Aquatic and Terrestrial Animal Genomics
Theme Leaders:
Andy Potter (Vaccine and Infectious Disease Organization, University of Saskatchewan) and
Steve Moore (University of Alberta)
Lead Centres:
Genome Prairie
Pre-Draft with new Strategic Areas and Deliverables graph, a rough-in of a
new executive summary and highlights of areas for review as recommended
and placeholders for some success stories – May 22
1
Executive Summary
“Investment is made for future opportunity and by not preserving a questionable status quo. The knowledge
intensive bio-economy is real, is here today, and will create potentially huge new value for agriculture in the
future.” Canadian Agri-Food Policy Institute 2007
The theme: The Aquatic and Terrestrial Animal Genomics, ATAG, theme harnesses the internationally competitive
Canadian agriculture and aquaculture industries, the nation’s abundant natural resources of land and water and the
federally and provincially supported research initiatives that have made Canada a natural global bio-resources leader.
Agriculture and food related industry employs one in eight Canadians. The research developed within this theme will
create a knowledge base critical to improvements in animal production, improved human health outcomes and industrial
and export food processing creating more than $XX billion in new wealth and savings for Canadians over the next
decade. Canada is poised to be a major contributor to international food security through improved utilization of the
nation’s natural assets at a time in history when food supplies are considered inadequate to meet global needs and
demand for protein is at record levels. These research outcomes will add stability and profitability to the nation’s livestock
and aquaculture industries, often plagued by poor economic margins, and provide healthier food for a healthier Canada.
Animal welfare will be improved, building on Canada’s international reputation as a source of premium quality food.
Research activities under this theme would promote discovery and development in four strategic areas: genomics
and animal resource profiling; animal productivity, health and welfare; ecosystem health; strategic planning for
change in animal agriculture and aquaculture –each including GE3LS issues of the legal, ethical, environmental,
economical, and social impact of ‘omics research and animal and aquatic livestock production and harvest.
The ‘omics: Genomics technologies provide tools to assess and track wild populations, improve animal production
systems though marker assisted selection and development of novel traits, monitor the environment and determine
impacts of agriculture and aquaculture on our natural resources. A strong Canadian genomics research community
means that it can better access and contribute to global genomic resources and develop tailored genomics tools to meet
the needs of a modern, world class industry. The ATAG theme research and planned deliverables of improved tools of
production and protection focus on strategic development of existing Made-in-Canada ‘omics solutions and novel
developments to promote sustainable growth of animal agriculture and aquaculture. In addition it will use these
resources to assess, monitor and safeguard wild animal populations and their environments, and build opportunities to
secure Canada as a leader in animal health and welfare. ATAG will enable research into the potential benefits of
production improvements, such as increased feed conversion, and subsequent impact on methane, nitrogen and
phosphorus in terrestrial production waste. This will provide solutions for sustainability in the face of an ever expanding
demand for animal protein. Further, GE3LS research will assess the potential for rural and aboriginal community
developments and socio-economic benefits of resulting from animal harvesting and production system expansion.
Canada’s Advantage: Canada has 25% of the world’s coastline and 16% of the world’s fresh water which gives
Canada a unique advantage in large-scale aquaculture and terrestrial animal production. Its fisheries and aquaculture
industries produced over $2.9 billion and $715 million respectively in 2005. Canadian animal health systems are among
the world’s best, and have enabled disease eradication for a number of production systems. Canada has unparalleled
animal identification protocols which positions our country as a world-leader towards the implementation of animal
product traceability. Finally, Canada has invested richly in infrastructure and early development of genomics tools, and
ATAG proposes research that will capitalize on this investment.
Projected Deliverables: Together with reference sequences and other genome based tools, the large-scale research
partnerships supported by this theme will enable improved description of genetic variation and biodiversity, allow better
monitoring of animal population and environmental gene flow, support marker assisted selection and genome-wide
approaches to breeding, help optimize production and environmental efficiency, and inform the creation of valuable new
tools (diagnostic tests) for managing disease and animal health. In addition, the ATAG theme will foster the creation of
bioinformatic and biological sample repositories as well as animal registries to optimize resource use and access in
current and future genomics research. These repositories will not only support genomics research, but promote
traceability and support Canada’s competitiveness within the global food industry.
With advances enabled by the above described genomics tools and resources, the ATAG theme provides a blueprint to
enable a 20% increase in efficient, healthy animal production – a critical need for Canada in the face of increasing costs
of production, health, and ever expanding global food demands.
2
This theme offers excellent short term value on the investment. A national ATAG program budget of $120-170 million
would enable at least 8 major four-year projects or initiatives with an average budget of $15-20 million. Based on
provincial and industry enthusiasm, and international opportunities, this theme could assume a 50/50 funding formula,
thus leveraging Genome Canada’s contribution of between $60 and $85 million. In return, this investment would allow
for the development of high-impact research assets with immediate and future commercial value. Even a modest change
(0.5%) in animal based trade would translate into hundreds of millions of dollars per year. Prevention and management
of future diseases could have even greater value, while the maintenance of biodiversity could prove invaluable. At the
same time, research training and recruitment of Highly Qualified Personnel will be enhanced, productivity improved,
resources conserved, and sustainability enhanced, all of which will strengthen Canada’s Brand and improve health –
both now, and in the future.
Recent examples such as BSE and SARS demonstrate both the critical need for better genomics approaches and, at the
same time, the enormous potential and capability that exists in Canada. Moreover, increased concern around obesity
prevalence and the growing interest in organic and nutritionally enhanced foods speaks to the public’s appetite for action
in this area.
3
INTRODUCTION
Animal-based industries including aquaculture* are critical sectors to Canada’s economy. This fact is
illustrated by the strength of Canada’s exports and industry related employment. One in eight
Canadian jobs is related to food and agriculture1. In 2002, prior to BSE, the red meat industry was
ranked fourth among Canada’s manufacturing industries with annual shipments worth $14.6 billion2†.
This position is underpinned by Canada’s reputation for the safety and quality of its animal products;
2004 (post-BSE) cattle and beef exports were 48% of their 2002 level3. Canada has benefited from its
growing strength in animal genetics, (which has impacted trade in breeding stocks as value-added
products), and has the expertise and the abundant natural resources (e.g. land and water; geographical
isolation) to further strengthen the Canada Brand‡ for food and agriculture products. Canada has 25%
of the world’s coastline4 and 16% of the world’s fresh water5. Its fisheries and aquaculture industries
produced over $2.9 billion and $715 million in 2005, respectively, and provide many thousands of jobs
in coastal, rural, and aboriginal communities6. Genomics is poised to have a significant impact on these
industries; however, continued support is needed to realize this impact and to ensure the
maintenance and improvement of sustainable animal agriculture and aquaculture in accordance
with consumer demand, ethical considerations and respect for the environment.
From conception to consumption, genomics has begun to influence all stages of livestock production
and the potential of approaches such as marker assisted selection and marker assisted management
have been demonstrated7. Canada has also taken a leadership role in fisheries and aquaculture
genomics, as evidenced by a $40M investment for international projects on fish species that are
important to the Canadian economy: cod, halibut and salmonids8. Future research holds promise for
providing tools to augment our current strengths in areas such as food safety and quality, wild species
management and genetic conservation, animal health and for increasing biological knowledge through
insights into human health and disease issues, including zoonoses§. Over the next decade, animal
genomics research will determine the industry’s future international competitiveness.
Canada’s researchers in this field are among the best in the world; the research community has the
required technologies, expertise, animal resources and physical infrastructure in our Genome Centres,
universities, research institutes, federal research labs, and companies. Canada also has considerable
strength, resources, and support available in its animal based industries. Canada is well-positioned to
make major advances in this field and to continue to lead the international scientific agenda. The next
step is the development of national resources by the Canadian research community to solve priority
issues, establish networks and to address emerging issues on a timely basis. A strong national program
is now needed to co-ordinate these world-class facilities and research groups, and to fulfill the
potential of animal genomics, in order to create tangible outcomes that benefit Canadians now and in
the future. The ATAG theme’s research outcomes will benefit Canada’s wild and cultured animal
species through discovery and development in the following areas:
Definition – Animal: any member of the kingdom Animalia
More recently, meat processing sales totaled $15 billion with exports to over 120 countries (Canadian Meat Council,
Industry Statistics, 2005), although some sub-sectors continue to suffer the lasting effects of BSE (Ref 3).
‡
“Quality is in our nature” www.brandcanada.agr.gc.ca
§
Definition – Zoonoses: diseases that cross from one species to another (humans in particular). The H5N1 strain of bird
flu is an example.
*
†
4
Strategic Area
Genomics and
Animal Resource
Profiling
Animal Productivity,
Health and Welfare
Ecosystem Health
Growing Forward:
Strategic Planning
for Change
GE3LS
Deliverables
 Further development of genomic resources (e.g. high-quality
reference genome sequences, Single Nucleotide Polymorphisms
(SNPs), high density maps) for species important to Canada
 Incorporation of the data and results into a coordinated
bioinformatics strategy to provide a database and analysis
framework
 High throughput genome wide analysis and association studies to
identify underlying biological processes
 Other
 Marker development
 Development of strategies for protection of marker-associated
Intellectual Property (IP) and analysis of market potential for Canadian
marker-based IP
 Marker Assisted Selection to yield production increases for
aquaculture and terrestrial species
 Collection and curation of detailed phenotypic characterization of
animals and their environments (including high throughput
approaches to describe phenotypes such as microarray-based
expression profiling)
 Harnessing naturally occurring genetic diversity and Canada’s
genomics potential to address public issues of animal health and
welfare, food safety and sustainability, and disease prevention
 Building and using genomics tool to assess, monitor and safeguard
wild animal populations and their environments, and build
opportunities to secure Canada as a leader in animal health and
welfare
 Other
 Further development of genomic resources to monitor and assess
wild animal species populations
 Development of genomics resources to assess impacts of animal
production systems on aquatic and terrestrial ecosystems
 Other
 Identify and predict change and future needs related to animal
production, health and welfare
 Exploration related to novel traits including trait identification,
development, evaluation, risk assessment for GMOs and development
of risk mitigation strategies
 Regulatory science
 Modeling to demonstrate Canada’s potential for expansion in animal
production and harvest.
 Enhancing Canada’s advantage through optimized use of resources
 Other
GE3LS deliverables will be integrated with deliverables for the above four
strategic areas. Deliverables will relate to Regulatory and Environmental
Science, Policy and Societal Impact, etc. Examples:
 Modeling benefits of improvements such as increased feed conversion
and subsequent impact on methane and phosphorus in terrestrial
production waste.
 Assessment of the potential for rural and aboriginal community
development and socio-economic benefits resulting from
improvements in animal production systems.
5


Land use policy development.
Other
In the sections that follow, this paper outlines the importance of these research areas, focusing on the
social, the market, the sustainability, and the strategic significance of this theme. Elaborating on the
need for research in terrestrial and aquatic animal genomics, this paper presents a vision that
emphasizes co-ordinated large-scale research that capitalizes on Canadian strengths, harnesses
industry resources, and expands Canada’s capacity for the physical characterization of animals. GE 3LS
research opportunities are highlighted throughout with emphasis on enabling communication and
knowledge utilization. Finally, expected outcomes and impact are outlined, and a budget proposed.
This theme is well aligned with Industry Canada’s recently released framework for Mobilizing Science
and Technology to Canada’s Advantage, as is highlighted throughout, and is a reflection of the large and
diverse multi-sector and multi-national input that has been incorporated into the creation of this
document.
Sound science is the foundation on which the government manages the diverse range of human activities in
our waters, including fishing, aquaculture, transportation, and oil and gas exploration. Because these
decisions can affect people’s lives in a variety of ways—from the livelihood of Canadians in coastal
communities to the protection of the environment for current and future generations—decisions must be
based on the highest-quality science available. In turn this requires cutting-edge technology in the hands of
top-notch researchers, long-term monitoring, data management and the ability to interpret and transform new
knowledge into sound science advice. - Canada’s Federal S&T Strategy 2007
IMPORTANCE OF THE RESEARCH THEME
Social and Cultural Significance
Canada has a long cultural history founded on the richness and diversity of its animal resources. Our
economic health has long been bolstered by our animal food resources. Canada’s animal resources are
essential to the jobs and economic prosperity associated with the food industry. Canada has enormous
natural resources, and the responsibility and opportunity to manage animal and aquatic resources in a
sustainable way.
World food supply issue 2008 and Canada’s role – here
Today, Canada faces myriad local and global challenges to the long term competitiveness of its animalbased industries. Globalization has resulted in a food system that is increasingly interconnected and
strained by the exponential growth of world income (particularly in some developing countries) and
by food production capacity limitations9. The demand for food is confounded on a global scale by
issues such as climate change, water scarcity, increasing input costs, limited distribution
infrastructure, infectious disease, and maintaining biosecurity**. The intensification of agriculture in
the developing world could be environmentally catastrophic and a dangerous source of disease unless
there is significant advancement in the technical ability to safely raise food animals. Belatedly, we have
begun to perceive that, without advances in science and industry, our ability to sustain animal
production may be limited10.
Consumers are increasingly aware of the role that processed food plays in chronic diseases like
obesity, diabetes, and cardiovascular disease. With SARS and H5N1, the risk of infectious disease
associated with food or animal products has increasingly been in the public eye. The meat industry, in
particular, has also been challenged over potential links between red meat consumption and cancer
incidence. A 2003 Globescan report showed that China, Canada and the U.S.A. all put food safety and
nutritional value above price11. This heightened awareness has manifested in rapid changes in both
producer and consumer positioning in the food market place. Genomic approaches will help improve
**
Industry Canada priority. Ref 23 p.21.
6
the understanding of basic biological processes and the influence of the environmental aspects that
will play an increasing role in helping assure food safety and quality.
Similarly, concerns about the welfare of farm animals have also been increasing in recent years. For
example, in a large European Union survey of over 29,000 respondents12, 34% said that animal welfare
was of the highest possible importance. The consequences of such attitudes are important factors in
Canada’s global competitiveness. A demand for higher animal welfare standards places pressure on
export countries like Canada. Genomics provides opportunities for enhancing animal welfare, for
example by reducing or eliminating traits and behaviors, such as aggressiveness, that lead to
preventable animal suffering.
Given the importance of Canada’s food animal industry, we must take a leadership role in developing
and implementing technology and production practices. These technologies will be critical in securing
a healthy and sustainable animal-based food supply for Canada and the world and to ensure
environmental sustainability. A key goal of this theme is to harness the power of genomics to ensure
the efficiency and health of Canada’s animal resources.
Market Significance
Canada enjoys a prominent position and an excellent reputation in global industries associated with
animal agri- and aquaculture. Improving this position is important to Canada’s future prosperity.
These industries employ approximately 0.75 million people (one in eight Canadian jobs are related to
food and agriculture) and have a combined GDP approaching $4 billion (2005 at basic prices)13. In
2005, red meat industry annual shipments (excluding poultry) totaled $15 billion and Canada's fish
and seafood exports were valued at $4.3 billion14.
Canada is not immune, however, to rising global challenges associated with agri- and aquaculture;
current challenges include BSE, Avian Influenza and the decline in many of the world’s large fish
stocks15. Rising demand for oceanic protein, concurrent with limited supplies from wild fisheries, will
likely be met by aquaculture; however, increasing pressure on smaller fish species that are used for
fish meal can drive up the cost of fish meal used in aquaculture. Taken together, these realities may
jeopardize Canada’s multi-billion dollar fishery and aquaculture industry16 and many thousands of jobs
in coastal, rural, and aboriginal communities. Similar pressures are also impacting land-animal feed
costs, as renewable energy crops begin to replace feed-crops, thereby driving up input costs in animal
food production. Insert latest world grain stocks/price data here when report comes out June 8.
Urbanization, disease, and climate change may also have profound and disruptive impacts on Canada’s
land and aquatic animal resources.
Sustainability Significance
While animal and land resources continue to decline, rapid expansion in the demand for animal
protein will continue to create substantial economic and environmental challenges. In most developing
countries, agriculture is the most water-intensive sector of the economy and, unlike manufacturing,
consumes much of the water that it uses17††. As a result, water tables are now falling in countries that
contain over half the world's people. Future water shortages will make it much more difficult to
produce enough food to stay ahead of rising consumption. Urbanization and renewable energy land
usage are also growing concerns. At the same time there is an opportunity to address greenhouse
gases (methane, in particular, is a significant by-product of the animal industry). There is a critical
need to optimize animal-based agriculture in ways that reduce the environmental impact - a need that
can be alleviated, in part, by genome-based selection of production animals. Role of potential Canadian
research project here.
Logic suggests that water-intensive activities should be undertaken in water-rich locations. Economic
arguments against moving grain to animals are even more compelling. Instead of subsidizing
††
Less than 30% of the water used is returned to sources such as rivers and lakes (Ref 16).
7
production through trade distortions, technological advancement could be used to develop the most
productive areas of the globe and to improve the efficiency of sustainable production where it makes
sense. Canada possesses some of the world’s largest reserves of fresh water, a considerable proportion
of the world’s arable land, and an animal population density that is low and, therefore, generally
favourable for biosecurity and animal health. Importantly, Canada also has access to a considerable
diversity of animal species, a critical resource for the long-term sustainability of production
populations. Together with advanced genomics capabilities and value-added genetic leadership ability,
Canada is well positioned to assume a leadership role in developing enhanced sustainability resources
and practices in the agri- and aquaculture industries.
The agriculture community, as a key source of food, has a huge role to play in the
health of Canadians, and can help reduce burgeoning health-care costs. Indeed, both humanhealth
and the agriculture industry stand to benefit greatly from an integrated agrifood policyframework.
An appropriate vision for Canadian agriculture might constitute the foundation of a healthy and
sustainable Canadian society. CAPI Dec 2007
Strategic Significance
Food safety, security (enhanced with current news and world food stocks issues), and supply are
obviously critical national strategic concerns. Major issues associated with animal-based industries
include diseases that affect the food supply and human health. Growing global food demands require
ever larger sources of animal-based resources, leading to the intensification of agriculture and
aquaculture practices. Disease is a particular threat to these large scale operations, especially in
populations with relative genetic homogeneity. Fish diseases, in particular, present a significant threat
to farmed fish populations where diseases, such as infectious salmon anaemia virus, can lead to
widespread mortality. Terrestrial animals, particularly those raised in high population densities, are
also susceptible, as demonstrated by a recent epidemic of Porcine Reproductive and Respiratory
Syndrome virus, which claimed 1 million pigs in China as recently as 200618 and remains a threat to
global pig populations.
The intensification of agriculture and the increase in trade brought about by globalization is also
causing the emergence of new life-threatening zoonotic diseases. Researchers report that 80% of
emerging public health challenges are zoonoses (human infections arising from animal sources)19. We
can document 38 illnesses (exemplified by SARS) that have made the jump from animals to people in
only the last 25 years20. Experts in the field of infectious disease believe that intensification of animal
rearing, the competition of humans and animals for space, and climate change are causing increasingly
more virulent strains of pathogens to emerge and sweep across continents. Currently, the greatest
zoonotic threat – H5N1 avian flu - has emerged largely due to the high density and proximity of
animals and people in Asia. BSE demonstrated that being free from reportable disease is a critical
success factor for the North American animal industry. VIDO/Inervac/Guelph mentions?
Diseases are not the only threat to food production. Increasingly, centralized food production and
processing systems create the potential for significant widespread food-safety problems. The CDC
identified 17,252 confirmed cases of food poisoning in 2006, including 6,655 cases of Salmonella and
590 cases of E.coli O15721. These figures are recognized as being gross underestimates of the actual
burden of disease.
Genomics technology offers potential solutions for maintaining and expanding global animal resources
by providing information to increase efficiency, fight disease and improve biosecurity. A new
understanding of host-pathogen interactions based on genomics research offers the promise of
improved vaccines, new gene-based targets for treatment, better response times to new threats and
the potential to breed healthier animals. The latter may produce animals that better respond to
vaccination, or carry a lower burden of zoonotic organisms, so that greater food safety can be delivered
8
through the food chain. At the same time, genomic information and infrastructure will provide a
critical component to advance biosafety programs with improved traceability, allowing rapid
identification of disease outbreaks or food chain contamination.
THE SUCCESSES – THESE ARE SUBJECT TO DEBATE
VIDO and InterVac – at home on the range
A success story and the potential.
Immunogenomics and animal breeding programs at the University of Guelph successful
research. A success story and the potential.
The Cod Genomics and Broodstock Development Project – a placeholder for Cod research
Traditional fisheries provide an important basis of cultural and economic activity in Atlantic Canada,
although the fisheries for some species such as Atlantic salmon and Atlantic cod have severely declined. The
decline in Atlantic salmon stocks served as an incentive to develop today’s aquaculture sector, which
generates more than $200 million of annual revenue in New Brunswick alone. One approach towards
maintaining growth and stability of the aquaculture industry is diversification into rearing other species such
as Atlantic cod. Current estimates show that cod farming in Newfoundland alone could generate more than
$100 million in new wealth while meeting consumer demand for a high quality food resource. Dr. Sharen
Bowman, a specialist in genome sequencing and annotation at Genome Atlantic’s DNA Sequencing Centre
(located in Halifax, Nova Scotia) and Dr. Ed Trippel of Fisheries and Oceans Canada’s St. Andrews
Biological Station (located in St. Andrews, NB) are project co-leaders of Atlantic Cod Genomics and
Broodstock Development Project (CGP) which encompasses cod broodstock development in New Brunswick
and Newfoundland. Cod breeding programs are also being developed in countries such as Norway and
Iceland. The Canadian aquaculture industry recognizes that broodstock selection is essential in order to
produce superior cod stocks for farming. The CGP is a partnership with industry, universities, government
and Not-for-Profit organizations and will apply genomics technologies combined with family-based selective
breeding methodologies to identify cod with traits of commercial importance, such as improved growth,
delayed age of sexual maturation and resistance to disease and stress. The project will sequence genes in
order to identify molecular markers that are associated with superior performance under farming conditions.
To date, the CGP has dramatically improved availability of genomic resources for cod. Approximately
158,000 sequences have been submitted to GenBank. Genes of interest have been selected and development
of a 20,000 element oligonucleotide microarray is underway. Development of gene-linked markers and a
high density genetic map is ongoing. Marker identification has yielded >4,500 “predicted informative” SNPs
and >140 microsatellite markers. A substantial investment has been made by Genome Canada and other
partners to fund the CGP (www.codgene.ca). Resources developed by the CGP will enable marker assisted
selection, and provide valuable tools for researchers interested in Atlantic cod.
Alberta’s Bovine Genome Project
THE CHALLENGE
The Need
Realizing the promise of genomics for animal-based industries requires a rate-step change in Canada’s
approach to genomics research. Canada’s previous investments have laid the foundation and
demonstrated the tremendous potential of this new technology. However, an integrative pan-Canadian
approach is now required to implement truly large-scale research and fully address the needs and
opportunities of the animal-based industries and consumers. Information about how the genetic makeup of an animal impacts its physical characteristics (or phenotype‡‡) is critical to harnessing genomic
‡‡
Definition – Phenotype: the set of observable characteristics of an individual resulting from the interaction of its
genotype with the environment. Genomics seeks to study and find variation in genes that contribute to the phenotype.
9
information, but is difficult and expensive to quantify. Thus far, the small-scale, slow-pace, or
inability to link genomic features with physical characteristics have contributed to what is essentially a
“phenomic roadblock” to the utilization of genomic information; that is, there is presently a dearth of
phenotypic information for many different biologically, environmentally, and economically important
traits to inform how the genome is physically manifested§§. Similarly, the relatively small animal
research populations that have been used in the past have not had sufficient statistical power for the
discovery of genes involved in complex genetic traits (e.g. traits conferring efficiency or disease
resistance). The large-scale collection of genomic-phenotypic data coupled with an IT-driven
bioinformatics platform represents a critical next step for Canada’s animal genomics research
communities. Canada also needs to make the critical investment to create high quality reference
sequences as part of international consortia, so that collected phenotypic data can be appropriately
matched to a complete, high confidence genomic map. Both efforts require an integrated approach***
with the participation of all sectors, including academia, government, and industry, together with
international partners, in order to achieve the necessary scale. Only through a large-scale biology
approach will researchers be able to tackle global problems, develop greater insights, and make faster
progress than is possible by using only models or experimental systems.
The sustained development of genomic approaches in medicine has led to breakthroughs in
understanding the molecular basis of human diseases. Parallel research in agriculture is beginning to
impact farmed animals though the identification of production-relevant traits (e.g. milk production,
meat marbling). Likewise, continued development of genomic resources for animals, coupled with an
integrated effort to collect richer phenotypic information (including information on the environments
where animals are produced), together with experimental and commercial applications of these tools
and integrated GE³LS research, will allow Canadian scientists to retain their current competitive edge
and to build upon established interactions with complementary international programs (e.g. USA, EU,
Australia, NZ for pigs and cattle; Norway, UK, Japan for fish). This approach is in line with international
best practices, exemplified by the UK BioBank and the Wellcome Trust Case Control Consortium
(WTCCC), which recently reported the analysis of almost 10 billion pieces of DNA, collected from
17,000 people. Their findings, reported in Nature, reveal novel insights into complex disease that
would not have been possible without this scale of research. Included in the discoveries are new
evidence for genetic linkages with Type 2 diabetes and obesity, and the identification of DNA regions
previously unrecognized for their role in disease22. The ATAG theme will create the animal equivalents
of the BioBank and WTCCC, although its scope will be beyond common diseases. This research will
provide essential information for Canadian industry, stakeholders and policy makers to address rising
international competition and to focus on climate change, environmental footprints, food safety and
sustainable production.
State of the Science
Genomics underpins biological research based on the accumulation of significant resources such as
DNA libraries, expressed sequence tags (ESTs), microarrays, single nucleotide polymorphism (SNP)
panels - resources that are now, or soon will be, supported by genome sequences for chicken, cow, pig
and horse. Many of the resources have been generated by international consortia, which include
significant contributions from Canadian scientists. Some of the most important genomic resources in
existence for fish species have been built in Canada using Genome Canada funding. Pioneering work on
the application of proteomics and metabolomics for the study of fish has also been undertaken in
Canada. These projects are creating the tools that can be used to improve Canada’s position in the field
of animal genomics.
Success depends on having rich descriptions of the phenotype (and the environment) of an animal as well powerful
genomic technologies (DNA sequence etc).
§§
Simply stated the areas that hold the greatest potential are those that are traditionally data scarce – because the traits
that need to be investigated are technically difficult and/or expensive to measure. This gap is consistent around the
world and there are significant rewards to be obtained for the groups that are able to take the lead in removing the block
(see Ref 30).
***
also advocated by Industry Canada (Ref 23).
10
Indeed, genomic resources for animals have now run ahead of our ability to apply them to the most
important questions and to create competitive advantage for Canadian industry. Enabling the
production of new products tailored to the changing demands of consumers is of vital importance and
an Industry Canada goal23. The challenge is to create a program that can translate the potential of
genomics into real benefits for Canada’s citizens and its economy. This challenge can only be tackled by
addressing the “phenomic roadblock”. Detailed characterization of phenotype (essentially, “case
definition”, as is well understood in the human health field, and exemplified by the Wellcome Trust
Case Control Consortium22) is crucial to the dissection of the complex traits that need to be studied.
The “phenomic roadblock” described above cannot be removed using academic research populations
alone; it requires industry participation, such that samples and data are created as a partnership. Such
a partnership would then be able to tackle global problems, develop greater insights and make faster
progress with their existing resources (including databases and research populations). Indeed, the
direct involvement of those rearing and using the animals will make it more straightforward for the
implementation stage of the research. Such an approach would also increase the attractiveness of
industry participation, allowing new opportunities for funding and in-kind contribution related to the
animal resources.
The theme will establish a research program capable of delivering on the key aspects of sustainability:
improved efficiency and improved animal health. Such an approach will truly mobilize existing
genomics resources to create new research outcomes that will provide applications within the next
five years. In addition, this theme will integrate GE³LS research to understand the implications of
potential applications, as well as how these applications might be integrated into existing policy,
industry and normative frameworks, to help realize the benefits of animal genomics. This next phase of
animal genomics will be based on Canada’s acknowledged strengths in animal breeding, production
and product processing as well as its proven ability to support the highest standards of animal health
and food safety. With this in mind, we believe that it is a realistic ambition for Canada to assume a
leading role in this coming stage of development.
A Vision of Efficiency and Health
The plummeting cost of gene scanning and the emergence of gene chip technologies over the last 2
years make this a better time than at anytime in the past to realize the promise of genomics for animal
research24. The Bovine Genome Sequencing project provides a good example in the recent
development of the 50,000 SNP chip, a breakthrough in high-throughput technology. By addressing the
“phenomic roadblock”, we will quickly be in the same position as human health researchers who can
scan the genomes of thousands of people and, by comparing the clinical and physiological profiles of
sick and healthy people, uncover markers for diseases such as diabetes, cancer and Alzheimers24. This
theme, will capitalize on state-of-the-art techniques developed in medical genomics by applying them
to animal research. By scanning the genomes of thousands of animals in different environments, and
by comparing different phenotypic classes - sick with healthy, efficient with inefficient, desirable with
undesirable - researchers will uncover markers and environmental influences they can use to deliver
healthier, higher quality, sustainable food to Canada and the world.
Large-scale population genomics will be statistically powerful. The ability to collect multiple sets of
information for the same animal and its relatives means that animal researchers can drive forward
with a speed and breadth of focus that exceeds that found in human genomic research (obviously,
dependant on the availability of resources). For example, we will be able to know the impact of a gene
variant that contributes to reduced load of Salmonella on traits such as feed conversion, organ
function, physical conformation and overall longevity. We will also be able to tease apart the
interactions between genotype and environment, including nutrition or disease treatment, which will
in turn provide benefits in improving human health. Creating these foundational resources will be a
critical feature in fostering investment and creating a climate that encourages entrepreneurship and
private sector investment.
11
Canada’s Advantage
Canada’s tremendous potential for genomics and existing value added genetic capabilities can be
attributed largely to previous and ongoing investments by Genome Canada and co-funders. Canada
also has a long history of successful investment in animal genetics and production that can be built
upon. Several projects in particular highlight the current level of interest and strategic leadership
already initiated by, or related to, investment by Genome Canada: The consortium for Genomics
Research on All Salmonids Project (GRASP), The Cod Genomics and Broodstock Development Project
(CGP), Pleurogene (halibut), Functional Pathogenomics of Mucosal Immunity (FPMI), Pathogenomics
of Innate Immunity (PI2) and the Alberta Bovine Genomics Program (including the Genome Canada
investment in the international bovine genome sequence consortium). Genome Canada has funded
successful GE3LS research projects related to animal genomics including both large-scale stand alone
and integrated GE3LS research projects25. The GE3LS component of Advanced Foods Materials
Network, highlights the successful investment in GE3LS related to food, health and biotechnology26.
Examples of specific outcomes are provided in Table 1.
Critical Components
Data collection
Significant resources will be required in order to achieve the quality and depth of biosamples,
and trait and genomic data needed to overcome the “phenomic block” and drive the research
to achieve the desired short and mid-range (i.e. five years) outcomes. This theme will also
incorporate the measurement of environmental contributors to the traits of interest such as
type of husbandry system, health treatments, measurement of toxins, diagnosis of pathogens
and disease, diet, physical activity, behaviour, and markers of stress. These aspects will be
incorporated into the bioinformatics aspects of the theme so as to construct a fully accessible
phenotypic database capable of sustaining the next phase of animal genomic research. In
addition, technologies suitable for use with stored biosamples will be expected to be fully
incorporated into the projects within the theme. These would include histological approaches
as well as transcriptomics, proteomics and metabolomics in order to provide the most
detailed phenotypic information possible, including data on structure and substructure within
samples (tissues, organs, etc.).
Linking basic data and phenotypic outcomes
Achieving coordination of resources is an important concept in this theme. In particular, this theme
will focus on enabling effective cross study analysis between large scale population studies and small
scale studies with the aim of complimenting both resources. This will require similar measures of traits
and environmental factors or the use of genetically related individuals (potentially, there would be the
opportunity to employ somatic cloning in the context of livestock). Accordingly, the theme will seek to
include a coordination activity, with an integrated strategy for sample collection and analysis, to
support the animal genomics initiative and maximize the use of the resources as they are developed.
Genome Canada has already pioneered the development of such approaches (e.g. BioMoby:
http://www.biomoby.org/) by supporting the creation of bioinformatics networks and infrastructure
that can support bioinformaticians embedded within research groups and their laboratories. By
harnessing these dispersed infrastructure pieces, it will be possible to create an integrated community
of animal researchers able to mine the assembly of resources without the need for extensive additional
IT infrastructure. Furthermore, linkages with human health research will extend the utility of these
resources to both animal and human researchers for an added level of multidisciplinary collaboration.
GE3LS Research - this area was of concern for reviewers (could use some project specifics)
This section needs additions/modifications to demonstrate capacity to deal with environmental health
and rural development.
Animal genomics research raises a number of ethical, environmental, economic, legal and social
challenges for industry, government, consumers/ citizens, animals, and the environment. These
12
challenges require social science and/or humanities research. For example, public surveys
consistently show greater public concern for animal genomics and biotechnology than for plant
genomics and biotechnology27. One challenge will be to create a program that will translate the
potential of animal genomics into real benefits for Canadian citizens and the economy. Thus it will be
critical to understand the ethical, environmental, economic, legal and social implications of potential
approaches to and outputs from animal genomics research. This theme will draw upon the
internationally recognized Canadian GE³LS community to incorporate both integrated and stand-alone
GE³LS projects that are relevant to the science of animal genomics.
A recent review of Canadian GE³LS research and interviews with Canadian GE³LS researchers suggest
a number of key social science and humanities research areas in animal genomics that are ripe for
study28. The most commonly citied research areas were governance and social acceptability, including
risk assessment, public perceptions and concerns, policy and regulatory responses, and public
engagement. Industry Canada’s framework for mobilizing science and technology calls for Canada to
become a “best-in-class regulator”29. Other research areas include industry innovation strategies and
associated employment and economic growth, the capacity for regulatory responses to developments
in animal genomics in light of rapid scientific developments, potential environmental risks, animal
health and welfare, knowledge translation of developments in animal genomics to communities and
policy-makers, and global equity. Throughout genomic research there is a need to better understand
public values, perspectives and perceptions on key technological, policy and ethical issues. Questions
that could be addressed include, for example: whether there is a public policy distinction between
genomic manipulation within species versus across species; how is the distinction unfolding and what
are the implications; what is the role of genetic researchers in protecting the welfare of animals; are
current policy frameworks for genomics appropriate, and what are the alternatives?
Experience to date on the sensitivities around genetically modified organisms (GMO’s) provides a case
in point; industry is increasingly interested in public opinion and, in particular, the potential influence
of the public’s perceived negativity toward genetically modified products and what impact this may
have on non-genetically modified applications derived from animal genomics. Similarly, concerns
around cloning and stem cell research highlight the need to conduct to research to understand the
perspective of policy makers and regulators in the area of animal genomics. Knowledge translation is
critical in these areas (as well as achieving industry application) and raises important questions
related to the dissemination of knowledge, such as: what are the best vehicles for knowledge transfer,
and the varying information needs of public and private stakeholders? Research undertaken as part of
this theme would address these questions within the context of each specific research project,
ensuring that beneficial outputs are maximized through optimal positioning and communication.
Considerable investment is required to support animal genomics and the economic consequences need
to be studied. GE3LS research would include key considerations for commercialization and
entrepreneurship involving science in this area, including: (1) intellectual property (e.g. patentability
of genotype/phenotype correlations) including research into the problem of differing institutional
intellectual property (IP) policies given the increasing pressure to build cross-institutional research
networks and collaborations; (2) the role of differentiation in market value (relevant to traceability of
food animals); and, (3) the impact of current policy and regulatory frameworks. GE3LS studies will
illuminate these issues and contribute to informed regulatory decision making on policy and public
safety concerns.
CANADIAN HUMAN RESOURCES AND INFRASTRUCTURE
As described in previous sections, this theme proposes an integrative large-scale partnership approach
to creating a pan-Canadian effort in animal genomics. Potential contributors to this effort include
industry, government, and academic groups, as well as international collaborators. A list of groups that
have expressed interest in participating in this theme is available on the website. At the time of writing
this group included 36 representatives from industry, 13 representatives from government, 56
researchers, and 21 correspondents from outside Canada (please refer to Table 2 and supplementary
13
web-page list of resources). Together, this group brings a tremendous array of genomic resources to
bear on this theme.
OPPORTUNITIES FOR LINKAGES WITH INTERNATIONAL EFFORTS – (LINKS TO AN INT’L PROJECT OR TWO)
The issues and opportunities identified here are international in scope. The need for enlarging the
scope of data that is collected on animal populations in order to harness genomics resources to deliver
the desired outcomes is widely recognized30. New research programs exist (e.g. the Cooperative
Research Centres in Australia, the European Seventh Research Framework Programme (FP7)) or are
being developed (e.g. by the USDA), that provide opportunities to establish significant international
collaborations for ATAG projects. In addition, we anticipate that there will be important opportunities
to develop collaborative efforts with countries where the demand for animal protein is increasing (e.g.
China). International collaboration is likely to be an essential feature for projects that focus on
genotype-environment or host-pathogen interactions. GE3LS research will provide further insight on
opportunities and best-practices in engaging international collaborators, and capturing maximum
value from opportunities outside Canada.
PROPOSED BUDGET
Canada has the capacity to conduct at least 8 major projects over the next four years with an average
project budget of $10-15 million. These would include the establishment of several strategic reference
population projects, particularly those involving large numbers of commercially relevant animals, and
support for several comparative genomics projects. ATAG will integrate GE3LS activity within the
major projects, but will also provide approximately five percent of the project funding for a standalone GE3LS project addressing the strategic needs of the theme. In addition, we envisage that a
significant component (up to $25 million) will need to be included for coordination and infrastructure,
including distributed bioinformatics and the archiving and curation of theme resources. Considering a
50/50 cost sharing funding formula, the Genome Canada contribution would be $60-85 million, with
the remaining contributions to come from industry partners, the provinces, the Canada Foundation for
Innovation and international collaborators.
In developing 8 major projects, the ATAG theme aims to develop outputs that will have a significant
impact on the Canadian animal industry sector. This will be achieved by improving the efficiency and
health of Canadian production. Animal breeding typically generates an improvement of two to three
percent annually for cattle, pigs, and poultry; an additional increase of as little as half a percentage
point as a result of ATAG provides a reasonably conservative estimate that, nonetheless, translates into
approximately $175 million per annum from a sector that currently has a value of $35 billion†††. This
provides a rapid payback on the investment proposed for ATAG. Other long-term benefits are also
anticipated, not least of which would be improved health resulting from infectious disease prevention
and nutritional advances impacting on chronic disease. Beyond this rough quantitative estimate, some
other intangible benefits that will accrue are illustrated by the following examples (see also Table 2):
 Improvements in animal productivity will result in a reduction in input costs and a
concomitant reduction in methane emissions;
 Improved rates of reproduction will lead to improvements in overall efficiency;
 Reduced variation in product quality will lower costs and improve customer satisfaction;
 Reduction in susceptibility to specific diseases will result in reduced treatment costs, improved
animal welfare and a lowered risk of antibiotic residues;
 Reduced carriage of zoonotic bacteria such as Salmonella, Campylobacter, E. coli 0157 leading
to a reduction in the number of cases of food poisoning in Canada;
 Improved response to vaccination leading to lower input costs and rates of disease
transmission;
†††
Red meat $14.6 billion www.agr.gc.ca/redmeat/factsheet06.pdf; Dairy $13.0 billion
http://www.dairyinfo.gc.ca/pdf/graph1.pdf, Poultry and eggs 5.1bn http://www.agr.gc.ca/poultry/prindc2006_e.pdf,
Livestock and Aquaculture; Aquaculture $2.5 billion (see Ref 6).
14



Improved management and conservation of genetic diversity (biodiversity) including the
impact of agriculture and aquaculture on wild populations;
Increased transparency on food origins and quality enabled by genomic traceability;
Health benefits arising from reduced levels of food related chronic disease
ANTICIPATED OUTCOMES - NEEDS WOW STATEMENT AT THIS POINT
This theme is uniquely positioned to address key Canadian operational mandates for federally
performed science and technology as outlined by Industry Canada31. In particular, unlike most
research themes, research proposed under this theme will simultaneously impact health, food safety,
and environmental protection, and do so in a way that promotes Canada’s knowledge, people and
commercial advantage. The expected outcomes of the ATAG theme further reflect this uniqueness, with
impact on GE3LS issues, Health issues, and Animal and Food Industry competitiveness.
GE3LS impact – this area was of concern for reviewers
Improvements in our quality of life and standard of living will depend on our success in bringing
scientific and technological innovations to life through social, ethical and legal discourse on scientific
developments. Some of the key benefits that Canada can achieve through a more comprehensive,
strategic approach to science and technology include, encouraging high-quality, well-paying,
knowledge economy jobs, helping to improve our world through scientific discovery, and having a
stronger voice on the world stage. Specifically, GE3LS research to be conducted under this theme is
expected to improve communication about genomics in Canada. This includes understanding public
perceptions, opportunities for linking discovery to commercialization, enhancing the uptake of
scientific knowledge, and informing regulators on current and upcoming issues relevant to the field.
GE3LS research will improve animal welfare through better understanding and communication of
priorities and opportunities within public and stakeholder communities. A priority of GE 3LS research
will be understanding regulatory considerations and implications of work in this area, so as to inform
Canadian regulators, and support Canada’s excellence in regulatory leadership. This research will also
segue into improved positioning on regulatory harmonization and understanding opportunities for
industry advantage and international integration. This will allow GE3LS research in this theme to
increase commercial productivity and international impact. Finally, research supports the promotion
of training and recruitment by communicating issues around productivity, opportunity and
reimbursement to support the attraction and retention of people, towards Canada’s people advantage.
Improved Health – increased detail – Johnes/Crohn’s and …
Animal health and disease prevention are at the heart of this proposal. Research in this theme will
create resources that would make the identification of disease traits possible, enabling approaches to
disease prevention. Economically, it has been estimated that the cost to control a single alien livestock
disease in the US could be as much as $14 billion per year32. This estimate does not include the direct
costs associated with lost animal production or the potential losses that may follow if there is a loss of
market access. In a similar vein, the cost of foodborne illness in Canada has been estimated to incur an
annual cost approaching $3.7billion33. In this light, the proposed investment in genomics research,
which could yield improved diagnostics and biosecurity, is relatively small when compared to the
potential benefits.
It is anticipated that the theme will also provide insights and outcomes on biological pathways that
have application to human health issues. Examples may include obesity and diabetes, muscle and bone
disorders (including osteoporosis), reproductive health, and host-pathogen interactions (infectious
disease and immune response). As a specific example, the cost of sub-clinical Johne’s disease
(Mycobacterium avium subspecies paratuberculosis) is estimated to be $200-250 million per year in
the US and at least $15 million per year in Canada34. Intriguingly, emerging epidemiological evidence
hints at a possible link between Johne’s disease and Crohn’s disease in humans35, potentially
transmitted by pasteurization resistant bacteria in the milk of infected cows. Should such a link be
confirmed, Johne’s disease would emerge as a significant zoonotic infection and its prevention a
priority in terms of both animal and human health. For diseases like Johne’s a major impediment to the
15
prevention strategies is the ability to diagnose preclinical infections. Genomics could provide the
tools to allow this type of pre-clinical diagnosis to occur. Functional genomics is also being used to
analyze responses in infected cattle prior to the emergence of clinical disease. This will provide
another critical component in disease diagnosis and control since cattle with preclinical infections
shed a large number of bacteria into the environment and possibly contaminate the food chain. This is
but one example of an economically important animal disease that also has the potential to affect
human health.
The potential to add value in these areas will be significantly increased over the current state of the
field through the requirement to create detailed phenotypic and genotypic characterization of
environmental factors and the gene by environment interactions. The large population studies
required to target complex polygenic traits and diseases can only be delivered through integration
with partner industries and participants (e.g. livestock producers, aquaculturists, veterinarians,
packers and processors), which in turn creates the opportunity to further enhance the value of the
phenotypic characterization by extending sample and data collection through the value chain.
Examples include carcass and quality evaluation, process interaction, eating quality, and consumer
preference. The samples generated will be well-suited to the application of the latest genomic
technologies, including genome-wide association technology, either as discovery or in validation on
additional samples. This effort will lead to the identification of genetic variants associated with
complex traits and diseases through high throughput, genome-wide approaches (“SNP chips”,
transcriptomics) as well as new diagnostics, vaccines and new “drugable” targets.
Impact on the Agri-Food Industry – Increased detail on livestock breeding
This theme will develop a pan-Canadian initiative for animal genomics to deliver new research
outcomes in the next five years. The theme will maintain and improve Canada’s strengths in animal
genetics, production and processing. An initiative for all animals makes sense at this time; the
sequencing of the genomes of the major livestock species is near completion and tools to compare and
contrast information from different species are available. Such information will increasingly facilitate
rapid progress through the use of comparative genomics to address species specific questions and to
move between model species and experimental or commercial populations of livestock and fish. Where
appropriate, this information will also provide insights for questions relating to human biology and
disease. Bioinformatics will be an essential element of the initiative, ensuring that information is
available for efficient networked collaboration, efficient transfer between species and for translation to
commercial applications.
The vision presented here will have a significant impact on the animal sector, especially for complex
traits such as those impacting animal health, efficiency, reproduction, and product quality and safety.
The opportunity at hand is for Canada to lead the development of genomic-based tools that will be
required to develop sustainable animal breeding and production now and for the future.
CREDITS
This paper has been created through an iterative and broad consultative process aimed at presenting
the perspective of animal genomics stakeholders from a variety of sectors at academic, government,
and industry levels from Canada and internationally. It was initiated from the Expressions of Interest
round of the process. A number of discussions and meetings culminated in the Genome Canada
sponsored workshop of research and industry leaders that took place in Ottawa in May (more than 40
attended). Throughout the writing process draft versions have been made available by wide
circulation and on the theme webpage. Nearly 100 individuals (including 32 from industry) have
expressed support for the paper within 4 days of the latest draft been available by hyperlink. The
writing team is therefore, proud to advance this document as a community initiative compelling the
need for aquatic and terrestrial animal genomics research.
16
APPENDIX
Canada’s Relative Position
Figure 1: Change in Dependency on Food Imports (Source: FAO, 2005);
Figure 2: Change in Food Exports (Source: FAO, 2005)
Figure 3: The ATAG Context
Figure 4: The ATAG Roadmap
Figure 1
Figure 2
1993
billion USD
2003
70
6.4%
60
2.5%
50
2.4% 3.6%
40
4.4%
7.6% -0.7%
10
20
3.8%
0%
3. Netherlands
2. France
15. Hong Kong
14. S. Korea
13. Russia
12. Mexico
11. Canada
10. Spain
9. Belgium
8. China
7. Netherlands
6. Italy
5. France
4. UK
3. Japan
2. Germany
3.1% 17.6%
10
0
0
5.5% 2.7% 3.3%
Figure 4
Figure 3
Global Meat/Protein Supply
Chain
Canada
ATAG Roadmap
World
DNA
Sequences
Genomic and Phenotypic knowledge adds value across the entire Supply Chain
ATAG Theme
Genomics
Sustainability
Efficiency
Value
Health
Phenotype
Gene
Function
13. Argentina
5.9%
4. Germany
5.8%
3.4% 5.6%
15. Thailand
4.9% 8.2% 8.0%
5.7%
3.8%
20
14. Denmark
30
10.6%
12. Australia
4.6%
11. China
2.8%
10. UK
30
9. Canada
3.3%
8. Italy
5.3%
7. Brazil
1.5%
6. Spain
40
1. U.S.
2003
2.7%
5. Belgium
50
1993
billion USD
1. U.S.
60
17
18
Table : Selected Resources Relevant to the ATAG Theme
Species
Bovine
Description
Draft 3.1 of the complete bovine genome sequence
>2m SNPs
50,000 SNP panel in final production phase
Trait markers available for Marker Assisted
Selection/Management
DairyGen announce intention to begin systematic storage of
DNA in Canada for dairy cattle
Rapid response to BSE crisis leading to favorable OIE status
change in May 2007
Porcine
ArrayPipe public analysis of large sets of microarray data.
Format adaptable to any species with annotated arrays.
Whole genome long-oligo expression array now available in
Canada.
Platforms for control of zoonotic bacterial pathogens
developed: world’s first vaccine for E. coli 0157 licensed in
2006
Genome sequence initiated
Trait markers available for MAS
CCSI managed trait database and now include DNA sample
curation.
Maple Leaf create first full-traceability system for pork to
support exports to Japan
Aquaculture
species
Established genomic toolkits for major fish species including
mapping resources
Salmonid cDNA microarrays (now 16k with next generation
24-30k in production). e.g. used to identify host genes
responding to infection P. salmonis, Aeromonas salmonicida
and amoebic gill disease as a route to the development of
effective diagnostics, vaccines and therapeutics.
Aeromonas salmonicida microarray used for investigating
strain-specific differences
Production of cod cDNA microarrays (10-15k) underway
focused on response to pathogens and environmental stress
Production of halibut oligo microarray containing 38,000
features representing 9280 unique genes.
Comment
Co-funded by Genome Canada
Ditto
Alberta Bovine Genome Program
is one of the 3 groups providing
this resource
Significant input from Canada
(ABGP, University of SK)
www.ccnmatthews.com/news/relea
ses/show.jsp?action=showRelease&a
ctionFor=653182&searchText=false
&showText=all
Hokamp et al. 2004. Nucleic Acid
Res. 32: W457-9
Elsik et al. 2006. ISAG
Public-private partnership, UBC,
USask, CMCI, ARC and BNC
Opportunity for Canadian
researchers to ensure that a high
quality sequence exists through a
contribution to sequencing and
SNP identification
CCSI involved in validation and
implementation for Canadian
industry
http://investor.mapleleaf.ca/phoeni
x.zhtml?c=88490&p=irolnewsArticle&ID=547938&highlight=
Led by Canadian researchers
including funding from Genome
Canada
GRASP (Genomics Research on All
Salmonids Project)
NRC-GHI program
The Cod Genomics and
Broodstock Development Project
Pleurogene
19
Multiple
species
Production of halibut genetic linkage map
Canadian Centre for Genetic Conservation established (SK)
InnateDB, a public domain database of pathways involved in
innate immunity for multiple species, established at Simon
Fraser University.
Microarrays (cDNA and oligo) established for avian, bovine
and porcine studies for use in host-pathogen interaction
studies and establishment of innate immunity pathways in
multiple hosts
Establishment of InterVac, Canada’s largest Level III animal
containment facility in SK.
Funding from Genome Canada
“Functional pathogenomics of
mucosal immunity” (FPMI) and
“Pathogenomics of innate
immunity” (PI2)
FPMI & PI2; Bill & Melinda Gates
Foundation consortia
CFI, Govt of Canada & SK-funded
project ($110m).
20
Table 2: Examples of Financial impacts
Impact
Impact on the
environment
Description
$65-155 million cost: Walkerton,
Ontario - Animal by-product related
E. coli O157:H7 outbreak.
Impact on food
safety
$650 million cost: U.S. direct and Frenzen, P.D. et al. (2005)
indirect costs of food-borne E. coli Economic cost of illness due to E.
O157 infections per year.
coli 0157 infection in United
States. J. Food Prot. 68: 262323 million: pounds of meat recalled 2630.
due to contamination in 2002.
Impact on
economy of
BSE
Impact of
genetic
improvement
References
Livernois, J. (2001) The
Walkerton Inquiry: The
Economic Cost of the Walkerton
Water Crisis.
$74 million cost: Contamination of Di Pietro, J. (2005) Risk
spinach by E. coli O157:H7 in the USA Governance for Water Utilities.
and Canada; cost to spinach Bridge-soft Presentation
producers alone.
(www.bridge-soft.com)
$2.7 billion cost: food industry in
recalls, destroyed food, control Meat & Poultry, February, 2003
measures and lost demand due to
loss of consumer confidence in the
U.S. alone.
33%: decrease in family farm Mitura, V. and di Piétro, L. (2004)
receipts after BSE.
Canada’s beef sector and the
impact of BSE on farm family
$5.7 billion cost: estimated negative income 2000-2003. Agriculture
impact of BSE on the Canadian and Rural Working Paper Series.
economy.
Working Paper No. 69. Statistics
Canada Agriculture Division.
75,000: jobs lost after BSE.
Catalogue no. 21-601-MIE- No.
069.
1 month: reduction in time for an
Provided by the Canadian Centre
average pig to reach market weight
for Swine Improvement
over the past 20 years.
1.7 days/year: current rate of
genetic change on time to market.
$14 million: annual benefits of
weight related time reduction on 32
million hogs.
$54 million: annual benefit resulting
from improvements in litter size, lean
yield and feed efficiency
21
Endnotes
1
Agiculture and Agri-Food Canada, 2005. An Overview of the Canadian Agriculture and Agri-Food
System, p.6.
2
Agriculture and Agri-Food Canada, Animal Industry Division. Factsheet 2006
(http://www.agr.gc.ca/redmeat/factsheet06.pdf.)
3
Agiculture and Agri-Food Canada, 2005. An Overview of the Canadian Agriculture and Agri-Food
System, p.viii.
4
Fisheries and Oceans Canada, Fastfacts (http://www.dfo-mpo.gc.ca/communic/facts-info/factsinfo_e.htm)
5
Agriculture and AgriFood Canada, Industry Overview - Canada's Fish and Seafood Industry (http://atnriae.agr.ca/seafood/industry-e.htm)
6
Fisheries and Oceans Canada, Fastfacts (http://www.dfompo.gc.ca/aquaculture/sheet_feuillet/figures_e.htm)
7
For examples, see: Application of genomics to the pork industry, 2005, J. Anim. Sci 83 (E Suppl):E1-E8;
Strategy for applying genome-wide selection in dairy cattle, 2006, J. Anim. Breeding and Genetics, 123:
218-223; Salmonid genetic maps and microarray resources have been produced to find genes impacting
traits such as temperature tolerance and resistance to disease, 2007, Rise et al. in Aquaculture Genome
Technologies ed. Z Liu, Blackwell Publishing, in press.
8
Atlantic cod ($18.2m), GRASP & cGRASP ($20.9m) and PLEUROGENE (~$2m) see
http://www.genomecanada.ca/xresearchers/researchPrograms/projects/index.asp?o=d&d=1&l=e
9
Drivers of Global Change, Oct. 20, 2006 ( http://www.mnp.ca/04library/documents/)
10
Paraphrased from Ted Bilyea (formerly President, Maple Leaf Foods International) speaking notes,
Animal Genomics workshop May, 2007.
11
Globescan, 2003.
12
Eurobarometer, 2007. Attitudes of EU citizens towards animal welfare. Special Eurobrometer 270
(March, 2007). Available at: http://ec.europa.eu/public_opinion/archives/eb_special_en.htm.
13
CANSIM data in The Agricultural Policy Framework (APF) (http://www.agr.gc.ca/cb/apf/index_e.php)
14
Agriculture and AgriFood Canada
(http://www.ats.agr.gc.ca/supply/factsheets/4226_e.pdf and http://www.ats.agr.gc.ca/invest/3840_e.pdf )
15
FAO, The State of World Fisheries and Aquaculture 2006 (FAO Fisheries Department, Rome, 2007).
16
Agriculture and AgriFood Canada, Invest in Canada’s Fish and Seafood Industry – projected value of the
industry in 15 years (http://www.ats.agr.gc.ca/invest/3840_e.pdf)
17
Agriculture and AgriFood Canada (http://www.agr.gc.ca/nlwis-snite/pub/hw_se/pdf/intro_e.pdf)
18
http://www.chinadaily.com.cn/china/2007-06/11/content_891811.htm
19
http://www.avma.org/onlnews/javma/jul04/040701d.asp
20
Attributed to Mark Woolhouse of the University of Edinburgh
21
Centre for Disease Control, 2007.
22
“Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls”
June 2007, Nature 447: 661-678.
23
Mobilizing Science and Technology to Canada’s Advantage (2007). (http://ic.gc.ca/epublications)
24
GENOME-WIDE ASSOCIATION: Closing the Net on Common Disease Genes, Science 316: 820-822,
11 May 2007.
25
http://gels.ethics.ubc.ca:8213/ge3ls-arch/animal-welfare; http://codgene.ca/investigators.php;
http://gels.ethics.ubc.ca:8213/collaborative-projects/cgrasp
26
http://web.uvic.ca/csrs/research/gels.php
27
Epstein, R. 2002. Redesigning the World: Ethical Questions about Genetic Engineering Issues in
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Mobilizing Science and Technology to Canada’s Advantage (2007). p.68. (http://ic.gc.ca/epublications)
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