The Canadian Cattle Genome Project (CCGP) celebrated the completion of 2 huge milestones on April 1, 2014. The project completed sequencing of 315 animals and genotyping (770K and 50K) of over 10,000 animals. Most of the animals sequenced and genotyped are key historic bulls (including some animals born as early as 1900) that have had a major influence on our current Canadian herds.
Decisions on which animals to sequence and genotype were based on an analysis of the pedigree and breed structure for each breed. The top 30 key ancestors for each breed were chosen for sequencing with the goal of representing 50-60% of the effective genome. Further animals were chosen for genotyping based on strategies developed to cover over 90% of the genetic base and to avoid duplication of close relatives.
The CCGP is in the final year of its 3-year project. All of this sequence and genotype data will now be used in the development of improved imputation tools to deliver imputed genotypes. These imputed genotypes will establish the reference training data sets for future delivery of genomic selection for purebred and crossbred animals. As well, appropriate methods for application of genome-wide selection using the imputed high density and sequence genotypes will be implemented.
From the large number of sequenced animals, we have identified millions of sites of variants in the bovine genome, most of which (more than 80%) are previously unknown. With the data from the 1000 Bulls Genome Project, we will be able to get more than 30 million sites of variation, all of which will be used for imputation and phenotype association studies in the project.
The Canadian Cattle Genome Project (CCGP) is a large international project that includes researchers from Alberta, Ontario, Australia, USA, Ireland, Scotland and New Zealand. But the project’s collaborations go even further than that. The CCGP is very pleased to be part of another large scale project that is bringing together a large number of bovine genomes. The 1000 Bull Genomes Project, as the name implies, is planning on combining sequence data on 1000 Bull Genomes. In fact, they have already surpassed this goal and currently have 1147 whole genome sequences, with more coming. These sequences are available to any research team from around the world who contributes a certain amount of data to the project. By sharing data, everyone gains. The CCGP has contributed 315 sequences from key ancestors to the project and this is the largest input so far. In return, we have gained access to the 1147 sequences.
Our lead investigator, Dr. Paul Stothard from the University of Alberta is on the steering committee of the 1000 Bull Genomes Project and was a key investigator for the recent publication in Nature Genetics. This publication shows results from Phase I of the project in which 234 bull sequences were used to discover important genetic mutations that could improve animal health.
To find out more about the 1000 Bull Genomes project, follow these links:
To access the Nature Genetics paper, use this link:
Daetwyler D.D., et al. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nature Genetics, 2014; DOI: 10.1038/ng.3034.
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