Bovine Genome Project

About the Project

The BCM-HGSC sequenced and analyzed the bovine genome (Bos taurus). The initial bovine genome assembly and analysis and the study of cattle genetic history were published April 24, 2009. Later efforts centered around finishing the Y chromosome. The most recent efforts to improve the genome are using Pacific Biosciences long-read data. We have produced 19-fold coverage of long read sequence data and combined these with the existing genome assembly using the PBJelly2 software. A de novo genome assembly using higher coverage PacBio data is planned in collaboration with Timothy Smith and Juan Medrano.

The source of the BABovineC library DNA was Hereford bull L1 Domino 99375, registration number 41170496. Dr. Michael MacNeil's laboratory, USDA-ARS, Miles City, MT, provided the blood. The DNA for the whole genome shotgun sequences was provided by Dr. Timothy Smith's laboratory, U.S. Meat Animal Research Center, Clay Center, NE, from white blood cells (for the Sanger data) and spleen (for the PacBio data) from L1 Dominette 01449, American Hereford Association registration number 42190680 (a daughter of L1 Domino 99375). A skin cell fibroblast cell line from the same animal is available from Dr. Carol Chitko-McKown's laboratory, although there is no sequence from that cell line.

Current improvement efforts are funded by the United States Department of Agriculture National Institute of Food and Agriculture (2013-67015-21228) with support from the National Human Genome Research Institute (NHGRI U54 HG003273), which is part of the National Institutes of Health (NIH). Past funding for this project was also provided by: NHGRI U54 HG003273 as well as the U.S. Department of Agriculture's Agricultural Research Service and Cooperative State Research, Education, and Extension Service (USDA ARS Agreement No. 5 9-0790-3-196 and CSREES Agreement No. 2004-35216-14163); the state of Texas; Genome Canada through Genome British Columbia, The Commonwealth Scientific and Industrial Research Organization of Australia (CSIRO); Agritech Investments Ltd., Dairy Insight, Inc. and AgResearch Ltd., all of New Zealand; the Robert J. Kleberg, Jr. and Helen C. Kleberg Foundation; and the National, Texas and South Dakota Beef Check-off Funds.

Genomic Resources

Genome Assemblies

Date Released Release Name Coverage Comments
December 2015 Btau_5.0.1 25x Improved draft assembly combined 19x PacBio data with UMD 3.1 using PBJelly.
July 2012 Btau_4.6.1 7.1x Draft assembly replaced data in Btau_4.5 with high quality finished data where available.
October 2009 Btau_4.5 7.1x Draft assembly incorporating additional Whole Genome Shotgun (WGS) contigs from Btau_2.0 into Btau_4.0
April 2009 Btau_4.2 7.1x Draft assembly Btau_4.0 data replaced with high quality finished sequence where available.
October 2007 Btau_4.0 7.1x Draft assembly using (WGS) reads from small insert clones and BAC sequences. Mapped to chromosomes using refined mapping information.
August 2006 Btau_3.1 7.1x Draft assembly (WGS) reads from small insert clones and BAC sequences.
March 2005 Btau_2.0 6.2x Preliminary assembly using (WGS) reads from small insert clones and BAC end sequences.
September 2004 Btau_1.0 3x Preliminary assembly using (WGS) reads from small insert clones.

Additional Resources

Project History

Sequencing of the bovine (Hereford) genome consumed a large part of 2004-06 BCM-HGSC resources. The project was staged to produce an initial 3x WGS assembly followed by a second 6x WGS assembly to allow gene predictions for preliminary annotation, and a final assembly including BAC sequences for improved local assembly refinement. The 3x assembly was used by Ensembl to test their pipeline on low coverage genome assemblies. The 6x WGS assembly was released and gene predictions from Ensembl and NCBI have been made public. The final assembly has been completed using the Atlas assembler and BAC data from equal numbers of BACs sequenced individually or by the CAPSS clone pooling strategy.

WGS samples from six other breeds were sequenced to identify SNPs for genetic studies. A panel of 10,000 SNPs were mined at the HGSC from this interbreed dataset and genotyping reagents were developed. 227 animals representing 9 breeds were genotyped and analyzed. An expanded set of markers (32,000) was applied to a more extensive group of animals (449). The results form the basis of a Bovine HapMap Project. Affymetrix now markets a bovine genotyping chip based on this work, allowing broader translation of the genome project into applications.

A meeting of sixty bovine researchers in Houston in March 2005 began coordination for overall genome analysis and the future of bovine research. A working group for annotation selected themes for analysis (Global analyses; Muscle, Immune function; Lactation; Energy partitioning, Metabolism, Rumen function; Reproduction, Endocrinology, Sex determination, Development; Imprinted genes, HDACs, Methyl transferases; Bovine models of human diseases; Non-coding RNA; Genetics/Genotyping; Behavior, Maternal nurturing; Prion protein). The Bovine Genome Project leveraged NHGRI funds with funds from other sources. This allowed the utility of the sequence to be enhanced by genetic analysis, outside the scope of the standard basic genome project deliverables.

Related Publications

Zimin AV, Kelley DR, Roberts M, Marçais G, Salzberg SL, Yorke JA. Mis-assembled "segmental duplications" in two versions of the Bos taurus genome. PLoS One. 2012 ;7(8):e42680.

Elsik CG, Tellam RL, Worley KC, Gibbs RA, Muzny DM, Weinstock GM, et al. The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science. 2009 ;324(5926):522-8.

Tellam RL, Lemay DG, Van Tassell CP, Lewin HA, Worley KC, Elsik CG. Unlocking the bovine genome. BMC Genomics. 2009 ;10:193.

Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, Gill CA, et al. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science. 2009 ;324(5926):528-32.