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Precision fertility and resiliency phenotyping in dairy cattle

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Overview

As the world’s 5th largest exporter of agricultural products, Canadian farmers are poised to play a decisive role in meeting the 70% increase in world food demand expected by 2050. In 2017, $14.3 billion worth of manufactured shipments of milk and dairy products were made, with approximately 33% of those coming from Ontario farms (https://www.milk.org/corporate/pdf/media-ontariomilkindustry.pdf, site accessed December, 2018). Canadian dairy genetics exports are also a growing source of revenue, rising 45% during the last decade to a total value of $155.2M in 2017;  in particular, semen sales rose by 80% ($127M in 2017) (http://www.dairyinfo.gc.ca, site accessed December, 2018). The Semex Alliance, which is owned by three well-established Canadian genetics organizations, delivers innovative genetic solutions both within Canada and globally. With its headquarters in Guelph Ontario, Semex is well aware of the importance of addressing the anticipated environmental changes associated with climate change.

Dairy cow performance (such as growth, milk production, and reproduction), as well as animal welfare and health, can be strongly influenced by air temperature, humidity, and other climatic factors. Genetic selection plays a key role in breeding livestock that can better cope with changing climate, and more specifically, tolerate extreme temperatures and humidity and changes thereof. This project will provide novel and innovative methods for genomically selecting robust dairy animals which are resilient to environmental stressors, such as extreme hot/cold temperatures, while maintaining health, production, and reproductive efficiency. This proof-of-concept project integrates phenotypic data collected using automated sensor technologies with high-throughput genotypes of dairy cows through application of machine-learning algorithms to identify the underlying associations therein. In this way, a sustainable and economically profitable genomics-derived process for identifying healthy, fertile, resilient animals for use in genomic selection programs will be demonstrated and ready for large-scale realization, thus strengthening Ontario’s leadership in this field.

Probiotics for plants to increase crop yields

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Overview

Ceragen is developing probiotics for plants that help hydroponic fruit and vegetable growers increase crop yields 10-20%. Ceragen’s inoculants are formulated with plant growth promoting microbes that increase crop yields by increasing nutrient uptake and improving the plants’ response to environmental stress. The company currently has two products on the market and is working to develop products for all hydroponically grown crops.

Animal-free gelatin from pulse starch

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Overview

Using engineering biology, Liven produces sustainable and animal-free protein ingredients with functionality equivalent to or superior to animal products. Liven is establishing a bioprocess and fermentation platform to transform food industry side streams into these protein ingredients, allowing scalable, environmentally friendly, and cruelty-free protein production to feed the growing population. Liven’s first product is animal-free collagen, a versatile protein ingredient with an $8 billion market.

Evolved (formerly Caro Meats): Creating cultivated pork belly that is identical to conventional pork belly

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Overview

Global demand for meat is expected to rise by over 75 % by 2050, and conventional agriculture will have to be supplemented by new methods, such as cultivated meat production, to meet this need sustainably. The majority of cultivated meat products in development are equivalent to current processed meat options and contain additives to enhance taste and texture and provide structure.

Evolved intends to create whole cuts of scaffold-free cultivated meat that are structurally and biochemically identical to conventional meat products. Using their proprietary cell sheet engineering techniques and transitioning their products from muscle to meat, Evolved will create cultivated meat products, from any livestock species, that align with consumer preferences and consumption habits. Focusing here on pork, Evolved will develop a 4-step quality control system:

  • Create a proteomic data set (baseline) for conventional pork by acquiring and testing different cuts from different breeds of pig
  • Test the proteomic data from Evolved’s porcine samples against the baseline data
  • Perform targeted protein studies on Evolved’s porcine samples for known biomarkers of meat quality
  • Evaluate the organoleptic properties of their porcine samples against the data obtained

Moreover, the proteomic data set for conventional pork will be made open-source for access by interested parties in the cellular agriculture ecosystem.

Cell Ag Tech: Scaling up the manufacturing of fish muscle stem cells from a 2D to 3D culture system with proteomic assessments of the cells

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Overview

The global seafood industry has a first-sale value of over $400B annually, and growth is forecast to continue. With commercial fishing and aquaculture unable to meet growing market demand, cell-cultured seafood can play an integral role in helping to supply the global market in a sustainable manner. As most of the seafood production in Canada occurs in the coastal regions, cell-cultured seafood provides Ontario with a unique opportunity to participate in the seafood economy.

Working with CCRM/Cytiva, a global leader in scaling up cell manufacturing, CELL AG TECH intends to grow snapper cells in 2D and 3D, to lay the foundation for commercial-scale production and commercialization. Proteomic assessments will be performed on muscle precursor cells from 2D and 3D cultures to:

  1. Determine the differences in protein expression between 2D and 3D
  2. Regulate the environment the cells are grown in to achieve optimal conditions and outcomes
  3. Better understand the nutritional value of the cells
  4. Provide data for regulatory processes.

This level of scale-up will move our organization closer to commercial scale production and price competitiveness, as well as allowing us to produce a greater number of cells for our experiments and R&D initiatives, such as valuable optimization parameters and creation of additional food product prototypes.

Ardra Inc.: Developing fermentation-based production of heme as a natural flavour ingredient

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Overview

Alternatives to animal protein are targeted towards disrupting the global meat industry, a >$800B market, with total sales of plant-based foods in 2021 around $10B. To further grow the market share, plant-based foods need improvements in matching meat-based products’ flavour, texture, nutrition, and cooking behaviour. Addressing these challenges is believed to be a significant driver for greater adoption of meat alternatives and satisfying consumer demands.

A significant focus of the Canadian alternative meat industry is supplying pulse-based plant ingredients. However, Ontario has an opportunity to support the alternative meat industry and potentially enable more Canadian-produced products by leveraging its engineering biology and biotechnology expertise to supply/create ingredients to enhance these products.

Ardra’s project focuses on developing a very well understood ingredient called heme, found in animal blood, which alone provides a core element of the taste of meat. Ardra has demonstrated production of animal-free heme by precision fermentation and has active requests for larger sample amounts from several major flavour companies. Their AcCELLerate-ON project objective is to reach pilot-scale for heme production, validation of their key ingredients by these potential customers, and to establish a clear path to market.

Applying genomic signal processing methods to accelerate crop breeding

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Overview

Selective breeding improves plant and animal products by identifying desirable traits such as quality, yield, and ability to grow in difficult conditions, ensuring that that there is sufficient production for food, fuel and raw materials. Factors like climate change and population growth are making selective breeding more important than ever. One of the largest challenges facing the plant research community is identifying the suite of genes that make organisms well adapted to their environment and using this information in breeding programs.

Drs. Lewis Lukens, Cortland Griswold and their team are using bioinformatics tools to understand how organisms that adapt well to their environments can be selected to accelerate the development of new plant varieties.

Sustaining and securing Canada’s honey bees using ‘omic tools (2014)

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Honey bees play a critical role in Canadian agriculture. They produce 75 million pounds of honey each year and are responsible for pollinating many fruits and vegetable crops, nuts and oil seeds like canola. Through these activities, they contribute more than $4.6 billion to the Canadian economy each year. Given this critical role, the high rate at which bee colonies are dying off is particularly alarming, posing a serious threat to the productivity of Canadian agri-­food industries and jeopardizing Canada’s food security. Canadian beekeepers have lost more than a quarter of their colonies each winter since 2006-­07 with certain provinces experiencing significantly higher death in some years. Replacing these losses by purchasing queen bees from offshore, as beekeepers have been doing, risks importing new diseases or invasive strains of honey bees (such as “killer” bees from  the US). Dr. Leonard Foster of the University of British Columbia and Dr. Amro Zayed from York University are leading a project to guard the safety and sustainability of the beekeeping industry in Canada. The team will develop genomics and proteomics tools that will provide markers to selectively breed 12 economically valuable traits. This will enable beekeepers to quickly and cost­effectively breed healthy, disease-­resistant, productive bee colonies that are better able to survive harsh Canadian winters. While this will lessen, it will not eliminate, the need to import bees from other regions, so the team will also develop an accurate and cost-effective test to detect bees with Africanized genetics (“killer” bees). The team will work with beekeepers and other stakeholders and end users to ensure its tools are implemented and accessible to beekeepers by the end of the project. This will provide measurable economic benefits to Canada, including to beekeepers and the agri-­food industry and social benefits to the Canadian public. These benefits range in value from $8 million to $150 million per year.

Increasing feed efficiency and reducing methane emissions through genomics: A new promising goal for the Canadian dairy industry (2014)

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he Canadian dairy industry adds $16.2 billion to Canadian GDP each year (2011 figures). That figure is forecast to increase as international demand for dairy products grows in the coming years, due to growing middle classes in emerging economies, demand for high-quality milk proteins in developing countries and world population expansion more generally. That figure can also grow (by an estimated $100 million annually) by improving two key traits in dairy cattle: their ability to convert feed into increased milk production and a reduction in their methane emissions (methane being a powerful greenhouse gas). Dr. Filippo Miglior of the University of Guelph and Dr. Paul Stothard of the University of Alberta are leading a team that will use genomics-­based approaches to select for cattle with the genetic traits needed for more efficient feed conversion and lower methane emissions. To date, it has been both difficult and expensive to collect the data required for such selection. The latest genomic approaches and the award-winning phenotyping platform developed by Growsafe in Alberta offer an opportunity to address these problems and collect and assess the required data to carry out the selection. The results of this project will assist dairy farmers and the industry more broadly to develop cattle that will carry these two important traits. Farmers will save money (as feed is the single largest expense in milk production), while the international competitiveness of Canada’s dairy industry will increase. The environmental footprint of the dairy industry will also be reduced, in part due to lower methane emissions, but also because more feed efficient animals produce less manure waste. Broad application of the project’s findings will be enhanced by the involvement of several industry organizations and international research partners in the project, not only benefiting Canada’s dairy industry, but also contributing to global food security and  sustainability.

Genome Alberta Press Release

Towards a sustainable fishery for Nunavummiut (2014)

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Affordable access to safe, nutritious and culturally relevant food is one of the biggest challenges facing the Nunavummiut, the people of Nunavut. Food costs are 140 per cent higher in Nunavut than in the rest of Canada with eight times more Inuit households facing moderate to severe food insecurity. This lack of affordable, nutritious foods is linked to growing health problems, including diabetes and childhood rickets. Accelerated melting of Arctic sea ice due to climate change is increasing access to arguably the last remaining under-­exploited fishery in the Northern Hemisphere. This increased accessibility, primarily to Arctic char, but also to Arctic cod and Northern shrimp, coupled with a developed, sustainable, science-­based fishing plan will offer opportunities for employment and economic benefits for Nunavut communities as well as greater food security. It is the Nunavummiut that should be the beneficiaries of these resources, rather than foreign fishing fleets. Understanding the genetic differences among these fish populations is key to developing that plan. Dr. Virginia K. Walker of Queen’s University and colleagues together with the Nunavut communities will integrate traditional and local knowledge with leading-­edge genomic science and bioinformatics to gain an understanding of the genomes of these fish populations. This will allow monitoring of their migration, characteristics and adaptation and inform strategies to maintain genetically diverse and healthy stocks. The project will work toward strengthening Nunavut fisheries, augment sovereignty claims in the Canadian Arctic, increase employment and economic development opportunities, ensure access to a healthy food source, and improve food security for the people of Nunavut. The Walker Project website is www.arcticfishery.ca