Progress 07/01/00 to 09/01/04
Outputs
1. What major problem or issue is being resolved and how are you resolving it (summarize project aims and objectives)? How serious is the problem? What does it matter? Currently, it takes too long (years) to identify a DNA marker with a reliable association with a trait. Most traits are affected by many genes so multiple markers are required for each trait. A BAC physical map reduces the time required to identify associations between DNA markers and traits. This report serves to document research conducted under a specific cooperative agreement (see in-house CRIS 5438-31000-071- 00D entitled "Bioinformatics for Livestock" for more details) with The Michael Smith Genome Sciences Centre, Vancouver, BC (http://www.bcgsc.bc. ca/projects/bovine_mapping/). This work was done in collaboration with the International Bovine bacterial artificial chromosome (BAC) Mapping Consortium (IBBMC), including laboratories in the US, Canada, UK, Australia, New Zealand, Brazil and
France. A bovine BAC physical map would reduce the time required to identify genes affecting economically important traits, improve the effectiveness of marker-assisted selection and permit anchoring assembled genomic sequence segments to chromosomes. The Genome Sciences Centre will 1) fingerprint over 300,000 BAC clones, 2) generate over 75,000 BAC-end sequences, and 3) maintain a publicly accessible web site to disseminate the data. A bacterial artificial chromosome (BAC) map of the bovine genome would reduce the time required to identify genes affecting production efficiency, disease, meat quality and food safety; improve the effectiveness of marker-assisted selection; and facilitate assembling the genomic sequence. A BAC map can be used to anchor assembled sequence segments to the bovine genome and to similar sequence on other mammalian genomes. A bovine BAC map will probably accelerate technology development which may be instrumental in maintaining or improving the
competitiveness of U.S. beef production. This research addresses the following goals of the National Program Action Plan for Food Animal Production 101: IV Genomic tools with emphasis on 1. Comprehensive maps, and 5. Bioinformatics and statistical analysis tools. 2. List the milestones (indicators of progress) from your Project Plan. Year 1 (FY 2002) Fingerprint using fragment sizes derived from restriction digests of 300, 000 bovine BAC clones. Year 2 (FY 2003) Sequence both ends of 75,000 bovine BAC clones (150,000 end-sequences). Year 3 (FY 2004) Maintain data on a publicly accessible web site. 3. Milestones: A. List the milestones that were scheduled to be addressed in FY 2004. How many milestones did you fully or substantially meet in FY 2004, and indicate which ones were not fully or substantially met, briefly explain why not, and your plans to do so. Maintain data on a publicly accessible web site. The bovine BAC fingerprint data is accessible from a web site
(http://www.bcgsc.bc. ca/projects/bovine_mapping/) maintained by the Michael Smith Genome Sciences Centre. The BAC-end sequences are accessible at GenBank. Met. B. List the milestones that you expect to address over the next 3 years (FY 2005, 2006, and 2007). What do you expect to accomplish, year by year, over the next 3 years under each milestone? This project is scheduled to terminate in FY 2004. This is the final report. 4. What were the most significant accomplishments this past year? A. Single Most Significant Accomplishment During FY 2004. Bovine BAC fingerprint data is publicly accessible at http://www.bcgsc. bc.ca/projects/bovine_mapping/. BAC-end sequences are publicly accessible at GenBank. Scientists at MARC and elsewhere use these resources to associate bovine chromosomal regions with bovine BAC clones and genes annotated on the human genome. These resources are available to anyone with an Internet connection. This report serves to document research conducted
under a specific cooperative agreement (see in-house CRIS 5438-31000-071-00D entitled "Bioinformatics for Livestock" for more details) with The Michael Smith Genome Sciences Centre, Vancouver, BC. This work was done in collaboration with the International Bovine bacterial artificial chromosome (BAC) Mapping Consortium (IBBMC), including laboratories in the US, Canada, UK, Australia, New Zealand, Brazil and France. B. Other Significant Accomplishment(s). None. C. Significant Activities That Support Special Target Populations. None. D. Progress Report. None. 5. Describe the major accomplishments over the life of the project, including their predicted or actual impact. A bovine BAC physical map is needed to assemble the genomic sequence and identify genes affecting economically important traits. A bovine BAC physical map was constructed through a specific cooperative agreement (see in-house CRIS 5438-31000-071-00D entitled "Bioinformatics for Livestock" for more details) with The
Michael Smith Genome Sciences Centre, Vancouver, BC. This work was done in collaboration with the International Bovine BAC Mapping Consortium (IBBMC), including laboratories in the US, Canada, UK, Australia, New Zealand, Brazil and France. The bovine BAC physical map will reduce the time required to identify genes affecting economically important traits, improve the effectiveness of marker-assisted selection and permit anchoring assembled genomic sequence segments to chromosomes. The Genome Sciences Centre fingerprinted over 300,000 BAC clones and generated over 75,000 BAC-end sequences. The fingerprints are accessible from a publicly accessible web site (http://www.bcgsc.bc.ca/projects/bovine_mapping/) and the BAC- end sequences are accessible at GenBank. Scientists at MARC and elsewhere use these resources to associate bovine chromosomal regions with bovine BAC clones and genes annotated on the human genome. These resources are available to anyone with an Internet connection.
Milestones: Fingerprint using fragment sizes derived from restriction digests of 300,000 bovine BAC clones in FY 2002. Sequence both ends of 75,000 bovine BAC clones (150,000 end-sequences) in FY 2003. Maintain data on a publicly accessible web site in FY 2004. Action Plan components: National Program 101 - IV Genomic tools with emphasis on 1. Comprehensive maps, and 5. Bioinformatics and statistical analysis tools. 6. What science and/or technologies have been transferred and to whom? When is the science and/or technology likely to become available to the end- user (industry, farmer, other scientists)? What are the constraints, if known, to the adoption and durability of the technology products? The restriction-digest BAC fingerprint data are available via the World- Wide-Web (http://www.bcgsc.bc.ca/projects/bovine_mapping/) to the public (other scientists, agribusiness, pharmaceutical industry, farmers). BAC- end sequences are available at GenBank. The bovine BAC physical
map is a relatively basic research tool so benefits will trickle-down to different user groups. The impact or benefit of the bovine BAC physical map will ultimately depend on the success of each user group (scientists, genetic testing companies, cattle breeders and commercial producers) in implementing available technology for the purpose of providing a safe, healthy, tasty and affordable product to the consumer. Scientists use the bovine BAC physical map to develop improved markers with stronger associations with economically important traits. Genetic testing companies use these markers to provide improved tests. Cattle breeders improve genetic and management decisions resulting from access to new and better genetic tests. Commercial cattle producers have access to improved breeding animals at a reasonable cost because cattle breeders make better selection decisions based on more accurate markers.
Impacts
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Publications
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