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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