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

GigaScience

Stephen P. Miller³  Stephen Moore⁵  Flavio Schenkel⁷  John A. Basarab²  John J. Crowley⁴  Mehdi Sargolzaei⁷  Graham S. Plastow⁴  Colin Coros¹  Mary De Pauw⁴  Adriano S. Arantes⁴  Xiaoping Liao⁶  Paul Stothard⁴ 

[1] Delta Genomics, Edmonton, AB, Canada;Alberta Agriculture, Food and Rural Development, Lacombe Research Centre, Lacombe, AB, Canada;AgResearch Limited, Invermay Agricultural Centre, Mosgiel, New Zealand;Department of Agricultural, Food and Nutritional Science / Livestock Gentec, University of Alberta, Edmonton, AB, Canada;Queensland Alliance for Agriculture & Food Innovation, University of Queensland, St Lucia, Australia;Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China;Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada

关键词: Dairy;    Beef;    Bos taurus;    Whole-genome sequencing;   

Others  :  1232004
DOI  :  10.1186/s13742-015-0090-5

 received in 2015-05-21, accepted in 2015-10-13,  发布年份 2015

【 摘 要 】

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.

【 授权许可】

   
2015 Stothard et al.

【 图 表 】

Fig. 1.

Fig. 2.

【 参考文献 】

• [1]Stachowicz K, Larmer S, Jamrozik J, Moore SS, Miller SP. Sequencing and genotyping for the whole genome selection in Canadian beef populations. In: Proceedings of the Twentieth Conference of the Association for the Advancement of Animal Breeding and Genetics. Napier, New Zealand; 2013. p. 344–7.
• [2]Sargolzaei M, Iwaisaki H, Colleau JJ. CFC: a tool for monitoring genetic diversity. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production. Belo Horizonte, Brazil: 2006; paper 27–28.
• [3]Boichard D. Pedig: a Fortran package for pedigree analysis suited for large populations. In: Proceedings of the 7th World Congress on Genetics Applied to Livestock Production. Montpellier, France: 2002; paper 28-13.
• [4]Daetwyler HD, Capitan A, Pausch H, Stothard P, van Binsbergen R, Brøndum RF et al.. Whole-genome sequencing of 234 bulls facilitates mapping of monogenic and complex traits in cattle. Nat Genet. 2014; 46:858-65.
• [5]FastQC. http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Accessed 30 Aug 2012.
• [6]Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, Puiu D, et al. A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol. 2009;10:R42.
• [7]Li H, Durbin R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009; 25:1754-60.
• [8]McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A et al.. The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010; 20:1297-303.
• [9]Picard. http://broadinstitute.github.io/picard/Accessed 30 Aug 2012.
• [10]Thorvaldsdóttir H, Robinson JT, Mesirov JP. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration. Brief Bioinform. 2013; 14:178-92.
• [11]Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N et al.. The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009; 25:2078-9.
• [12]Stothard P, Liao X, Arantes AS, Pauw MD, Coros C, Plastow GS, et al. Bovine whole-genome sequence alignments from the Canadian Cattle Genome Project. GigaScience Database. 2015. http://dx.doi.org/10.5524/100157