Canadian Genomic Innovations and the Global Bioeconomy
Is Canada ready to deliver genomic solutions to solve the world’s biggest challenges? The list of challenges related to the bioeconomy is long. The energy transition from fossil fuels to sustainable alternatives needs to happen soon and some argue it is possible to get it done fast. Ensuring that enough food is produced to feed everyone is also a growing challenge as the demand for food quality and diversity is growing fast. The need for action and innovation to address the increasing impact of climate change is urgent. A circular bioeconomy, with genomics as a key driver, offers a way forward to tackle many of these urgent issues we face today.
The State of Canada’s Bioeconomy
We are fortunate to live in a time of great technological progress in genomics and computing. After 20 years of investment in research and innovation, genomics is now ready to start delivering concrete solutions to help us solve global challenges.
From high-throughput sequencing of whole genomes to measuring gene expression and epigenetic marks at the genome-wide scale and even at the single-cell and spatial level, genomic technologies are advancing and evolving faster than ever, making their applications towards a more sustainable and green bioeconomy increasingly tangible. In our recent book, we highlighted a fascinating collection of examples, including several in Canada, illustrating the concrete applications and impact that these new genomics technologies hold for the next phase of the global bioeconomy.
Applications of Genomics in a Bioeconomy
1. Synthetic Biology
One of the most hyped tools in this century is synthetic biology. A group led by Dr. Lenore Newman at the University of Fraser Valley in British Columbia is working on protein production using cellular agriculture, a technique that is rapidly nearing commercial scale. Genomics and synthetic biology technologies are currently being used for protein production including cell culture-derived proteins and fermentation-derived proteins.
“Genomics and synthetic biology technologies are currently being used for protein production.”
Using cell lines with specialized growth media, companies like Finless Foods (California, US) and Mosa Meat (Maastricht, Netherlands) are producing cultured fish meat and cultured beef meat respectively. Future Fields (Edmonton, Canada) goes upstream of the process and is using genetically modified fruit flies to produce custom growth factors which have the potential to address the high cost of humane growth material for cultured meat.
2. Environmental Monitoring
Another application of genomics in the bioeconomy is environmental monitoring. Dr. Caren C. Helbing and her team at the University of Victoria are leading the way in the use of Environmental DNA (eDNA) for monitoring a wide range of organisms and ecosystems. eDNA is the genetic material shed by organisms, micro or macro, into their environment which can be measured with powerful and cost-effective genomic tools.
Today, eDNA sampling is being integrated into large-scale biomonitoring programs and will be useful for informing policy and management decisions in the near future. From tracking invading species like the American bullfrog invading Belgium, to detecting pathogens like SARS-CoV-2 in wastewater for pandemic monitoring, eDNA has been recognized and applied around the world. To fully embrace the potential of eDNA, opportunities include relating eDNA to more conventional methods and standardizing protocols and reporting.
3. De-risking Offshore Oil Exploration
Genomics can also be used to de-risk offshore oil exploration. With sea ice melting at a record pace in recent years, maritime and industrial activity is mounting in the Arctic Ocean. This translates into an ancillary increase in the risk of offshore oil spills which are likely to result in challenging and expensive remediation efforts in such an unforgiving, cold and remote environment.
“Genomic surveys help predict the potential for biodegradation by identifying the presence of marine bacteria that can eat compounds from oil.”
This is where genomic data on baseline microbial communities can play a huge role. Dr. Casey R.J. Hubert at the University of Calgary and his team, are using genomic surveys to help predict the potential for biodegradation by identifying the presence of marine bacteria that can eat compounds from oil. This genomic mining work could help inform risk modelling and determinants of insurance premiums for marine shipping but also help understand ecosystem impacts to inform clean-up costs in the event of a marine oil spill.
4. Genomic Surveillance
Genomic surveillance can also be taken to the forests to help predict and prevent pest outbreaks, where invasive species are often not known. Forests are vital for the bioeconomy as they support entire communities by providing building materials, food and energy. Arguably, the most important contribution of our forests is their ability to capture and store carbon, which mitigates climate change.
“Genomics has revealed the causal agents of sudden oak death and ash dieback, two deadly pathogens that were previously unknown to science.”
However, forests are constantly challenged by invasions and pushed beyond the thresholds of sustainability. Dr. Richard Hamelin at the University of British Columbia is developing comprehensive genomic biosurveillance approaches to help ensure that these thresholds are not crossed. For example, genomics has revealed the causal agents of sudden oak death and ash dieback, two deadly pathogens that were previously unknown to science. Increasing demand will likely result in more access to powerful and cost-effective genomic tools being developed to ensure sustainable and healthy forests.
5. Agriculture
Another area where Genomics has played an important role in driving the bioeconomy is agriculture. Whether it is food or fibre, today’s crops have been selected or modified using a wide range of ancient methods but also the most modern genomic techniques. Dr. Erin J. Gilchrist and collaborators focus on a plant that is grabbing headlines everywhere: cannabis.
“The rapid growth of genomic tools is also supporting the improvement of the cannabis crop to produce and regulate the array of cannabinoids and terpenes in cannabis.”
Cannabis cultivation spans millennia, but despite its long-standing use, scientific research on the crop has been limited. The recent flux of restrictive legislation across the globe is changing this and has opened up new avenues for genomic research in cannabis. Besides a genome sequence published in 2011, a number of more recent publicly available databases have improved cannabis genomic resources. An interesting discovery has been the lack of a genetic basis for the commonly used designations “indica” and “sativa”. Although these terms are well-accepted in the cannabis industry and even used for medical prescriptions, genomic research has shown that these groups lack conserved genetic profiles as there are significant genetic differences within samples of the same strain. These differences could be exciting for recreational users but might have more serious implications for medical use where patients rely on strain-specific effects. The rapid growth of genomic tools is also supporting the improvement of the cannabis crop to produce and regulate the array of cannabinoids and terpenes in cannabis.
How to Advance Canada’s Bioeconomy
To fully deliver on the promise of genomics and the bioeconomy, Canada requires continued investments in our research ecosystem. Such funding is urgently needed to create new knowledge for the future of the bioeconomy and keep Canada competitive.
Policy and regulation are also fundamental to accelerating the deployment of a sustainable bioeconomy. Emily Marden from Sidley Austin LLP and the University of British Columbia calls on researchers and developers to stay up to date on regulatory developments and to be aware that requirements may differ amongst jurisdictions. Regulatory authorities across the globe are building policies and strategies to address questions about how to regulate products derived from genome editing and synthetic biology. Currently, there is a flux in regulatory oversight around these products and how fast-paced developments in food science and agricultural production are challenging US, Canadian and European Union regulators.
The power and the promise of genomic technologies in Canada are latent. To ensure broad and equitable access to these new technologies, Canada needs to continue supporting the extensive expertise and capacity in critical areas such as the agrifood, forestry, fisheries and environment sectors.