- Genomics research offers new way to protect Canada's agricultural exports
With the support of funding from the Genomics R&D Initiative, scientists have refined an existing DNA bar code test, providing a highly accurate way to distinguish quarantine insect species from similar-looking but harmless species. This helps to ensure Canadian agricultural exports are not refused unnecessarily, and invasive species do not enter Canada by mistake. DNA bar coding involves comparing specific sections of DNA where differences among species have been shown to exist. It is fast and accurate, but not perfect—different populations of the same species can have slightly different DNA. To make sure the right sections of DNA were being used for species of concern, the scientists compared the DNA of more than 200 populations of insects from 57 different species in 24 different countries. To further ensure accuracy, they have developed three tests, using different DNA sequences for each of three groups of closely related species.
- Oatmeal is good for you—technology is helping to make it even better
Canada is the world's largest exporter of oats and participation funded by the Genomics R&D Initiative in an international research project will help to ensure it can maintain this position. Despite the widely recognized health benefits of oats, progress toward varieties with more heart-healthy fibre and antioxidants has been slow. The oat genome is large and complex, making it difficult and expensive to apply the marker-assisted breeding techniques used with other crops. Co-led by Agriculture and Agri-Food Canada and the U.S. Department of Agriculture, the project succeeded in applying a relatively new technology called genotyping-by-sequencing to support marker-assisted breeding in oats. Now, instead of having only a handful of genetic markers to work with, oat breeders have a test that identifies tens of thousands of markers, at a cost of just $20 per variety. The project also developed the bioinformatics needed to analyse the DNA sequences, enabling breeders to select crosses with a much higher probability of success.
- Taking the guesswork out of breeding disease-resistant wheat
The Genomics R&D Initiative has funded research that promises to accelerate the development of varieties of wheat that are resistant to fusarium head blight, a disease that renders wheat unfit for consumption by humans or animals. The infection is spreading to ever-larger areas of major wheat-growing countries around the world, including Canada. While some varieties of wheat show resistance to the disease, none are suitable for food production. They can be used as breeding stock, but it can take as long as 15 years to determine whether a new variety has potential as a commercial crop. Now, with the capacity to conduct genomics research, scientists have identified several specific elements of the wheat genome that appear to play a role in disease resistance. Combined with gene marker-assisted breeding techniques also developed through GRDI-funded research, the breeding process can be better targeted toward disease resistance, and the commercial potential of a new variety determined in as little as five years.
- Canadian genomic research furthers quest for plants that make their own fertilizer
With support from the Genomics R&D Initiative, researchers are edging closer to understanding how some plants can feed themselves, obtain the nitrogen they need from the air, and potentially transferring that ability to other food crops. While modern agriculture would not be possible without fertilizer containing nitrogen, it is expensive, not very efficient, and its production and use have significant environmental impacts. Scientists are searching for the genetic mechanism that allows a few families of plants, such as peas and soybeans, to get nitrogen from the atmosphere. When they sense there is not enough nitrogen in the soil, these plants allow certain bacteria to enter their root cells. It is the bacteria that fix the nitrogen from the air so it can be used by the plant. The team has identified parts of the plant's genetic apparatus that allow friendly bacterial to enter root cells. It has also identified a gene that initiates the process by which root cells change to accommodate the friendly bacteria. This is similar to the way many other plants interact with a fungus to obtain the phosphate they need—offering hope that the genetic ability to obtain atmospheric nitrogen may be transferrable.
- Genetic discoveries open door to better control of costly soybean disease
Research funded through the Genomics R&D Initiative is helping soybean growers minimize the chances their crops will be damaged by soybean root rot. The fungus is estimated to cost Canadian soybean growers alone as much $50 million a year, with losses worldwide of some $2 billion annually. Research focuses on identifying which genes in the soybean provide resistance to different strains of the pathogen that causes the disease. Based on these findings, a series of genetic diagnostic tests is being developed that will enable rapid identification of different strains of the pathogen in the soil, allowing growers to plant soybean cultivars with the genes most likely to provide resistance to those strains of the pathogen. The team has benefitted from and contributed to genomics-based soybean research in other countries. This valuable collaboration would not have been possible without GRDI funding, which enabled federal scientists to develop the genomics capacity needed to participate.
- Canada part of international effort to protect global wheat crop
Research funded by the Genomics R&D Initiative is playing a key part in the international effort to protect one of the world's most important food crops from the growing threat of fusarium head blight. The disease attacks wheat, leaving behind a number of mycotoxins that can cause serious illness in people or animals who consume food or feed made from infected wheat. Beyond its impact on the food supply, it is estimated the disease has cost Canadian wheat producers alone more than $1.5 billion in lost income since the mid-1990s. A research team has helped to identify and position many novel genes that are part of the genome of the fungus that causes fusarium head blight. Thanks in part to this work, the international research community now has access to the most complete and accurate sequencing of the genome, an essential prerequisite to understanding how the disease infects the plant. The team has also identified specific genes the fungus uses to produce a number of different mycotoxins, as well as when and under what conditions they are produced.
- Genomics helps ease regulatory burden for Canadian soybean growers
Canadian soybean growers owe some thanks to the Genomics R&D Initiative for the Canadian Food Inspection Agency (CFIA) decision to lift regulations aimed at preventing the spread of soybean cyst nematode. Despites the regulations, which included things like requiring growers to clean machinery immediately after moving it from a field where the microscopic worm had been detected, the nematode continued to spread in soybean production areas. Once established, it is difficult to control. But when it is detected at the earliest stages of infestation, damage can be limited through careful and innovative management. A team at Agriculture and Agri-Food Canada developed a new genomics-based test that is both faster and more precise than the traditional method of using a microscope to look for adult nematodes in the soil. The new test detects the worm's genetic material in a soil sample, allowing nematodes to be identified quickly, in any quantity and at any stage of development, from egg to adult. With the capacity to detect nematodes at the earliest stage of infestation, the CFIA dropped the regulations and determined growers can implement measures to manage their production effectively without the need for regulatory controls.
- Protecting PEI potatoes
Genomics research capacity developed with funding from the Genomics R&D Initiative played a key role in protecting Prince Edward Island's potato industry after potato wart disease was detected there in 2000, leading the U.S. to impose an immediate ban on potatoes from PEI. In an attempt to prove the discovery was an isolated occurrence, the Canadian Food Inspection Agency began the time-consuming process of examining hundreds of thousands of soil samples from PEI farms under the microscope, the only test available at the time. Looking for a better approach, researchers at Agriculture and Agri-Food Canada developed a new genomics-based test through GRDI-supported research, allowing a soil sample to be tested in hours instead of days. The U.S. accepted the findings of the new test—that the fungus was confined to just one small section of one farm—and agreed to lift the ban, months earlier than might otherwise have been possible. The test also played a key part in pre-empting a possible ban when potato wart was detected in two other fields in PEI in 2012. Since then, the U.S. Department of Agriculture has adopted the Canadian method as its own standard test for potato wart.
- Yellow peas: a case of mistaken identity
Research funded through the Genomics R&D Initiative is helping to protect millions of dollars in profits on Canada's yellow pea exports to India. Since 2004, when the damaging nematode D. dipsaci was detected in a load of Canadian yellow peas, India has required every shipment from Canada to be inspected for the presence of the microscopic worm. If it were found, the shipment would have to be fumigated at a cost of hundreds of thousands of dollars. Thanks to genomics-based testing developed under the GRDI, Canada has been able to demonstrate that the nematode identified in Canadian peas in 2004 and many times since as D. dipsaci was in fact a harmless but virtually identical relative, D. weischeri.
- Applying toxicogenomics to new and emerging environmental issues
A research project funded by the Genomics R&D Initiative at Environment and Climate Change Canada is showing how genomics can enable precise identification of the causes of environmental problems. Already, the city of Montreal has used this research to support its decision to invest $250 million in an ozone-treatment system for wastewater. Even treated wastewater can contain thousands of bacteria, viruses, pharmaceuticals and industrial chemicals. Using traditional methods, it is very difficult to determine which of those may be responsible for a specific problem found downstream of the treatment outlet. The researchers have demonstrated that, with toxicogenomics—the study of how an organism's genetic information responds to a toxin—it is possible to pinpoint exactly which toxins are causing the problem. The same techniques are being used to determine the extent to which oil sands development may be adding to natural toxicity from the bitumen that has been leaching into the ecosystem for thousands of years.
- Fecal forensics track sources of water contamination
Research funded by the Genomics R&D Initiative is transforming the way municipalities in Canada and around the world manage water safety at public beaches, often increasing effectiveness while reducing costs. For decades, towns and cities have checked swimming areas for fecal bacteria contamination by testing for E. coli. If the E. coli level was too high, the beach would be closed to swimming. It was usually assumed the fecal contamination was sewage overflow or pet droppings washed into the waterway after heavy rain. Using new genomics-based test methods, researchers at Environment and Climate Change Canada discovered that E. coli in water samples from beaches often matched the DNA fingerprint of E. coli from seagulls and Canada geese—not sewage or pet droppings. Now that the source of contamination can be identified with confidence, municipalities can better target mitigation measures. In Ottawa, for example, rather than investing in an expensive renovation of its sewage system, the city has installed overhead wires at some beaches to discourage gulls and geese. The research findings have generated interest from cities around the world.
- Protecting biodiversity through understanding amphibian diseases
Genomics-based test methods developed as part of a project funded by the Genomics R&D Initiative at Environment and Climate Change Canada are allowing more accurate, efficient, and sustainable tracking of diseases that threaten Canada's frog populations—diseases that have been responsible for large die-offs of frogs in Canada and other countries. While previous methods of testing for infection usually meant the animal was sacrificed, the new technique is non-invasive—a swab of the amphibian's skin is taken, and then tested for genetic markers of the disease. This is especially important from a conservation perspective, since a number of species of frogs in Canada are already listed as endangered. The genetic information being collected may lead to new ways to protect native frogs by, for example, explaining why the virulence of a specific infection can vary significantly among different populations of the same species.
Fisheries and oceans
- Advanced genomics technologies may enable more cost-effective fishery management
With support from the GRDI, scientists have developed a cost-effective, non-invasive method of parentage-based tagging from genotypes of hatchery broodstock. Millions of juvenile salmon are released each year from salmon hatcheries operated by Fisheries and Oceans Canada and others to help maintain and rebuild vulnerable populations, including Chinook and Coho. This method makes it possible to tag all breeding stock for a given hatchery - a big improvement over the 10 percent that would have been tracked with standard coded-wire tags. Salmon DNA can then be sampled in the ocean and compared to genotypes in the database to identify fish from hatcheries. The ability to track tagged fish across multiple generations enables more efficient management of hatcheries to support sustainable harvesting and conserve vulnerable salmon populations.
- Genomics confirms fish farm escapees breeding with wild Atlantic salmon in Newfoundland
Researchers with Fisheries and Oceans Canada have confirmed that farmed salmon are interbreeding with wild Atlantic salmon in rivers along the south coast of Newfoundland. With funding from the GRDI, they were able to identify markers to quickly distinguish a wild Atlantic salmon from a salmon bred for aquaculture, and used them to study thousands of salmon specimens in 18 rivers along the south coast of the island. The results have been shared internationally and inform further studies on the impacts of interbreeding on wild salmon populations. Genomics-based identification also provides the capacity to trace an escaped salmon back to its farm of origin and informs aquaculture management measures.
- Genomics investments provide new tools to salmon enhancement program
With the help of funding from the GRDI, scientists at Fisheries and Oceans Canada have gathered data to identify which salmon are wild and which are from a hatchery, focusing on Chinook salmon populations that spawn in rivers along the west coast of Vancouver Island. As they collect fish that come up-river to spawn, they can now make a much more accurate assessment of the numbers of hatchery and wild fish that are successful in making it to the spawning grounds, and how many spawn successfully. This information enables the assessment of how hatchery Chinook salmons contribute to fisheries, and whether they are beneficial or detrimental in the process of rebuilding natural spawning populations.
- Revealing new discoveries of Canada's redfish
Based on research funded by the Genomics R&D Initiative, Fisheries and Oceans Canada is re-examining its approach to managing redfish stocks off Canada's east coast. Genetic markers identified by the scientists revealed that the Atlantic fishery includes not one, but two distinct species of redfish. Although very similar in appearance, the two species (the Acadian redfish and the deepwater redfish) are different populations that frequent different depths and regions of the Northwest Atlantic. By enabling a precise way to distinguish the two species, the research has enabled a greater understanding of redfish stock structure and contributes to more informed management strategies. For examples, it played a role in the 2010 decision by the Committee on the Status of Endangered Wildlife in Canada to classify the Northwest Atlantic population of deepwater redfish as 'threatened'.
- Shaping the Management of Northern Dolly Varden Charr
With support from the Genomics R&D Initiative, genomics research conducted at Fisheries and Oceans Canada has allowed for the re-opening of an important fishing ground for Indigenous people in Canada's North. The northern Dolly Varden charr is an important part of the diet, traditions and culture of the Inuvialuit and Gwich'in peoples in northern Canada. The species exists in six small populations and is particularly sensitive to habitat change and other stresses. In recent years, two of the populations dropped to critical levels, leading to fishing bans in some areas. However, with little understanding of how different populations mixed with one another, it was difficult to judge whether the bans were effective. The scientists identified genetic markers that provide an accurate way to differentiate fish from different populations, allowing more accurate assessments of the size of each population. Management actions by Fisheries and Oceans Canada are better informed and evaluated—already allowing for the re-opening of one local fishery that had been shut down for more than 10 years.
- Canadian test for pine wood nematode included in new international protocol
With funding from the GRDI, scientists from Natural Resources Canada and the Canadian Food Inspection Agency developed a molecular test that identifies the presence of living nematodes. Virtually all countries, including Canada, regulate wood imports to ensure damaging invasive species are not being imported along with the wood. If a quarantine pest is found, such as the pine wood nematode, the shipment may be turned away and future shipments put in jeopardy. This test gives Canadian exporters a fast and cost-effective way to make sure their phytosanitary processes are effective in eliminating the nematode from their wood products. The International Plant Protection Convention, a United Nations organization dedicated to protecting the world's plant resources from pests, has adopted a new standard diagnostic protocol for pine wood nematode that includes the test developed by GRDI scientists.
- Cutting tree breeding down to size
A research project funded by the Genomics R&D Initiative at Natural Resources Canada has developed novel methods that will revolutionize tree breeding. Among other management measures, Canada's forest industry plants some 650 million trees every year. These trees are bred for strong growth, resistance to disease, adaptation to climate, and desirable wood characteristics. Unfortunately, tree-breeding is a slow process—it can be 20 years or more before a tree reveals whether it has the hoped-for traits. The scientists are studying the genomes of mature trees to identify genetic markers associated with the most desirable characteristics. This enables breeders to select trees at a very early stage, based on their genetic make-up, rather than waiting decades to see which specimens have the characteristics they want.
- DNA-based test helps protect Canadian forests
With funding from the Genomics R&D Initiative, researchers at Natural Resources Canada were able to develop a new, DNA-based test for Sudden Oak Death, a fungus-like disease that has killed a wide variety of trees and plants in California and Oregon. In an effort to keep the disease from gaining a foothold in this country, Canada restricts imports of plants from areas where the disease has been found. The Canadian Food Inspection Agency (CFIA) also checks plants in garden centres for Sudden Oak Death, testing leaf and soil samples for early signs of the disease. In the past, a garden centre could be quarantined for a month waiting for results of a test. The test developed by the GRDI is far more accurate, and is done in 24 hours. In use by the CFIA for several years, the new test has been adopted by the U.S. Department of Agriculture, and other countries are considering it as well.
- Genomics saves money, time and trees — and creates a new business
The capacity to conduct genomics research, delivered through the Genomics R&D Initiative, enabled researchers at Natural Resources Canada to accelerate approval of a new biocontrol agent needed to address a growing infestation of balsam sawfly threatening commercially important forests in western Newfoundland. The scientists knew of a naturally occurring virus that would attack only the balsam sawfly, but approval could take many years. Using genomics, the researchers showed that, genetically, their virus was largely similar to another virus already approved for use against another species of sawfly. As a result, many tests and trials did not have to be repeated—the virus was approved years earlier and at far less cost than would have been possible otherwise. Subsequently, a New Brunswick entrepreneur obtained a commercial license for the virus, and started a company to produce and market the biocontrol agent around the world.
- Canadian researchers recognized as key part of global effort to curb spread of gonorrhea
The Sanger Institute, one of the biggest and most influential centres for genomics research in the world, is working to incorporate NG-STAR into a broader gonorrhea sequencing project underway at Sanger headquarters at Oxford University in the UK. Gonorrhea is now a major public health concern as strains of the bacteria are increasingly showing resistance to currently used antibiotics. With the support of funding from the GRDI and working with researchers from the USA, UK, Australia, Sweden and the Netherlands, scientists at the Public Health Agency of Canada have created a sort of universal translator for drug resistance in gonorrhea—it's called NG-STAR, which stands for Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance. Researchers around the world can refer to this database to identify the strain of gonorrhea they are working on.
- SISTR born in Canada being adopted around the world
With support from the GRDI, researchers at the Public Health Agency of Canada have developed a genomics-based tool that is changing the way authorities have investigated incidents of salmonellosis for close to 100 years. Scientists have assembled computer algorithms that use next-generation sequencing data to type and subtype Salmonella: the Salmonella in Silico Typing Resource—SISTR. Researchers anywhere in the world can use this resource to type the Salmonella they want to identify. The Canadian Food Inspection Agency and Canada's National Microbiology Laboratory now use SISTR as their standard protocol for Salmonella investigation, and the U.S. Food and Drug Administration is expected to adopt SISTR. It is also used by EnteroBase, an international centre for web-based bacterial genomic analysis at the University of Warwick in England. SISTR represents a significant contribution to reducing the public health risk posed by Salmonella not only in Canada, but around the world.
- Genomics research to better manage risk of Listeria
Research funded by the Genomics R&D Initiative will help to reduce the risk posed by listeriosis—the foodborne illness responsible for the deaths of 24 Canadians during an outbreak in 2008. With any foodborne illness, the earlier the source of contamination is identified, the sooner action can be taken to limit the spread of the infection. Researchers at Health Canada identified genetic markers to differentiate among hundreds of different strains of Listeria, the bacteria that causes the disease. The project includes developing an automated test, so investigators can determine quickly whether Listeria collected in one place is the same strain as Listeria collected somewhere else—a key to figuring out the source of contamination. The researchers also found that the same markers can be used to determine the resistance of different strains of the bacteria to different types of sanitizers—information that will help food processors ensure their sanitation procedures are as effective as possible.
- Health Canada researchers leading the way to safer stem cell treatments
Research funded through the Genomics R&D Initiative is helping to overcome a major hurdle on the way to realizing the huge potential of mesenchymal stem cells (MSCs) to treat a wide range of ailments. MSCs have a unique ability to help other types of stem cells repair damaged tissue but, like all stem cells, they also have the potential to mutate and become cancerous. And, just as they help other stem cells make repairs, they can also help cancerous stem cells grow more cancer. With a team of international collaborators, researchers at Health Canada have identified a series of protein and gene changes that indicate whether a particular MSC has a high probability of becoming cancerous. Based on these findings, the researchers are now focused on developing a rapid test platform clinicians could use to screen MSCs to ensure their safety prior to use in treatment.
- Immunotoxicogenomics: big word—big potential
With funding provided through the Genomics R&D Initiative, researchers at Health Canada are using genomics technologies to study how exposure to certain chemicals can cause people to develop an allergy to something that has never bothered them before. The relatively new field of immunotoxicogenomics involves identifying changes to gene expression in immune cells when different chemicals are introduced. Using chemicals known to cause changes in immune responses, the researchers are looking for a link between the changes they see in immune cells when a particular chemical is introduced, and the physical manifestations observed when animals are exposed to the same chemical. It is believed that, eventually, these methods could help reduce the incidence of new allergies—testing proposed new food additives, for example. As an added benefit, immunotoxicogenomics has the potential to significantly reduce the need for using animals in testing the safety of chemicals.
- Canadian researchers leading development of better, faster, less costly ways to test safety of chemicals
Research made possible by the Genomics R&D Initiative has enabled Canadian researchers to place themselves among the leaders of a revolution in regulatory toxicology—the science behind the regulations that help to ensure everything from the medicines we take to the air we breathe is as safe as possible. Traditionally, toxicity has been studied by dosing laboratory animals with a chemical—usually much more than would ever be encountered in daily life—and watching for the effects. It is a slow, expensive and somewhat inexact process. At Health Canada, researchers are showing how toxicogenomics can bring unrivalled precision and speed to regulatory toxicology, allowing researchers to see how different amounts of a chemical affect cells at the molecular level—and not only what the chemical does, but how it does it, all while reducing the need for animal testing. Their efforts have earned Canada a place on a prestigious international committee developing global strategies for toxicogenomics in regulatory policy.
- Canadians win international recognition with new HIV test
Canadian researchers, supported by the Genomics R&D Initiative, have developed a faster and more effective test for drug resistance in HIV—an achievement recognized as a significant contribution to the global effort to eradicate AIDS. Detecting and responding to drug resistance in HIV at an early stage is critical, lest a drug resistant variety become established in a population, setting off a new epidemic of untreatable HIV. Conventional testing for HIV drug resistance involves freezing a blood sample and delivering it to a specialized lab for analysis. This is a particular challenge in sub-Saharan Africa, where testing facilities are limited, and transportation and refrigeration can be unreliable. The DNA-based test developed by researchers at the Public Health Agency of Canada requires no refrigeration, can analyze dozens of samples at once, and detects mutations in the virus that indicate drug resistance at a much earlier stage. The new test is already being rolled out in Africa and other parts of the world.
- Salmonella: genomics investment leads to faster, more accurate identification
Funding from the Genomics R&D Initiative played a key role in enabling the development of new, genomics-based test that significantly reduces the time and cost involved in tracking the source of Salmonella contamination in the food supply. Using the traditional method, which involves animal testing, it takes four days to identify the type of Salmonella found in a sample of food—knowing the type is key to tracking the source of the contamination—and the test can be done by only a handful of specially equipped labs. Developed by researchers at the Public Health Agency of Canada in collaboration with colleagues in the U.K. and Austria, the new test identifies the Salmonella type in less than a day. Already accredited by the International Organization for Standardization, the new test can be done by almost any lab at minimal cost, so it's also ideal for routine surveillance for Salmonella at food processing plants.
- Stage is set for breakthrough in food safety
Funding from the Genomics R&D Initiative has supported the development of a genomics-based tool that will enhance the ability of food safety investigators to track the source of one of the most common causes of food poisoning in Canada: campylobacter, which sickens as many as 400,000 Canadians a year. Although it is incredibly common, finding the source of an incident of campylobacter contamination has been almost impossible, because there was no way to identify specific strains of the bacteria—until now. Researchers at the Public Health Agency of Canada have identified a set of genes in the bacteria that acts like a fingerprint for a particular strain. Using this so-called "DNA bar-code," food safety investigators will be able to identify a specific strain of campylobacter in a matter of hours, and in turn, quickly and accurately identify and address the source of the contamination.
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