, Amritha Amalraj, Soňa Garajová, Yagnesh Nagarajan, Shane Waters, Haydyn D.T. Mertens and Maria Hrmova.

This article was written by Arwen Cross and the image was prepared by Maria Hrmova.

Sandra grows glowing plants in Cambridge

September 12, 2012

Filed under: Research — Tags: , — acpfg @ 12:19 pm

PhD student Sandra Schmoekel is just back from growing glowing plants at Cambridge University. She worked in Prof Alex Webb’s laboratory to study the signals that plants use to respond to salt stress.

The river at Cambridge University

At Cambridge, Sandra grew Arabidopsis plants which had been transformed to produce Aequorin, a protein from luminescent jellyfish which glows blue when bound to calcium (Ca2+), a common signalling molecule in plants and animals. Sandra used the glowing protein to investigate how plants detect salt in their roots. She compared salt-sensitive and salt-tolerant Arabidopsis varieties to see if there was a difference in Ca2+ signalling between the plants. (more…)

Fascination of Plants Day 2012

August 28, 2012

Filed under: Events — Tags: — acpfg @ 3:26 pm

The world celebrated Fascination of Plants Day for the first time in 39 countries on 18 May 2012. The day was organised by the European Plant Science Organisation (EPSO) to promote the importance of plants and plant science worldwide.

Australian events included a tour of the Aboriginal Garden at Monash University, plant experiments in the Q-lab at Questacon, a public lecture by Julian Cribb on global food security at the University of Queensland, and an online video competition. For a full list of events and a few photos see the Fascination of Plants Day website.

Public lecture on plant imaging at CSIRO

CSIRO held a public lecture on plant imaging technologies and how they’re used in plant science. This photo is by Erica Seccombe.

Radio interviews brought Fascination of Plants Day to Australians that couldn’t attend live events. ABC Brisbane interviewed Dr Paul Scott from the University of Queensland about why plants are so important in our daily lives. He went on to describe his research in developing biofuels from tree legumes. (more…)

Cracking a Salty Rice Riddle

July 31, 2012

Filed under: Research — Tags: , , — acpfg @ 3:39 pm

ACPFG research recently published in PLoS One descibes a model explaining how ancestral rice plants survive saline soils. Agricultural lands worldwide are getting saltier, and in Australia this is a particular problem in WA and SA.

Associate Professor Maria Hrmova described the impacts of her research on the ABC Rural SA Country Hour (listen to the podcast from 17 min for her interview). She explains that understanding how some rice plants are more salt tolerant than others will help develop salt-tolerant cereal varieties. (more…)

Swamped with saltwater: what a tsunami does to rice farmers

April 16, 2012

Filed under: Opinion — Tags: , — acpfg @ 4:07 pm

By Dr Darren Plett

Japan’s tsunami of March 11 2011 brought a wall of water laden with debris up to 5 kilometres inland from the sea. After the surge receded, the surrounding farming area was left covered in debris and a thick, black sludge. This sludge was extremely saline due to the sodium chloride from seawater.

Rice is the largest agricultural crop in Japan and the five prefectures affected by the 2011 tsunami are among the top producers of rice in Japan. Fortunately, less than 1.5% of Japan’s entire rice producing region was covered by the tsunami. Preliminary rice production statistics from the 2011 growing season show total rice production in Japan has hardly changed from 2010.

This all sounds fine on a national scale, but how did the tsunami affect the subsistence farmers in the tsunami-affected region? Reports indicate the 2011 rice production was severely decreased by salinity stress in the tsunami-affected region. This seriously affected the livelihood of these farmers.


The carpet of sludge and debris left by 2011’s tsunami wreaked havoc on paddyfields. AAP


Pretty wheat protein has biotechnology potential

March 13, 2012

Filed under: Research — Tags: , , , , — acpfg @ 11:08 am

A protein involved in moving lipids into wheat grains graces the cover of the Journal of Experimental Botany this month. Scientists at the Australian Centre for Plant Functional Genomics (ACPFG) discovered this protein, called TdPR61, while trying to find out how to express genes in the grain of wheat plants. The protein is expressed in specific parts of the grains of wheat, barley and rice, and it transports lipids (fats and oils). The new knowledge about where the gene is expressed can be used to improve grain quality or to increase the nutritional quality of grains. (more…)

Gene Patents

June 8, 2011

Filed under: Opinion — acpfg @ 2:01 pm

The very word “cancer” incites feelings of fear and dread; most of us do not understand where it comes from or why, the treatments seem unreliable and the outcomes are often miserable. Blocking gene patents is being supported by some cancer researchers because they are worried that access to critical information and materials will be stifled. They use emotive case studies to argue that somehow gene patents are inhibiting progress in curing patients. They are missing the point and surprisingly, as evidence based scientists, they are not applying the same techniques to critically examining the issues. There is little mention of the good outcomes that have been achieved using patented technologies. (more…)

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