Canadian Cattle Genome

The Canadian Cattle Genome Project – Request for Resources and Data Sharing Plan

The Canadian Charolais Association will provide the Canadian Cattle Genome Project with a pedigree file that contains the parentage of all animals registered with the Association. This pedigree file will be available to researchers at collaborating research institutions including those at 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). This file will be used for research purposes only and will not be published or shared with any non-Project personnel or other breed associations without the written permission from the Association.

The pedigree file will be analyzed by the Project’s researchers to identify key historical animals that have had a significant impact on the genetics of the current Charolais population(s). The researchers will create a list of key individuals that defines each animal’s total genetic contribution, marginal genetic contribution, and cumulative genetic contribution. This list will be provided to the Association by email, and will be made available on the Project’s website under the Association’s unique login that is not accessible to the public or the other breed associations. It will also be available to all Project researchers and collaborators. This list will be used for research purposes only and will not be published or shared with any nonProject personnel or other breed associations without written permission from the Association.

Based on the list of key animals, the Association will, to the best of their ability, source and provide the Project with samples containing a source of DNA (semen vials, semen straws, blood, tail hair, tissue) for each animal on the list provided to them by the Project. If possible, the Association will also provide information on how rare/difficult it is to replace each sample. Additional samples will be requested from the Association later in the Project from animals lower on the breeding pyramid for use in validating the imputation. These samples will also be procured by the Association to the best of their ability and provided to the Project.

All samples will be submitted for DNA extraction and sequencing and/or genotyping at a 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 Association is free to share all data it receives from the Project (on the samples provided by the Association) as it feels appropriate.

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 nonproject personnel or other breed associations without written permission from the Association.

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 (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’s 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.

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 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).