Minnesota-based Calyxt struck a deal with a processor to make oil from its GE soybeans, in which the genes responsible for trans fats have been ‘turned off.’

And SU Canola (a sulfonyurea herbicide-resistant variety) was given its Canadian commercial release a year ago by San Diego plant-breeding company Cibus.

One of the things that stands out about these two companies is their names. They are not Bayer, Syngenta, DowDuPont, or other big global players usually associated with ag biotech. Rather, both are relatively new, smaller companies for which relatively cheap GE technology has opened a new world of opportunity.

So where are the homegrown Canadian GE startups?

At this point, there are few as far as anyone knows. However, academic institutions and well-funded ag biotech companies are digging into the space, said Gijs van Rooijen, chief scientific officer with Genome Alberta, a major funder of public genomic research in the province.

“There is a lot of private research occurring at commercial entities that is not directly visible to the general public,” he said. “At the same time, there is significant research happening at publicly funded academic institutions.”

For researchers, private or public, the process of genome editing (also called gene editing) has greatly reduced costs. Technologies such as CRISPR/Cas9 allow for a much faster process — possibly up to 90 per cent faster, according to some experts — than traditional crossbreeding or transgenic mutation (the technology used to create genetically modified organisms). This has thrown open the field of ag biotech to a host of new players.

Genome Alberta is funding some of that work, particularly projects examining the genomics of cattle and what is possible in terms of reducing feed inefficiency and methane emissions. The findings may have implications for GE work in the future, but van Rooijen said any objectives will likely be realized through traditional breeding as there is currently little social licence for genome-edited cattle.

“To date, there are no genome-edited animals approved for commercial use and the question remains whether or not society will be comfortable with this technology as applied to animals,” said van Rooijen.

And even though genome-editing technology is relatively inexpensive, ag biotech is a tough business with high costs of entry, said van Rooijen.

In fact, any Canadian biotech startup with a new GE crop would likely want to look at commercializing it south of the border, where a far different regulatory approach exists. The U.S. Department of Agriculture has ruled GE plants are not GMOs, which allows genome-edited products to get to market faster and with minimal vetting.

The Canadian Food Inspection Agency, on the other hand, has ‘plants with novel traits’ regulations. Under this system, it doesn’t matter if a new plant breed comes via traditional crossbreeding, genetic modification or genome editing — if it’s got a novel trait, it is subject to a rigorous, and often lengthy approval, process.

While the U.S. approach may be good for GE developers, Canada’s product-focused regulatory approach is better from an overall safety perspective, said van Rooijen.

“I think regulating byproduct is the right way to go,” he said. “There are plant species that are not very healthy for humans to consume. If someone wanted to commercialize a toxic plant species for human consumption — even if the toxic trait has been removed — you really want to make sure they are regulated based on product to assure they are safe for human and animal consumption.”

In its simplest definition, genome editing involves the ability to turn plant genes ‘on’ or ‘off’ depending on what trait you’re focused on — there is no introduction of foreign material or lengthy crossbreeding necessary. Advances in gene sequencing have given researchers the ability to quickly identify where genes are located on the cellular level, enabling the genome editing process and making it faster.

Although not specifically related to GE, Genome Alberta is funding several genome sequencing research projects in livestock. Genome sequencing is an important precursor to genome editing because it helps researchers identify the traits and associated genes they wish to emphasize or silence. Public acceptance will need to be won before genome editing becomes an important tool in livestock researchers’ tool boxes, but a better understanding of the genome is also important for traditional breeding.

“Genomics is being used to learn everything there is to learn about the cow genome — which genes are responsible for particular traits and the benefits of breeding those traits into the commercial stock,” said van Rooijen. “It will be really informative to cow-calf breeders to determine which bull to breed with which cow in order to come up with a progeny that is going to be better than what they started out with.

“If you can try to understand what is causing that variation then you can start breeding for cows that have a reduced methane output. By doing so, we’re basically developing cows that are better for the environment.”

Meanwhile, government researchers are thinking about how GE technology can help alfalfa producers deal with climate change. Agriculture and Agri-Food Canada researchers Stacy Singer in Lethbridge and London, Ont. colleague Abdelali Hannoufa are looking at how to introduce resistance to drought, salt, and abiotic stresses into alfalfa.

“There are wild relatives of alfalfa that are very tolerant to drought and salt — much more so than cultivated alfalfa,” said Singer. “We’re trying to identify which genes are the cause of this enhancement in drought tolerance in these wild relatives compared to alfalfa.

“We are targeting different genes that AAFC London has shown previously to be involved in some of these processes,” said Singer. “We are trying out different strategies hoping that some might work better than others in alfalfa.”

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Researchers said Monday they have sequenced the genome of the carrot, an increasingly important root crop worldwide, identifying genes responsible for traits including the vegetable’s abundance of vitamin A, an important nutrient for vision.

The genome may point to ways to improve carrots through breeding, including increasing their nutrients and making them more productive and more resistant to disease, pest and drought, the researchers said.

The vitamin A in carrots arises from their orange pigments, known as carotenoids. The study identified genes responsible for carotenoids as well as pest and disease resistance and other characteristics. In addition to eyesight, vitamin A also is important for immune function, cellular communication, healthy skin and other purposes.

The researchers sequenced the genome of a bright orange variety of the vegetable called the Nantes carrot, named for the French city. The carrot genome contained about 32,000 genes, a typical total for plants, which average around 30,000 genes, which is more than the human genome.

“Carrots are an interesting crop to work on because of their wide range of diversity. They are familiar to everyone, and generally well-regarded by consumers, but like most familiar things, people don’t necessarily know the background stories,” said University of Wisconsin horticulture professor and geneticist Phil Simon, who led the study published in the journal Nature Genetics.

Worldwide carrot consumption quadrupled between 1976 and 2013 and they now rank in the top 10 vegetable crops globally, the researchers said. In the past four decades, carrots have been bred to be more orange and more nutritious, with 50 per cent more nutrients.

The earliest record of carrots as a root crop dates from 1,100 years ago in Afghanistan, but those were yellow carrots and purple ones, not orange ones. Paintings from 16th-century Spain and Germany provide the first unmistakable evidence for orange carrots.

Knowledge of the carrot genome could lead to improvement of similar crops, from parsnips to the cassava, the researchers said. Close relatives of carrots include celery, parsley, parsnips, coriander, cilantro, dill, fennel, cumin and caraway. The common weed called Queen Anne’s Lace is a wild carrot.

The wild ancestors of carrots were white, the researchers said. While orange carrots are most commonly grown, some purple and yellow carrots are grown from the Middle East to South Asia, while some red carrots are grown in Asia.

— Reporting for Reuters by Will Dunham.

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The International Wheat Genome Sequencing Consortium (IWGSC), a team co-led by Canadian researchers, announced Wednesday it has produced a whole genome assembly for Chinese Spring bread wheat.

The assembly “represents a major breakthrough for the IWGSC integrated strategy towards delivering a high-quality reference sequence for each of the 21 bread wheat chromosomes,” project leader Nils Stein, of German plant research centre IPK Gatersleben, said in a release.

Where the IWGSC’s strategy is to study wheat one chromosome at a time, the assembly announced Wednesday was charted using a combination of software, computer programming and bioinformatics tools to look at virtually the entire genome.

The new data can now be integrated with physical-map-based sequence data to produce a “high-quality, ordered sequence” for each wheat chromosome, precisely locating genes and other markers along the chromosomes and providing “invaluable” tools for wheat breeders, the consortium said.

The consortium now expects to have a complete picture of the wheat genome, 17 billion base pairs in all, with a clear idea of how the genes are ordered, within two years.

Given that the wheat genome is five times the size of the human genome, earlier estimates had suggested such work would take four or five more years, the University of Saskatchewan said in a separate release.

The new sequence “is an important contribution to understanding the genetic blueprint of one of the world’s most important crops,” another project leader, Curtis Pozniak of the U of S Crop Development Centre, said in the same release.

“It will provide wheat researchers with an exciting new resource to identify the most influential genes important to wheat adaptation, stress response, pest resistance and improved yield.”

The digital work, he said, has “generated a version of the wheat genome sequence that is better ordered than anything we have seen to date. We are starting to get a better idea of the complex puzzle that is the wheat genome.”

The result, he said, will be greater precision in wheat breeding. “Imagine that you have a blueprint for the order of important pieces of the wheat genome puzzle. With that information, it becomes far easier to assemble the puzzle more quickly into new and improved varieties.”

However, he said, “there is still much work to do to define the function of each of the genetic pieces so that breeders can identify the very best genes in the gene pool.”

While the work was done on just one variety, it’s expected to serve as the backbone to unlock the genetic blueprint for traits in other varieties as well, he said.

The public-private collaborative project, co-ordinated by the IWGSC, is co-led by Stein, Pozniak, Saskatoon researcher Andrew Sharpe of the Global Institute for Food Security and Jesse Poland of Kansas State University.

Project participants also include researchers from San Diego-based genetic sequencing firm Illumina, genomic data firm NRGene, Tel Aviv University and the French National Institute for Agricultural Research (INRA). — AGCanada.com Network

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The panels are used to identify animal traits like feed efficiency and carcass quality. Eight partners are now using SNP technology for parentage on a regular basis, while three new partners are working towards that goal. This has helped not-for-profit Delta Genomics add more than 15,000 samples to its biobank. The data will be used to identify more traits of interest.

For more information, see deltagenomics.com.

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This sequence information can be analyzed directly, used for comparing animals within a breed, or for comparing animals across breeds.

One category of genetic difference frequently used for comparison is Single Nucleotide Polymorphisms or SNPs. SNPs are used as genetic markers to track the ancestral heritage of regions of DNA or of individual animals. SNPs also can be used to predict the likelihood that a given animal will possess an individual or a series of desirable trait(s). The latter can only occur once an SNP or a collection of SNPs is linked to a particular trait.

In (Canadian Cattle Genome) projects, genotypes (the pattern of important SNPs), from a wide range of beef and dairy breeds will be used to develop accurate genomic prediction equations to assess the genetic potential of an individual animal.

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