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Antibiotics and the Emerging Superbug Threat

About 100 years ago bacteria spread through a cough or an open wound could easily kill us, thanks to antibiotics this is no longer the case. But bacteria are fighting back! New strains of bacteria known as superbugs are developing resistance to antibiotics. The World Health Organization has highlighted this as one of the greatest threats to human health. We spoke with Professor Matt Cooper about superbugs and potential


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Are GMOs and organic foods compatible?

Dr Lee Hickey chat with Professor Ian Godwin from The University of Queensland about genetically modified food crops.

Ian believes that GMO foods and organic agriculture are perfectly compatible. He explains that scientists are creating GMO plants to achieve a more sustainable agriculture. The idea is to create plants resistant to pests and diseases, that don’t require the use of chemicals, but provide the same productivity and food quality.
He points out that our beloved “organic” potato is actually sprayed with copper to control disease and the use of copper fungicides in organic farming may be resulting in increased levels of copper in the soil and the food we eat.
So maybe it’s time we embrace GMOs for more sustainable agriculture and healthier food?
If you are after more information about this topic, below are a few good articles to get you started.
This article illustrates Ian’s example about the potato, traditional breeding won't work and production requires a lot of pesticides:
A huge meta analysis showing how GMOs have reduced pesticide use wherever it has been adopted.

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Women getting to the root of global hunger


The challenge of feeding a world population set to hit nine billion by 2050 is driving University of Queensland research that could revolutionise cereal production.

Four female UQ scientists are tackling the problem by getting to the root of the issue – studying wheat and barley roots to improve crop quality and productivity in a changing environment.

PhD students Cecile Richard, Amy Watson and Hannah Robinson are working to revolutionise cereal production.
PhD students Cecile Richard, Amy Watson and Hannah Robinson are working to revolutionise cereal production.

The women have diverse backgrounds, but their wheat and barley research is complementary, allowing them to find new solutions.

PhD student Cecile Richard, originally from France, has developed a new research method that involves planting wheat in clear pots so the plants with better root system can be selected.

“Before, we were looking at the top of the plant because it was easier, but using this new method we can look below the ground and get useful information,” she said.

“With the clear pots we can see the root characteristics and look for the best ones – for example, deeper roots can mean more access to water and nutrients stored in the soil, so potentially a bigger yield of grain.

“Wheat is one of the most important sources of protein for most of the world’s population.

“There are many factors that can impact production – drought, frost, soil toxicity, disease, pests.

“It’s very important to us to develop new varieties that are very resilient to meet the demand in the future.”

Ms Richard works alongside PhD students Hannah Robinson (from Australia), Amy Watson (from New Zealand), and Honours student Anika Miller Cooper (originally from Argentina).

They each look at different aspects of the problem.

Ms Robinson investigates barley roots, and has identified a gene responsible for a deeper root system, leading to a yield increase.

Ms Watson is integrating DNA information for more efficient selection of wheat, while Ms Cooper examines roots in ancient wheat varieties to identify important genes that were lost during the process of domestication and selection.

Ms Richard said it was important to have women in science.

“Our team is a mix of cultures, generations and genders. The diversity brings together a new perspective,” she said.

“Women are just as capable as men. It’s about human talent: quality and productivity, just like wheat.”



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High throughput method for measuring root traits in wheat


PhD candidate Cecile Richard’s technique is cheap, simple and allows scientists to better adapt grain crops, such as wheat, to drought conditions. The method uses a system of clear-plastic pots, which allows scientists to see through the pot wall and view the roots of the plant.

Ms Richard from UQ’s Queensland Alliance for Agriculture and Food Innovation (QAAFI) said according to the climate-change predictions, drought episodes were likely to be more frequent and more severe in some areas.

“Crop improvement for drought tolerance is a priority for feeding the growing human population,” she said.

“Roots allow plants to access water stored in the soil and are crucial for reliable crop production.

“Even when rain is scarce, water is often still available deep in the soil.

“By increasing the length and number of roots, we can boost access to water and safeguard the crop.”

Ms Richard said the new method allowed scientists to combine favourable root characteristics in new wheat varieties that could improve the plant’s access to water – resulting in better yield stability and productivity under drought conditions.

“The roots are growing around the wall of the clear pot and it’s possible to measure different characteristics such as the angle and number of roots, based on images captured at ten days after sowing,” she said.

“These characteristics reflect the root growth pattern displayed by wheat in the field, which is important for the plant to access water.”

Previous techniques used for measuring roots had been time consuming and expensive.

“Planting wheat seeds around the rim of a clear-plastic pot to measure root characteristics has never been tried before,” Ms Richard said.

“This method is easy, cheap and rapid.”

Ms Richard’s technique was recently published in the open-access journal Plant Methods and could be one of the tools to help boost global wheat production.Her technique could speed-up selective breeding for drought-tolerant wheat strains.

“We hope to use the clear-pot technique to rapidly discover the genes responsible for these important root characteristics,” Ms Richard  said.

The research was partially funded by the Grains Research and Development Corporation of Australia, including a PhD scholarship for Ms Richard.

The research paper, ‘High-throughput phenotyping of seminal root traits in wheat’, by Cecile AI Richard, Lee T Hickey, Susan Fletcher, Raeleen Jennings, Karine Chenu and Jack T Christopher has been published in Plant Methods.

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To Russia in search of new genes in ancient wheats

Recently, QAAFI scientists Dr Lee Hickey and Prof Ian Godwin travelled to St Petersburg, Russia. Their travel to Russia formed part of a new project that seeks to rapidly discover and exploit novel disease resistance genes that are likely present in ancient wheat landraces – originally collected from around the world by the renowned Russian scientist Dr Nikolai Vavilov.

The Summer Palace in Peterhof, St Petersburg
The Summer Palace in Peterhof, St Petersburg

Born in 1887, Nikolay Vavilov was a prominent Russian and Soviet botanist and geneticist best known for his theory relating to “the centres of origin of cultivated plants”. He devoted his life to the study and improvement of wheat, corn, and other cereal crops that sustain the global population. He travelled the world collecting more seeds, tubers and fruits than any person in history. The collections, including many wheat landraces, were stored in a seedbank in Leningrad (St Petersburg), which is now known as the N.I. Vavilov Research Institute of Plant Industry .

Old photograph of Vavilov inspecting some wheat in the field.
Old photograph of Vavilov inspecting some wheat in the field.

During the “Siege of Leningrad” in World War II, which lasted 28 months, the seedbank comprising 250,000 samples of seeds, roots and fruits, was remarkably preserved by the Soviets. In fact, a group of scientists at the Vavilov Institute took shifts protecting them. Because it was considered so important to those guarding the seedbank, they refused to eat its contents. By the end of the siege in 1944, nine of them had died of starvation.

The seedbank was saved, but Vavilov himself faced an ironic fate. On 6th August 1940, Vavilov was arrested for criticising the non-Mendelian concepts of Trofim Lysenko, who had the support of Joseph Stalin. Vavilov was sentenced to death in July 1941. In 1942 his sentence was reduced to 20 years imprisonment, but he died in prison in 1943 of starvation.

The new QAAFI project also seeks to establish collaboration with the Russian

QAAFI scientists Dr Lee Hickey and Prof Ian Godwin gain some inspiration from the renowned Russian botanist and geneticist, Dr Nikolai Vavilov in St Petersburg, Russia.
QAAFI scientists Dr Lee Hickey and Prof Ian Godwin gain some inspiration from the renowned Russian botanist and geneticist, Dr Nikolai Vavilov in St Petersburg, Russia.

scientists that follow in the footsteps of the great Vavilov. Dr Hickey claims “by using a combination of new technologies we can rapidly discover new sources of disease resistance genes in the hidden treasures of the Vavilov seedbank”.

“We are focussing on some of the most important diseases of Australian wheat crops, such as yellow spot and rust pathogens” says Prof Ian Godwin.

Yellow spot is caused by the pathogen Pyrenophora tritici-repentis and currently contributes to the highest yield losses in in Australia, causing a very serious threat to the wheat industry. Yellow spot is a stubble-borne leaf disease, thus wheat-on-wheat crop rotations and zero or minimal tillage farming practices are contributing to the build-up of inoculum in farmer’s fields.

On the other hand, rust diseases of wheat (i.e. stripe, leaf and stem rust) are air-borne pathogens and can occur throughout most wheat growing regions of Australia. They have the ability to mutate and render resistance genes ineffective, thus wheat breeders require a constant supply of new genes to combat these rapidly evolving pathogens.

Dr Hickey has developed “speed breeding” technology at UQ in collaboration with colleague, Dr Mark Dieters. Their approach
uses controlled environmental glasshouse conditions fitted with lighting to accelerate plant development, thereby allowing up to 7 plant generations of wheat in just 12 months.

“Our rapid generation cycling will allow the new resistance genes to be plugged into Australian wheat cultivars within a short time” says Dr Hickey.

Dr Hickey and Prof Godwin also made time to enjoy some of the sights and delicious Russian food. They were hosted by Prof Olga Afanasenko, Head of Department of Plant Resistance to Diseases of All Russian Research Institute for Plant Protection (VIZR), who provided a short tour of the Summer Palace in Peterhof and Pushkin. “International collaboration is one of the perks of being a scientist” admits Prof Godwin.

Dr Hickey says “I hope this will be the beginning of a long-term collaboration with Russian scientist and I can’t wait to visit again next year”.

This project is funded a UQ Early Career Researcher Grant awarded to Dr Hickey.


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Searching for answers in the weeds of wheat fields in Morocco

Being a scientist, travel is certainly one of the perks of the job and our recent visit to Morocco was truly an eye-opening experience and one we rank highly among the many countries we have visited. Morocco is beautiful, home to friendly people, amazing food and perhaps most important, exquisite coffee.

The delicious Moroccan tagine we had for lunch while travelling to the research station of Annoceur.
The delicious Moroccan tagine we had for lunch while travelling to the research station of Annoceur.

While we certainly enjoyed these finer things in life, the main purpose of our visit centred on establishing new collaborations with both the wheat and barley breeding programs of ICARDA.

We were fortunate to have a fabulous host – Dr. Filippo Bassi (Durum breeder at ICARDA), who provided an authentic Moroccan experience. We travelled around the countryside, visiting the many field trials of ICARDA. One of the days, we travelled to the research station of Annoceur on the Atlas mountains, which is some 1,600m above sea level. ICARDA uses this location to test for cold resistance of wheat and barley, with temperatures during winter that reach -10 C and snow coverage that extends for two months (yes, Morocco can be cold too!). In summer, the cooler temperatures and availability of good irrigation water at this station allows for ideal off-season planting conditions. The early generations (F2 and F4) are typically grown at the high-plateau (420 m) station of Marchouch under rain-fed conditions (200 – 350 mm), harvested in early June and re-planted in Annoceur by early July.

The field site at Annoceur is a beautiful setting. For a wheat or barley breeder, it feels like you are in the middle of a fairy-tale. The cereal field trials are surrounded by trees and mountains – oh the serenity! The station also houses various fruit and herb breeding programs. Needless to say, in between looking at wheat and barley plots, the cherries in season were hard to resist.

Dr Hickey’s “selfie” with the elusive Anchusa
Dr Hickey’s “selfie” with the elusive Anchusa

In addition to this scenic backdrop, there were many small weeds with beautiful flowers – some blue, some red. The weeds in Australia certainly don’t appear as delightful. Dr Bassi pointed out that one of the weeds, which had small blue flowers was called Anchusa (A. Italica) – the alternate host of one of the wheat leaf rust pathogens, Puccinia tritici-duri, in Morocco. The amazing thing was that the Anchusa was even growing amongst the wheat and barley plots!

We don’t have any of the alternate hosts required for sexual recombination for wheat rust diseases in Australia. However, we do have the Star of Bethlehem, the alternate host of barley leaf rust (Puccinia hordei), growing throughout South Australia.


Revealing the hidden wheat leaf rust pathosystem 

Despite decades of intense research in cereal-rust pathosystems, there are still many questions to answer. Understanding the relationship and evolution between hosts and pathogens may provide the path to discovering new ways to manage crop diseases. The sexual stage of the wheat leaf rust pathogens has been generally regarded as an unimportant part of the epidemiological cycle of the disease. This is mostly due to the fact that research has shown that the P. triticinapopulations hold many characteristics of clonal populations. Moreover, high virulence diversity is observed in regions where Thalictrum spp., alternate host of Puccinia triticina, is absent or where no susceptible alternate host has been identified.  However, in the Mediterranean region a second wheat leaf rust pathogen Puccinia tritici-duri (P. recondita complex Group II) is known to occur. The P. tritici-durialternate host Anchusa italica, belongs to the Boraginaceae family and is distributed throughout the Mediterranean region and Asia. Ezzahiri et al., (1992) reported that in Morocco heavily infected durum wheat was observed in fields where A. italica was present.  Similarly, there are reports of P. tritici-duri samples collected in southern Portugal with virulence on durum and hexaploid wheat (Anisker, 1997). 

Despite these reports, little is known about the role of P. tritici-duri in this region and as part of the worldwide leaf rust disease complex. Thus, the extent of functionality of an alternate host in the Mediterranean and North African region represents an important question to answer for future disease management. Sexual recombination of the pathogen on the alternate host may lead to higher diversity and faster virulence evolution in the pathogen population. Moreover, durum wheat is extremely important in Morocco (nearly 1M ha), in North Africa (3M ha), and in the whole Mediterranean basin (approx. 6 M ha). It is a major component of the people’s caloric intake in this region, with nearly 8 meals per week derived from semolina products. Therefore, it is of significant interest to dissect the leaf rust pathogens regional epidemiological cycle and evolution.Current efforts by Maricelis Acevedo at North Dakota State University in collaboration with James Kolmer at the USDA aim to characterize the leaf rust pathogen population from leaf rust samples collected from bread (common) wheat and durum wheat from the region.

Acevedo plans to revisit the field locations in Morocco during the winter and early spring months when aecia on Anchusa should be evident in the lower altitudes.

Lee Hickey is a Research Fellow at the Queensland Alliance for Agriculture and Food Innovation (QAAFI) at the University of Queensland.  Follow him on Twitter @DrHikov.

Maricelis Acevedo is an Assistant Professor at North Dakota State University.  She received the Jeanie Borlaug Laube Women in Triticum Early Career award in 2010. Follow her on Twitter @MaricelisAceve1

Anikster, Y., W. R. Bushnell, T. Eilam, J. Manisterski, and A. P. Roelfs, 1997: Puccinia recondita causing leaf rust on cultivated wheats, wild wheats and rye. Can. J. Bot. 75, 2082—2096.

Ezzahiri, B., Diouri, S. & Roelfs, A.P. 1992. The-Role of the alternate host, Anchusa italica, in the epidemiology of Puccinia recondita f. sp. tritici on durum wheats in Morocco. In F.J. Zeller & G. Fischbeck, eds. Proc. 8th European and Mediterranean Cereal Rusts and Mildews Conf., 1992, p. 69-70. Heft 24 Weihenstephan, Germany.

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Gates Foundation supports wheat leadership


Lee Hickey


QAAFI Research Fellow Lee Hickey has been honoured with an invitation to take part in a Bill & Melinda Gates Foundation international workshop for early career scientists.

The three-day wheat leadership workshop in Heidelberg, Germany (16-19 Dec) is designed to help researchers  deal productively with challenges related to interpersonal aspects of their work.  

Dr Hickey is one of only two Australian wheat scientists invited to participate.

He will be joining 17 other early career scientists from countries such as USA, Israel, Uruguay and Kenya.

Read more about Dr Hickey’s research programs here.

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Scientists unveil new way to grow quality wheat faster



University of Queensland scientists have discovered a fast way to develop a new strain of wheat that is resistant to stripe rust and pre-harvest sprouting. The research team developed the wheat product using a new breeding strategy that slashes development time from more than 10 years to just two-and-a-half years.

Dr Lee Hickey, from UQ’s Queensland Alliance for Agriculture and Food Innovation, said the technology was set to benefit farmers in the next few years with field trials being grown in Victoria and New South Wales.

“Pending the performance of the wheat lines, we reckon that this new wheat variety with high-yield potential, resistance to stripe rust and pre-harvest sprouting tolerance could be available to southern growers in less than four years,” Dr Hickey said.

In collaboration with his PhD supervisor, Dr Mark Dieters, the research duo used a novel approach to transfer multiple genes for resistance to stripe rust and grain dormancy into the Australian wheat cultivar H45. The UQ geneticists are working with the Ballarat seed company GrainSearch.

“We developed 84 wheat lines, each 90 to 95 per cent genetically similar to the H45 variety, but with multiple genes for resistance to rust and pre-harvest sprouting,” Dr Hickey said.

“There are no wheat varieties available to Australian growers that offer adequate protection against pre-harvest sprouting, so this would be a first.

“The population also displays useful variation in physiological characteristics, including days to flowering, maturity, spike length, leaf width, seedling vigour, and grain size.

“These characters will be important for determining which line becomes the new wheat variety,” he said.

The UQ team has used the same techniques to rapidly produce disease-resistant strains of barley. Dr Hickey will be presenting the work at the Australian Barley Technical Symposium in Melbourne this week. The researchers are working with breeding companies and seed companies across Australia and overseas to speed-up grain improvement techniques.

More about H45

Released in the 1990s, H45 was a successful wheat variety with fast maturity and high-yield potential adopted by growers in Victoria and NSW. It has since been abandoned by most growers because it is susceptible to the current strains of stripe rust present along the east coast of Australia. As with all wheat varieties in Australia, H45 also lacks adequate grain dormancy to protect against pre-harvest sprouting, i.e. when germination of grain in the spike occurs in response to rainfall at crop maturity, resulting in grain crops being downgraded, resulting in less money for growers.


Initially formed in 2002 by a small group of innovative grain growers, GrainSearch has grown to be the largest grower-owned seed company in Australia with more than 200 grower-based shareholders. Their primary objective is to seek out, through the latest research and development techniques, new varieties of seed that significantly improve the productivity of shareholders, farming businesses and agricultural enterprises.

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