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. 2015 Oct 26:4:49.
doi: 10.1186/s13742-015-0090-5. eCollection 2015.

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

Paul Stothard  1 , Xiaoping Liao  2 , Adriano S Arantes  1 , Mary De Pauw  1 , Colin Coros  3 , Graham S Plastow  1 , Mehdi Sargolzaei  4 , John J Crowley  1 , John A Basarab  5 , Flavio Schenkel  4 , Stephen Moore  6 , Stephen P Miller  7
Affiliations

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

Paul Stothard et al. Gigascience. .

Abstract

Background: The 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.

Findings: We 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.

Conclusions: The 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.

Keywords: Beef; Bos taurus; Dairy; Whole-genome sequencing.

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Figures

Fig. 1
Fig. 1
Concordance between sequence-derived genotypes and Illumina HD panel genotypes. Animals were sequenced using Illumina (green) or SOLiD (red) sequencing platforms. Sequence-derived genotypes were compared to those from the Illumina BovineHD BeadChip array (770 K) to determine concordance. Two animals (dashed box) showed unusually poor concordance. These animals (CHACANM000000FMC409 and HOLCANM000005429693) are flagged in Additional file 1
Fig. 2
Fig. 2
Principal component analysis of purebred animals based on sequence-derived genotypes. The genotypes of individuals from the seven purebred populations examined in this study were compared. Three Charolais samples appear in the Hereford cluster and two Hereford animals appear in the Charolais cluster, suggesting potential issues with sample sourcing or sample handling. These five samples are included in the final set of sequenced animals but are flagged as potentially problematic in Additional file 1. Angus (ANG), Charolais (CHA), Gelbvieh (GVH), Hereford (HER), Holstein (HOL), Limousin (LIM) and Simmental (SIM)
See this image and copyright information in PMC

References

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