Designer root systems to maintain durum wheat yields in drought

A Queensland Alliance for Agriculture and Food Innovation (QAAFI) researcher has identified genes that improve durum wheat yields under drought conditions, as part of work focusing on the architecture of plant roots and how it contributes to yield stability.

Dr Samir Alahmad, who is a previous recipient of Monsanto’s Beachell-Borlaug International Scholarship, discovered the two genes while investigating traits that durum wheat uses to survive in water-limited conditions.

“In dry seasons like 2018 and 2019, farmers suffered significant losses due to reduced grain quality and yield,” Dr Alahmad says. His current research is part of a postdoctoral fellowship funded by GRDC.


Standing in front of the seed increase trial at Warwick in 2020, Dr Samir Alahmad holds one of the new experimental lines with modified root traits. The new lines will be evaluated in the coming 2021 season to determine the value of the root traits to support yield in key durum growing regions. Photo: Lee Hickey

Yield and quality

Stabilising yields and quality for the crop in a variable climate is a continuing challenge for growers, while demand from international markets is consistent. More than 80 per cent of Australian durum wheat exports go to Italy, where they are used for pasta production.

The first step in Dr Alahmad’s research was establishing links with durum breeder Dr Filippo Bassi at the International Center for Agricultural Research in Dry Areas (ICARDA) to source elite durum lines that were originally bred for very dry conditions in Syria.

Experimental population

Dr Samir Alahmad inspecting the roots of an experimental durum line carrying the narrow root angle gene on chromosome 6A.

Collaborating with Professor Jason Able at the University of Adelaide, Dr Alahmad then crossed the ICARDA lines with the leading Australian durum wheats DBA Aurora and Jandaroi, subsequently developing a large experimental population to study their traits.

“You need six generations to develop genetically stable lines that are suitable for evaluation,” Dr Alahmad says. “I used speed breeding technology, which involves growing plants under optimal light and temperature conditions, to reduce generation time, and refined the population in just one year.”

Garden pots

The next step was to study the durum wheat population for root growth angle using transparent garden pots. Dr Alahmad matched this information with DNA marker data to perform a genome-wide association analysis. The result was the discovery of a major gene located on chromosome 6A in durum wheat.

Over the following two seasons, he set up field trials in Queensland, South Australia and Morocco to better understand the value of the gene in improving yields under different drought conditions.

“We found there was an association between the root angle gene and grain yield,” he says. “In Queensland, root angle appeared to be important for maximising the length of the grain-filling period.”

In another genome-wide association analysis, the location of the gene responsible for high root biomass was identified on chromosome 6B.

“One of the most exciting aspects of the research was discovering that combining the root angle and root biomass qualitative trait loci resulted in a yield benefit of up to 0.9 tonnes per hectare under drought conditions,” Dr Alahmad says.

roots shallow versus deep
Root system architecture for durum variety DBA Aurora (left) versus an experimental line carrying the gene for narrow root angle (right). Photo: Lee Hickey

However, more insight is needed to determine how much root branching is beneficial at different soil depths to sustain grain yields in different environments. Another challenge is understanding the complex interactions between root and canopy traits that influence the timing of water use.

Now, Dr Alahmad’s postdoctoral research is focused on developing elite durum wheat pre-breeding lines with similar above-ground traits that comprise different root configurations. “These materials will enable us to more precisely determine the role of root traits to support yield under different drought scenarios.”

During 2020, seed of the elite lines with modified root traits was bulked-up at Hermitage Research Station, Warwick, Queensland. In 2021, field trials will be set up in Queensland and South Australia.

Future plans

To take the research to the next level, Dr Alahmad is using unmanned aerial vehicles to look at the effect of above-ground traits on drought tolerance.

“We will use this knowledge about the above-ground traits to better understand the value of root traits and the link between root and shoot dynamics,” he says.

“We want to help wheat breeders design future crops for farmers that provide more-stable yields across seasons despite variable rainfall. In the next 12 months we will try to understand the traits that sustain grain yield in different seasons.”

Dr Samir Alahmad is an early career plant breeder and geneticist. His main interest is dissecting the genetics of complex traits that contribute to enhanced yield under drought and disease stresses. His research is focused on better understanding the genetics of drought adaptive traits such as root system architecture and canopy development. He is currently working on two GRDC funded projects that aim to develop elite bread and durum wheat varieties with optimal root system architecture for yield improvement.

Research contacts:  Dr Samir Alahmad, Postdoctoral Research Fellow, QAAFI, Centre for Crop Science,, M:  +61 405 946 915
Associate Professor Lee Hickey, Principal Research Fellow, QAAFI, Centre for Crop Science,, T: +61 7 336 54805, M: +61 408 210 286

Media: Photos and video files for media use. 

Source: Originally published in GRDC’s GroundCover Issue 151, March-April 2021, Written by Nicole Baxter, Published online 30 January 2021. View online.


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DIY crop speed breeding system to boost drought research

DIY Speed breeding news story image

Plant speed breeding could be part of the solution to minimise the devastating effects of drought and climate change on crops in the future, according to a University of Queensland researcher.

UQ Queensland Alliance for Agriculture and Food Innovation(QAAFI) Senior Research Fellow Dr Lee Hickey said the technique can enable researchers and plants breeders to deliver more tolerant varieties of crops to farmers sooner.  

“It can take up to 20 years to develop an improved crop variety, but the speed breeding technique can slash this time because it enables growing up to six plant generations in a single year, rather than just one in the field,” Dr Hickey said.

“This technique works for a range of crops like wheat, barley, chickpea and canola, and uses specially modified glasshouses fitted with LED lighting to grow plants under extended photoperiods – accelerating crop research and the development of more robust plant varieties through rapid cross breeding and generation advance.

“With scientists from the John Innes Centre in the UK, we’ve now taken the next step in our research and developed the protocols to scale-up speed breeding to large glasshouse facilities as well as instructions on how to build your own low-cost speed breeding cabinet.

“Information on speed breeding has been in high demand, so by sharing our protocols it means researchers and plant breeders around the world can help tackle the impacts of climate change by accelerating their research or development of better crops, even on a shoestring budget.”  

Climate change is presenting a huge challenge for food production globally – currently many farmers in Australia and Europe are experiencing severe crop losses due to drought and heat.

With extreme weather expected to be more common in the future, there is a need to develop drought-resistant and more tolerant varieties of crops such as wheat, barley, oats, canola and chickpea rapidly.

John Innes Centre wheat scientist Dr Brande Wulff said the international team’s protocols could be adapted by researchers to work in vast glass houses or in scaled-down inexpensive desktop growth chambers.

“We built a miniature speed breeding cabinet with bits and pieces we got off the internet and it was very cheap,” he said.

“We know that more and more institutes across the world will be adopting this technology and by sharing these protocols we are providing a pathway for accelerating crop research.”

The paper has been published in Nature Protocols.


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Space age plant breeding lights the way for future crops

NASA experiments to grow wheat in space were the inspiration for University of Queensland scientists to develop the world’s first ‘speed breeding’ procedures here on planet Earth.

UQ Queensland Alliance for Agriculture and Food Innovation(QAAFI) Senior Research Fellow Dr Lee Hickey said the NASA experiments involved using continuous light on wheat which triggered early reproduction in the plants. 

“We thought we could use the NASA idea to grow plants quickly back on Earth, and in turn, accelerate the genetic gain in our plant breeding programs,” Dr Hickey said.

Dr Hickey was part of the UQ team that began trialling speed breeding techniques to cut the length of plant breeding cycles more than 10 years ago.  

“By using speed breeding techniques in specially modified glasshouses we can grow six generations of wheat, chickpea and barley plants, and four generations of canola plants in a single year – as opposed to two or three generations in a regular glasshouse, or a single generation in the field,” Dr Hickey said.

“Our experiments showed that the quality and yield of the plants grown under controlled climate and extended daylight conditions was as good, or sometimes better, than those grown in regular glasshouses.”

Dr Hickey said information on how to use speed breeding was increasingly in demand from other researchers and industry.

“There has been a lot of interest globally in this technique due to the fact that the world has to produce 60-80 per cent more food by 2050 to feed its nine billion people.”

The speed breeding technique has largely been used for research purposes but is now being adopted by industry.

UQ scientists, in partnership with Dow AgroSciences, have used the technique to develop the new ‘DS Faraday’ wheat variety due for release to industry in 2018.

DS Faraday is a high protein, milling wheat with tolerance to pre-harvest sprouting,” Dr Hickey said.

“We introduced genes for grain dormancy so it can better handle wet weather at harvest time – which has been a problem wheat scientists in Australia have been trying to solve for 40 years,” Dr Hickey said.

“We’ve finally had a breakthrough in grain dormancy, and speed breeding really helped us to do it.”

Dr Hickey said the level of interest in speed breeding led to his collaborators at the John Innes Centre and the University of Sydney to write theNaturePlantspaper, which outlines all the protocols involved in establishing speed breeding systems and adaptation of regular glasshouse facilities.

UQ PhD student Amy Watson was a co-author of the paper and conducted some of the key experiments that documented the rapid plant growth and flexibility of the system for multiple crop species.

Dr Hickey believes the sky is the limit for the new technology and he is now investigating the integration of speed breeding with other modern crop breeding technologies.

“It could also have some great applications in future vertical farming systems, and some horticultural crops,” Dr Hickey said.

The paper has been published in Nature Plants.

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Ancient genes to protect modern wheat


Scientists from The University of Queensland are undertaking world-first research into ancient wheats to ensure the crop’s future.

Queensland Alliance for Agriculture and Food Innovation’s Dr Lee Hickey said humans domesticated wheat about 10,000 years ago.

“Modern breeding and a switch to monoculture cropping has greatly improved yield and quality, but the lack of genetic variation has caused crops to become more vulnerable to new diseases and climate change,” he said.

“Diversity in ancient strains could hold the key to the future.”  

Dr Hickey said disease and drought cost the industry millions of dollars every year, and climate change was likely to make the situation worse.

Fortunately for today’s researchers, Russian scientist Nikolai Vavilov devoted his life to the improvement of cereal crops.

During the early 1900s, Vavilov travelled the world collecting seeds that he stored in a seed bank in Leningrad, now known as the N.I. Vavilov Institute of Plant Genetic Resources.

“Vavilov’s unique seed collection represents a snap shot of ancient wheats grown around the world prior to modern breeding,” Dr Hickey said.

Following in the footsteps of the Russian scientist, UQ PhD student Adnan Riaz has performed the world’s first genome-wide analysis of Vavilov’s seeds.

“A total of 295 diverse wheats were examined using 34,000 DNA markers,” Mr Riaz said.

“The genomic analysis revealed a massive array of genes that are absent in modern Australian wheat cultivars.

“The ancient genes could offer valuable sources of disease resistance or drought tolerance.”

The Hickey Lab has offers the research community open-access to this resource, including the pure seed of the ancient wheats, along with DNA marker information.

“We hope this will empower scientists and wheat breeders to rediscover genetic diversity lying dormant in our seed banks,” Dr Hickey said.

The Hickey Lab research, ‘Into the vault of the Vavilov wheats: old diversity for new alleles’, is published in Genetic Resources and Crop Evolution.

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Farming in 2030: Researchers cast the net for the next generation of farmers

Dr Lee Hickey's version of 2030 features robots, drones and intelligent machines as common place on farms, helping to reduce labour costs and chemical use. 

The University of Queensland researcher has crafted a narrative based around "Farmer Tim" in 2030. 

In the story, which Dr Hickey told at an Australian Academy of Technology and Engineering conference, it's June 2030, mid-way through the winter wheat growing season and Tim gets an urgent message. 

One day Tim receives a notification on his iPhone version 26.

His crop management app is warning him of an outbreak of yellow spot, a pretty nasty disease. The monitoring drone has detected the disease in the paddock while Tim was taking a shower. Tim slides through his management options and instructs his sprayer drone to take care of the problem. The drone, like the tractor, knows every inch of the farm and flies straight to the paddock with the disease. But instead of deploying a traditional fungicide, the drone applies to the crop, RNA that is specially designed to silence the gene in the pathogen that is required for producing the spores.

So instead of spending eight hours spraying his crop, Tim goes to the footy with his mates. In his lab, Dr Hickey has developed a process called "speed breeding", in intensive 24 hour lighting and controlled temperatures - a process inspired by how NASA grows food for astronauts in long space missions. 

"A big limitation in developing new varieties can take up to 20 years," Dr Hickey said.

"But in speed breeding we can achieve up to seven generations of wheat per year under constant lighting.

"It's a fantastic tool for selecting for traits and manipulating genes in the right combinations. So we can fast track the variety developing down to five to six years."

Read more here

Dr Lee Hickey and Anika Molesworth discuss the future of farming in Australia and southeast Asia

Drones in agriculture will soon detect crop diseases, and send alerts to farmers and researchers ( photo by: ABC News-Nadia Daly)
Drones in agriculture will soon detect crop diseases, and send alerts to farmers and researchers ( photo by: ABC News-Nadia Daly)
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Digging deep to drought-proof Australian barley

PhD student Hannah Robinson

In a world first, researchers from The University of Queensland have identified a key gene in barley that enables the plant to access water stored deep in the soil during droughts.

Queensland Alliance for Agriculture and Food Innovation’s Dr Lee Hickey said the gene promoted narrow root growth, which allowed the plant to grow roots that penetrate down to water stored deep within the soil.

“This may be one of the most exciting research findings to ever come out of my lab,” he said.

“PhD student Hannah Robinson has undertaken the first study of its kind that aims to connect root architecture to yield in barley. Her findings will impact everything from predicting yield to modelling.

“Even in a drought, there is water deep underground and to be able to breed plants with the type of root system to access this water means growers can maintain barley yields in drought conditions.”  

A former medical student turned plant scientist, Ms Robinson has identified the gene across the barley and wheat species. “Our latest findings demonstrate that the gene for narrow root growth provides a significant yield advantage throughout Queensland and New South Wales,” Ms Robinson said.  

“Even before the harvesters hit the paddock, the lack of rain caused by the current El Niño has stripped around half a billion dollars in yield from the wheat industry and looks set to also have a major impact on the barley industry,” she said.

“While barley crops on the Australian east coast enter the critical grain filling period, there appears to be no relief in sight as the next few months are forecast to be drier than average.”

Australia is the 8th largest barley producer worldwide, producing around 7.5 million tonnes of barley annually.

Most barley in Australia is used for animal feed and beer production, but in North Africa and Southwest Asia, barley is a main staple food.

“Worldwide, the largest limitation on barley production is water,” said Ms Robinson.

“Dry seasons mean lower yield and less profit for farmers. The effect is more severe in droughts and El Niño weather events.”

Ms Robinson’s barley research has been undertaken with support from a Grains Research Development Corporation scholarship.

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speed breeding and drones are the future of wheat production

Integrating modern plant breeding technologies to wheat production is vital to sustain global populations in the future, according to some researchers. Dr Lee Hickey, research fellow at the University of Queensland, will be running a workshop looking at 'speed breeding' and the use of drones at the 9th International Wheat Conference in Sydney next week. Dr Hickey and other scientists at the university developed speed breeding in 2013 from technologies developed by NASA.



Speed breeding accelerates the genetic gain in wheat, and is resistant to stripe rust and pre-harvest sprouting, which are common reasons for yield loss. "It's a great tool to develop wheat varieties faster [because] wheat breeding is slow; it can take 10 sometimes 20 years to develop a new and improved variety," Dr Hickey said.

"Companies are starting to use it now to breed varieties in Australia which is fantastic."  Dr Hickey said other emerging technologies are also proving valuable for farmers on the field. He said the workshops at the global conference are aimed at early career breeders and scientists. "It's very important that we are attracting young people into science and wheat improvement," he said.

"We need new ideas, we need to be thinking outside of the box because we face some pretty big challenges in the future to grow a growing population."

source: abc website


lee-hicley-speed-wheat researcher-speeds-wheat-breeding
Lee Hickey is growing plants under lights to speed the breeding process up six times.
"We need new ideas, we need to be thinking outside of the box  because we face some pretty big challenges in the future to grow a growing population.
Lee Hickey, University of Queensland research fellow
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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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