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Bovine: the companion papers for the publication of the bovine genome sequence

The cow (Bos taurus) is an important model organism for biomedical research and development, in addition to being agriculturally important. This special series of companion papers includes work from both the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium.

  1. Research article

    Genomic characteristics of cattle copy number variations

    Copy number variation (CNV) represents another important source of genetic variation complementary to single nucleotide polymorphism (SNP). High-density SNP array data have been routinely used to detect human ...

    Yali Hou, George E Liu, Derek M Bickhart, Maria Francesca Cardone, Kai Wang, Eui-soo Kim, Lakshmi K Matukumalli, Mario Ventura, Jiuzhou Song, Paul M VanRaden, Tad S Sonstegard and Curt P Van Tassell

    BMC Genomics 2011 12:127

    Published on: 23 February 2011

  2. Commentary

    Unlocking the bovine genome

    The draft genome sequence of cattle (Bos taurus) has now been analyzed by the Bovine Genome Sequencing and Analysis Consortium and the Bovine HapMap Consortium, which together represent an extensive collaboration...

    Ross L Tellam, Danielle G Lemay, Curtis P Van Tassell, Harris A Lewin, Kim C Worley and Christine G Elsik

    BMC Genomics 2009 10:193

    Published on: 24 April 2009

  3. Research article

    A high resolution RH map of the bovine major histocompatibility complex

    The cattle MHC is termed the bovine leukocyte antigen (BoLA) and, along with the MHCs of other ruminants, is unique in its genomic organization. Consequently, correct and reliable gene maps and sequence inform...

    Candice L Brinkmeyer-Langford, Christopher P Childers, Krista L Fritz, Ashley L Gustafson-Seabury, Marian Cothran, Terje Raudsepp, James E Womack and Loren C Skow

    BMC Genomics 2009 10:182

    Published on: 24 April 2009

  4. Research article

    Cross-species mapping of bidirectional promoters enables prediction of unannotated 5' UTRs and identification of species-specific transcripts

    Bidirectional promoters are shared regulatory regions that influence the expression of two oppositely oriented genes. This type of regulatory architecture is found more frequently than expected by chance in th...

    Helen Piontkivska, Mary Q Yang, Denis M Larkin, Harris A Lewin, James Reecy and Laura Elnitski

    BMC Genomics 2009 10:189

    Published on: 24 April 2009

  5. Research

    The bovine lactation genome: insights into the evolution of mammalian milk

    The newly assembled Bos taurus genome sequence enables the linkage of bovine milk and lactation data with other mammalian genomes.

    Danielle G Lemay, David J Lynn, William F Martin, Margaret C Neville, Theresa M Casey, Gonzalo Rincon, Evgenia V Kriventseva, Wesley C Barris, Angie S Hinrichs, Adrian J Molenaar, Katherine S Pollard, Nauman J Maqbool, Kuljeet Singh, Regan Murney, Evgeny M Zdobnov, Ross L Tellam…

    Genome Biology 2009 10:R43

    Published on: 24 April 2009

  6. Research article

    Two-stage genome-wide association study identifies integrin beta 5 as having potential role in bull fertility

    Fertility is one of the most critical factors controlling biological and financial performance of animal production systems and genetic improvement of lines. The objective of this study was to identify molecul...

    Jean M Feugang, Abdullah Kaya, Grier P Page, Lang Chen, Tapan Mehta, Kashif Hirani, Lynne Nazareth, Einko Topper, Richard Gibbs and Erdogan Memili

    BMC Genomics 2009 10:176

    Published on: 24 April 2009

  7. Research article

    Bos taurus genome assembly

    We present here the assembly of the bovine genome. The assembly method combines the BAC plus WGS local assembly used for the rat and sea urchin with the whole genome shotgun (WGS) only assembly used for many o...

    Yue Liu, Xiang Qin, Xing-Zhi Henry Song, Huaiyang Jiang, Yufeng Shen, K James Durbin, Sigbjørn Lien, Matthew Peter Kent, Marte Sodeland, Yanru Ren, Lan Zhang, Erica Sodergren, Paul Havlak, Kim C Worley, George M Weinstock and Richard A Gibbs

    BMC Genomics 2009 10:180

    Published on: 24 April 2009

  8. Research article

    Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits

    The goal of genome wide analyses of polymorphisms is to achieve a better understanding of the link between genotype and phenotype. Part of that goal is to understand the selective forces that have operated on ...

    William Barendse, Blair E Harrison, Rowan J Bunch, Merle B Thomas and Lex B Turner

    BMC Genomics 2009 10:178

    Published on: 24 April 2009

  9. Research article

    QTL global meta-analysis: are trait determining genes clustered?

    A key open question in biology is if genes are physically clustered with respect to their known functions or phenotypic effects. This is of particular interest for Quantitative Trait Loci (QTL) where a QTL reg...

    Hanni Salih and David L Adelson

    BMC Genomics 2009 10:184

    Published on: 24 April 2009

  10. Research article

    Analysis of the complement and molecular evolution of tRNA genes in cow

    Detailed information regarding the number and organization of transfer RNA (tRNA) genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the ident...

    Dave TP Tang, Evgeny A Glazov, Sean M McWilliam, Wesley C Barris and Brian P Dalrymple

    BMC Genomics 2009 10:188

    Published on: 24 April 2009

  11. Research article

    Gene synteny comparisons between different vertebrates provide new insights into breakage and fusion events during mammalian karyotype evolution

    Genome comparisons have made possible the reconstruction of the eutherian ancestral karyotype but also have the potential to provide new insights into the evolutionary inter-relationship of the different euthe...

    Claus Kemkemer, Matthias Kohn, David N Cooper, Lutz Froenicke, Josef Högel, Horst Hameister and Hildegard Kehrer-Sawatzki

    BMC Evolutionary Biology 2009 9:84

    Published on: 24 April 2009

  12. Research article

    An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle

    Identifying recent positive selection signatures in domesticated animals could provide information on genome response to strong directional selection from domestication and artificial selection. With the compl...

    Sean MacEachern, Ben Hayes, John McEwan and Mike Goddard

    BMC Genomics 2009 10:181

    Published on: 24 April 2009

  13. Research article

    Molecular evolution of the Bovini tribe (Bovidae, Bovinae): Is there evidence of rapid evolution or reduced selective constraint in Domestic cattle?

    If mutation within the coding region of the genome is largely not adaptive, the ratio of nonsynonymous (dN) to synonymous substitutions (dS) per site (dN/dS) should be approximately equal among closely related...

    Sean MacEachern, John McEwan, Alan McCulloch, Andrew Mather, Keith Savin and Mike Goddard

    BMC Genomics 2009 10:179

    Published on: 24 April 2009

  14. Research article

    Functional genomics of HMGN3a and SMARCAL1 in early mammalian embryogenesis

    Embryonic genome activation (EGA) is a critical event for the preimplantation embryo, which is manifested by changes in chromatin structure, transcriptional machinery, expression of embryonic genes, and degrad...

    Alper Uzun, Nelida Rodriguez-Osorio, Abdullah Kaya, Hongfeng Wang, John J Parrish, Valentin A Ilyin and Erdogan Memili

    BMC Genomics 2009 10:183

    Published on: 24 April 2009

  15. Research article

    Characterization of the bovine pregnancy-associated glycoprotein gene family – analysis of gene sequences, regulatory regions within the promoter and expression of selected genes

    The Pregnancy-associated glycoproteins (PAGs) belong to a large family of aspartic peptidases expressed exclusively in the placenta of species in the Artiodactyla order. In cattle, the PAG gene family is comprise...

    Bhanu Prakash VL Telugu, Angela M Walker and Jonathan A Green

    BMC Genomics 2009 10:185

    Published on: 24 April 2009

  16. Research article

    A high density linkage map of the bovine genome

    Recent technological advances have made it possible to efficiently genotype large numbers of single nucleotide polymorphisms (SNPs) in livestock species, allowing the production of high-density linkage maps. S...

    Juan A Arias, Mike Keehan, Paul Fisher, Wouter Coppieters and Richard Spelman

    BMC Genetics 2009 10:18

    Published on: 24 April 2009

  17. Research article

    Transcriptional reprogramming of gene expression in bovine somatic cell chromatin transfer embryos

    Successful reprogramming of a somatic genome to produce a healthy clone by somatic cells nuclear transfer (SCNT) is a rare event and the mechanisms involved in this process are poorly defined. When serial or s...

    Nelida Rodriguez-Osorio, Zhongde Wang, Poothappillai Kasinathan, Grier P Page, James M Robl and Erdogan Memili

    BMC Genomics 2009 10:190

    Published on: 24 April 2009

  18. Research article

    High-resolution haplotype block structure in the cattle genome

    The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup spec...

    Rafael Villa-Angulo, Lakshmi K Matukumalli, Clare A Gill, Jungwoo Choi, Curtis P Van Tassell and John J Grefenstette

    BMC Genetics 2009 10:19

    Published on: 24 April 2009