A large and diverse collection of bovine genome sequences from the Canadian Cattle Genome Project

Abstract

BackgroundThe Canadian Cattle Genome Project is a large-scale international project that aims to develop genomics-based tools to enhance the efficiency and sustainability of beef and dairy production. Obtaining DNA sequence information is an important part of achieving this goal as it facilitates efforts to associate specific DNA differences with phenotypic variation. These associations can be used to guide breeding decisions and provide valuable insight into the molecular basis of traits.FindingsWe describe a dataset of 379 whole-genome sequences, taken primarily from key historic Bos taurus animals, along with the analyses that were performed to assess data quality. The sequenced animals represent ten populations relevant to beef or dairy production. Animal information (name, breed, population), sequence data metrics (mapping rate, depth, concordance), and sequence repository identifiers (NCBI BioProject and BioSample IDs) are provided to enable others to access and exploit this sequence information.ConclusionsThe large number of whole-genome sequences generated as a result of this project will contribute to ongoing work aiming to catalogue the variation that exists in cattle as well as efforts to improve traits through genotype-guided selection. Studies of gene function, population structure, and sequence evolution are also likely to benefit from the availability of this resource.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-015-0090-5) contains supplementary material, which is available to authorized users.

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: I: feed efficiency and component traits

“…first from the 50 K SNP panel (33,321 SNPs) to the Affymetrix Axiom Genome-Wide BOS 1 Array (Affymetrix, Inc., Santa Clara) (termed "HD" hereafter), and then from imputed HD (428,895 SNPs) to the full whole-genome sequence (WGS) variants. A multibreed reference panel made up of 4059 animals genotyped with the Affymetrix HD chip from different Canadian breeds was assembled to impute the 50 K SNP panel (33,321 SNPs) to HD, and a panel of 1570 animals with WGS variants from run 5 of the Bull Genomes Project [73,74] was used for imputation from imputed HD to the WGS variants. To start the imputation, the 50 K SNP panel (33,321 SNPs) in the top strand SNP format were converted to Affymetrix HD sequence format based on the DNA strand designation and allele determination in each coding format and using guidelines from Illumina and Affymetrix.…”

Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits

“…Functional annotation of SNPs or DNA variants on the 30,155 SNPs and on the 7,853,211 DNA variants was provided in the companion paper [23]. The WGS DNA variants were annotated through run 5 of the 1000 Bull Genomes Project, which included 379 full genome sequences from the Canadian Cattle Genome Project [64]. DNA variants were then assigned to a functional class based on their overlap with gene features described in the Ensembl database (release 81), using an updated version of the NGS-SNP annotation system [65].…”

Population Structure Analysis of Bull Genomes of European and Western Ancestry

“…Recognizing the importance of cattle genome diversity in genome-wide association studies, genomic predictions, and optimal breeding, there have been substantial efforts to obtain genome-wide genotypes of multiple breeds in diverse geographical locations123. The 1000 Bull Genomes Consortium has successfully collaborated with institutions from more than 20 countries to collect 1577 whole genome sequences (as of version 5).…”