Download List of Successful Pre-Applications

2014 Large-Scale Applied Research Project Competition:
Genomics and Feeding the Future
Successful Pre-Applications
Lead Genome Centre
Co-Lead Genome Centre
Genome British Columbia
Project Leader
Last Name
Cross
Co-Project Leader
Last Name
First Name
Suttle
Curtis
Lead Organization
Title of Registration
First Name
Stephen
University of Victoria
Adapting to Climate Change - Applied
Genomics for the Development
of Sustainable Shellfish Aquaculture
Keywords
Research Areas
Methods/ Technologies
shellfish production; pathogen discovery, impacts and High throughput sequencing, molecular pathogen
monitoring; ocean acidification impacts; quantitative monitoring platform, high throughput quantitative PCR,
trait loci; marker-assisted selection
genetic selection, functional genomics
Genome British Columbia
Genome Quebec
Davidson
William S.
Bernatchez
Louis
Simon Fraser University
Enhancing Production In Coho: Culture,
Community, Catch (EPIC4)
Coho Salmon; population genomics and adaptive
variation; conservation units; hatcheries and
enhancement effectiveness; aquaculture.
SNP discovery by de novo next generation sequencing;
high-throughput SNP genotyping; population genomics;
parent and population assignments; genome wide
association studies and gene mapping.
Genomics, proteomics, genotyping, animal breeding
Genome British Columbia
Ontario Genomics Institute
Foster
Leonard
Zayed
Amro
University of British Columbia
Sustaining and securing Canada’s honey
bees using ‘omic tools
Genome British Columbia
Rieseberg
Loren H.
Burke
John M.
University of British Columbia
Genomics of Abiotic Stress Resistance in
Wild and Cultivated Sunflowers
Genome Alberta
Basarab
John
Berry
Crowley
Donagh
John
Alberta Agriculture and Rural
Development
Development and deployment of next
generation genomic technologies in the
beef cattle industry
Selective breeding, marker-assisted selection,
disease resistance,
pollination, importation
Abiotic stress resistance, agricultural genomics,
Association mapping, high-throughput genotyping and
ecophysiology,
phenotyping, gene
evolutionary genomics, wild and cultivated sunflowers regulatory analyses, physiology of abiotic stress resistance,
population
genomic analyses
Feed efficiency, carcass quality, methane emissions, Genomic prediction models, multi-trait selection indices,
beef sustainability; Economic and environmental
cost-effective low density genomic panels, vast sequence
impact of multi-trait genomically enhanced selection data; Farm level simulation and optimisation modelling to
indices, public acceptance of genomically enhanced determine economic values of performance traits,
selective breeding, societal value of environmentally interviews, surveys to develop profile of cow calf producers
friendly beef production, stakeholder perception on
as early to middle to late adopters of technology, focus
emphasis on feed efficiency in breeding goals,
group engagement throughout, surveys to ascertain social
market level socio-economic impacts of research
values associated with environmentally enhanced feed
adopted by cow calf producers
efficient beef production, market level modelling of trade in
cattle, beef and genetics impacts on producer, consumer
and social welfare in Canada and the rest of the world.
Genome Alberta
Genome Prairie
Dyck
Michael
Harding
Kemp
John
Bob
University of Alberta
Application of Genomics to Improve
Disease Resilience and Sustainability in
Pork Production
Pig health and welfare, reduction of antibiotic use,
health and immunocompetence, gut microbiota and
immunity, economics and adoption, pig robustness to
disease challenge; Public attitudes, producer
perceptions and behavior; Complementarity of
vaccination, antibiotic use and genetic selection for
increased pig robustness to diseases; Social benefit;
Sustainability
Transcriptomics, metagenomics, computational biology,
phenotyping, genotyping and sequencing with genome wide
association studies, genetic and genomic selection, disease
challenge studies; Public focus groups, surveys & economic
experiments to determine stated and revealed behavior;
farmer focus groups, surveys and simulation models to
extrapolate impact of different technologies across time
given producer behavior and public acceptance;
experiments with farm input suppliers (breeding companies
etc.) to determine likely competitive strategies for
sales/promotion of different technologies to farmers
Genome Alberta
Genome Quebec
Guan
Leluo
McAllister
Tsang
Tim
Adrian
University of Alberta
Genomics-based enhancement of fibre
digestion in cattle
Rumen microbiome, Fibre digestion, Host-microbial
interactions, Transcriptomics, Proteomics; Economic
analysis, Drivers of technology adoption, Impacts of
land-use change on carbon sequestration and
biodiversity, Communication and economic
modelling, Public perceptions
Amplicon sequencing, RNA-seq, Mass spectrometry,
Enzyme characterization, Microbiome transfer; Cost/benefit
analysis, Mathematical programming with partial equilibrium
/factor analysis, Focus groups, Models of science
communication, Deliberative public dialogues
Genome Alberta
Ontario Genomics Institute
Miglior
Filippo
Stothard
Paul
University of Guelph
Increasing feed efficiency and reducing
methane emissions through genomics: a
new promising goal for the Canadian dairy
industry
Genomic selection for feed efficiency and reduced
methane emission, Use of milk spectral records to
predict feed efficiency and methane emission, Use of
whole-genome sequencing, variant discovery and
functional studies to identify key genomic areas and
genes that affect feed efficiency and methane
emission; 1) Socio-economic impacts of dairy
genomic selective breeding for feed and
environmental efficiencies; 2) Determinants of
producer adoption of genomic information in breeding
decisions; 3) Market level implications of producer
adoption of genomic selection in terms of prices,
costs, structure of dairy industry in Canada; 4)
International market effects of the use of genomic
selection on exports of dairy genetics; 5) Public
support for the use of genomic information in
selective breeding for feed efficiency in dairy
production.
Genomic evaluations, genome wide association study, fine
mapping, gene discovery, cost-benefits economic study; 1)
Public focus groups, surveys, and economic modelling; 2)
Dairy producer focus groups, surveys and farm level bioeconomic models reflecting diversity in farms and farmers
across the country; 3) Market level models for the dairy
industry in Canada and the global dairy genetics market; 4)
Market level modelling of greenhouse gas impact based on
producer adoption and carbon credits for greenhouse gas
abatement.
1
2014 Large-Scale Applied Research Project Competition:
Genomics and Feeding the Future
Successful Pre-Applications
Lead Genome Centre
Co-Lead Genome Centre
Title of Registration
First Name
Randall
Co-Project Leader
Last Name
First Name
Rahman
Habibur
Lead Organization
Genome Alberta
Project Leader
Last Name
Weselake
University of Alberta
Genomic Tools and Selection for High
Performance Canola (GTS-HPCan)
Genome Alberta
Wishart
David
Facchini
Peter
University of Alberta
PhytoMap – Using Omics to Understand
and Improve Canadian Food Crop Yields,
Quality, Sustainability and Health Benefits
Application of Genomics to Innovation in
the Lentil Economy (AGILE)
BlueAG (Breeding Linum Enhancements
through Applied Genomics)
Genome Prairie
Bett
Kirstin
Vandenberg
Bert
University of Saskatchewan
Genome Prairie
Genome British Columbia
Booker
Helen
Deyholos
Mike
University of Saskatchewan
Genome Prairie
Genome British Columbia
Potter
Andrew
Hancock
Bob
University of Saskatchewan
Genome Prairie
Pozniak
Curtis
Sharpe
Andrew
University of Saskatchewan
Genome Prairie
Sharbel
Tim
Ontario Genomics Institute
Grbic
Miodrag
Ontario Genomics Institute
Pauls
K. Peter
Ontario Genomics Institute
Somers
Daryl
McCourt
Ontario Genomics Institute
Walker
Virginia K.
Ontario Genomics Institute
Wright
Stephen I.
Genome Québec
Belzile
Genome Québec
Dent
Vojislava
Genetic diversity, adaptation, domestication,
molecular breeding, lentil
Genomic selection (GS), flax, Linum usitatissimum ,
Genomic estimated breeding value (GEBV); Reverse
genetics
Johne’s disease, bovine tuberculosis, vaccine, gene
expression
Reverse Vaccinology Approach for the
Prevention of Mycobacterial Disease in
Cattle
2
chromosome sequencing, gene regulation,
Canadian Triticum Applied Genomics (CTAGWheat,
)
epigenetics, recombination
Comparative genomics of apomictic plants: Apomixis, heterosis, niche breeding, biodiversity,
a first step towards niche breeding
seeds
University of Saskatchewan
Grbic
Keywords
Research Areas
Methods/ Technologies
Increasing seed oil content and yield in Brassica
Comparative functional genomics (transcriptomics and
napus through genomics-assisted breeding;
metabolomics); Targeting Induced Local Lesions in
comparative functional genomics of embryo specific Genomes (TILLING) and whole-genome sequencing; plant
and maternal effects; identification and validation of biochemistry, developmental biology and genomic selection;
molecular targets; implement in combination with
assessment of different Brassica populations and
known molecular targets to generate new improved
computational biology including identification of causal
canola lines; Willingness-to-pay for improved canola variants from high-density markers responsible for oil
cultivars; segregation and supply chain economics;
content and yield; Contingent valuation and choice
differentiated products and international trade;
experiments; representative farm modelling; producer,
acceptance of genomics-based improvements by
consumer and processor surveys; trade simulations;
producers, processors and consumers; regulatory
behavioural economics experiments
systems
Food plants, primary and specialized plant
Next-generation sequencing and transcriptomics,
metabolism, agriculture and horticulture,
bioinformatics, metabolomics, metabolic engineering; Public
nutraceuticals; Public perception from farm to table, surveys and science cafes, focus groups and demand
food genomics regulation, food labeling in the postsystem modelling of consumer behaviour, in-depth
genomics era, updating and refining the Canadian
interviews with food producers and processers, engagement
Nutrient database to reflect more accurate measure with public policy makers, patent surveys.
of current nutrient content of foods, patent landscape
and knowledge translation
Re-sequencing, phenotyping in field setting, association
mapping, database development and integration
GS statistical models based on the relationship between
phenotypes and genome-wide dense genetic markers;
genomics based technologies
Reverse vaccinology, bioinformatics, gene expression,
kinome
Next generation sequencing, transcriptome analyses, allele
mining, bioinformatics, phenomics
Single molecule sequencing, Nano channel array mapping,
epigenome profiling, evolutionary genomics
University of Western Ontario
Translational Genomics in Agricultural Pest Plant-pest-environment interaction; Plant host
Integrative and comparative genomics, metabolomis,
Management, Trans GAP-M
resistance; Pest adaptation to plant hosts/pesticide
transcriptomics, proteomics, bioinformatics
resistance; Development of plant-derived
biopesticides; Development of bioinformatics tools for
the integration of ‘omics’ data
University of Guelph
Applying Idiotype Breeding in a Post
Phenotype, genotyping, agronomic performance
Genomic Era to Increase Bean Productivity, (yield, production efficiency), seed quality
Healthfulness and Sustainability
(healthfulness, nutraceuticals); Cost-effective
molecular tools for improved genomics-based
selection; Investigate the effects of polymorphisms in
noncoding regions; promoter, intergenic, small RNA,
retrotransposon; effectiveness of Canada-wide
genomic ideotype selection; Determine consumer
preferences (GELS component)
Genotyping by sequencing 1000 Canadian bean breeding
genotypes, provide end data to publicly accessible genomic
databases such as Genebank; Phenotyping in field settings
for yield, disease resistance, N2 fixation ability , seed coat
colour; Characterization of value – added biochemical and
healthful properties of bean breeding lines; Use and
ideotype approach to breed internationally competitive bean
varieties for production in distinct geographic regions in
Canada; Bean variety development, registration and
commercialization
Peter
Vineland Research and Innovation
Centre
Improving the resilience of Canada’s
tomato crop to climate and abiotic stress
Abiotic stress, tomatoes, greenhouse production,
temperature extremes, light intensity
Reverse genetics, forward genetics, protein-interaction
networks, marker-assisted breeding
Lougheed
Steve
Queen’s University
Stinchcombe
John
University of Toronto
Towards a sustainable fishery for
Nunavummiut
Population genomics of herbicide
resistance: improved prediction and
management of herbicides in Canada’s and
North America’s worst agricultural weeds.
Fish stocks, genetic diversity, microbiome,
pathogens, contaminants
Herbicide resistance, weed science, agricultural
genomics
Bioinformatics, next generation sequencing, Illumina ddRAD
SNPs, Ion Torrent metagenomes
Population genomics, genome-wide association studies,
comparative genomics
François
Bélanger
Richard
Université Laval
SoyaGen: Improving yield and disease
resistance in short-season soybean
Soybean, maturity, yield, disease resistance,
adaptation
Joseph
Prichard
Roger
McGill University
Identification, validation and diagnostic
testing of drug resistance markers in
nematode parasites of livestock
nematodes, parasites, anthelmintic resistance,
sheep, cattle
Whole-genome resequencing, genotyping by sequencing,
genomic selection, DNA markers, race/biotype-specific
markers
sequencing, bioinformatics, surveys, genotyping
2
2014 Large-Scale Applied Research Project Competition:
Genomics and Feeding the Future
Successful Pre-Applications
Lead Genome Centre
Co-Lead Genome Centre
First Name
Frédéric
Co-Project Leader
Last Name
First Name
Robert
Claude
Lead Organization
Genome Québec
Project Leader
Last Name
Fortin
Title of Registration
Genome Québec
Goodridge
Lawrence
Levesque
Roger
McGill University
A Syst-OMICS approach to ensuring food
safety and reducing the economic burden
of Salmonellosis
Comparative analysis of genomic diversity of
Salmonella serovars, virulence and pathogenicity,
biofilms, foodborne pathogenic bacteria and
attachment to plants
Crop microbiomes, agroecosystem, nutrient use
efficiency, cropping systems, mycorrhizal fungi
Research Areas
Use of Novel Phenomic and Genomic
Deep phenotyping of pigs, genomic evaluations,
Technologies to Optimize Pig Performance, epigenomics and transcriptomics, productivity and
Welfare and Carcass Value
welfare, product quality
CDPQ
Keywords
Methods/ Technologies
Emerging technologies (computer vision,
nanotechnologies,etc.),
SNP genotyping and whole genome sequencing,
development of low density SNP panels and imputation,
breeding program optimization
Whole genome sequence analysis, bacteriophage based
biocontrol,
Improved diagnostics and more discriminatory bacterial
strain subtyping
methods
Metagenomics and metatranscriptomics; amplicon
sequencing, MiSeq, HiSeq and shotgun sequencing;
genomics, bioinformatics & biostatistics; qPCR & TaqMan
probes; agronomic field trials, field surveys & greenhouse
assays.
High throughput transcriptome sequencing, Bioinformatics,
Genome Québec
Genome Prairie
Hijri
Mohamed
Hamel
Gan
Chantale
Yantai
Université de Montréal
Microbiome-driven soil fertility to enhance
major crop productivity while reducing
fertilizer use
Genome Québec
Genome Atlantic
Stromvik
Martina
Tai
Helen
McGill University
The Potato Leaf Doctor: A genomics tool to Potato
guide fertilizer use in potato
Gene expression indicators
Environmental sustainability
Best Management Practices (BMP) for fertilizer
management
Precision agriculture
The Economic, Social and Policy
1. What are the economic impacts on agricultural
Implications of Next Generation DNA
producers of different management practices to
Sequencing for Animal Disease and
address animal disease and AMR?
Antimicrobial Resistance Prevention
2, Are consumers willing to pay for increased food
safety and reduced AMR?
3. What is the economic impact on the agriculture
and food value chain of developing the NGS platform
and new policy environment?
4. How will the development of the NGS platform and
database tools impact animal disease transfer, AMR,
and human health?
5. What are the macroeconomic impacts of
developing an NGS platform to prevent animal and
human disease and reduce AMR?
Genome Québec
Thomassin
Paul
McGill University
3
Field experiments, Multi-Spectral imaging, RNA biosensors
System Dynamics Modelling, Choice Modelling,
Representative Farm Modelling, Input-Output Modelling,
Computable General Equilibrium Modelling