Data Sharing Plan

The Canadian Cattle Genome project is working with the major Canadian cattle breed associations, partnering institutions, and commercial companies to sequence and genotype cattle to develop procedures to provide low-cost but accurate genome-wide selection methods for breeders. In order to accomplish this samples containing DNA (semen vial, semen straw, blood, tail hair, tissue) from key sires, both current and historical, are being acquired from the breed associations and individual breeders and farmers. Here we describe what will be done with that data.

For farmers and breeders

Any person or group that provides a sample (semen vial, semen straw, blood, tail hair, tissue) to the project will have access to the data from that animal (DNA sequence and/or genotype). This information may be shared with the relevant breed association at his/her discretion. All data will be accessible through the Project’s website (www.canadacow.ca) under a unique login that will be provided. This information will be stored on the website for a minimum of 2 years after the completion of the project.

The Project will sequence approximately 30 individual cattle from each breed and complete high density (HD) genotyping (680K or 770K) on approximately 480 cattle and 50K genotyping on approximately 500 cattle in each population, depending on strategic importance to the project, and considering available resources. Additional individuals may be genotyped (e.g. RFI tested animals) but this will be at the discretion of the Project researchers and will be based on scientific merit.

All data will be shared with researchers at the research institutions involved in the Canadian Cattle Genome Project including Agriculture and Agri-Food Canada, New Zealand AgResearch, the Australian Cooperative Research Centre for Beef Genetic Technologies, United States Department of Agriculture, the Scottish Agricultural College, and Teagasc (Ireland). Commercial groups involved in the project (BIO and SEMEX) will have access to the data that will become publically available. All project members will use the data generated for research purposes only and will not publish or share the raw data with any non-project personnel.

For Breed Associations

All samples provided to the Canadian Cattle Genome Project will be submitted for DNA extraction and sequencing and/or genotyping at the facility chosen by the Project. All sequence and genotype data that results from samples provided by the Association will be accessible to the Association through the Project’s website (www.canadacow.ca) under a unique login. This information will be stored on the website for a minimum of 2 years after the completion of the project.

The Project will sequence approximately 30 individuals from each breed or population at approximately 5-fold coverage. The coverage of each animal may change depending on the Project’s resources and the scientific data requirements of the project.

All sequence data generated by the Project will have the animal ID associated with it and will be made available to: the Association through the project’s website; researchers at collaborating research institutions; and Dr. Ben Hayes (Department of Primary Industries Victoria, Biosciences Research Division, Bundoora, Australia) for use in the 1000 Bull Genomes Project (www.1000bullgenomes.com). All project members will use the sequence data generated for research purposes only and will not publish or share the raw data with any non-project personnel or other breed associations without written permission from the Association. Commercial collaborators such as BIO and SEMEX will have access to all sequence data with the animal IDs as this data will become publically available (see below).

All sequence data will be stored at the University of Alberta, and subsets of data (processed sequence reads) will be mirrored on a server maintained by Ben Hayes. Once the project is nearing completion the sequence data with the associated animal ID will be placed in public databases (http://www.ncbi.nlm.nih.gov/sra).  

The Project will complete high density (HD) genotyping (680K or 770K) on approximately 480 cattle and 50K genotyping on approximately 500 cattle in each population depending on strategic importance to the project, and considering collaborating resources. Additional individuals may be genotyped (e.g. RFI tested animals) but this will be at the discretion of the Project researchers and will be based on scientific merit.

All genotype data generated by the Project will have the animal ID associated with it and during the project will be made available to: the Association through the project’s website and researchers at collaborating research institutions. Commercial collaborators such as BIO and SEMEX will have access to all genotypes but without the associated animal ID as this data will become publically available (see below). All project members will use the data for research purposes only and will not publish or share the raw data with any non-project personnel or other breed associations without the written permission from the Association. Once the project is nearing completion the genotype data, without the associated animal ID, will be placed in public databases (if any are available) or on the project’s website and will be accessible to the public. At the end of the project, the Project will also provide data that will allow the Association to genotype animals at a facility of their choice and impute the data from 50K to HD, as enabled through the project (dependent on success of project).

Meet The Canadian Cattle Genome Project Stakeholders

Contacts

Paul Stothard
Project Leader
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Steve Miller
Project Leader
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Steve Moore
Project Leader
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Mary De Pauw
Project Manager
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