Cattle and sheep genome publications

By February 1st, 2011

The following publications detail the work involved in deciphering the cattle and sheep genomes.

Gibbs R, Weinstock G, Kappes S, Schook L, Skow L, Womack J, Bovine Genomic Sequencing Initiative – Cattle-izing the Human Genome

The Bovine Genome Project (Baylor College of Medicine)

Van Eenennaam A, Commercially-available DNA tests for beef cattle

Key papers

Turner LB, Harrison BE, Bunch RJ, Neto LRP, Li YT, Barendse W, 2010, ‘A genome-wide association study of tick burden and milk composition in cattle’, Animal Production Science, 50: 235-245.

Barendse W, Harrison BE, Bunch RJ, Thomas MB, Turner LB, 2009, ‘Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits’, BMC Genomics, 10: 178.

Elsik C, Tellam RL, Worley K, Dalrymple BP, 2009, ‘The Genome Sequence of Taurine Cattle: A window to ruminant biology and evolution’, Science, 324: 522-528. (Senior authors; the paper contains a total of 307 authors)

Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, et al., 2009, ‘Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds’, Science, 324: 528-532.

Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, McGrath A, Wilson P, Ingersoll RG, McCulloch R, McWilliam S et al., 2009, ‘A genome wide survey of SNP variation reveals the genetic structure of sheep breeds’, PLoS One, 4: e4668.

Lemay DG, Lynn DJ, Martin WF, Casey TM, Kriventseva EV, Rincon G, Barris WC, Hinrichs AS, Molenaar AJ, Pollard KS, Neville MC, Maqbool NJ, Zdobnov EM, Tellam R, Medrano JF, German JB, Rijnkels M, 2009, ‘The bovine lactation genome: insights into the evolution of mammalian milk’, Genome Biology, 10: R43.

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

Barendse W, Reverter A, Bunch RJ, Harrison B, Barris W, Thomas M, 2007, ‘A validated Whole Genome Association study of efficient food conversion in cattle’, Genetics, 176: 1893-1905.

Dalrymple BP, Kirkness EF, Nefedov M, McWilliam S, Ratnakumar A, Barris W, Zhao S, Shetty J, Maddox JF, O’Grady M et al., 2007, ‘Using comparative genomics to reorder the human genome sequence into a virtual sheep genome’, Genome Biology, 8: R152.

Khatkar MS, Zenger KR, Hobbs M, Hawken RJ, Cavanagh JA, Barris W, McClintock AE, McClintock S, Thomson PC, Tier B, Nicholas FW, Raadsma HW, 2007, ‘A primary assembly of a bovine haplotype block map based on a 15 036-single-nucleotide polymorphism panel genotyped in Holstein Friesian cattle’, Genetics, 176: 763-772.

Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Aerts J, et al., the International Bovine BAC Consortium, 2007, ‘A physical map of the bovine genome’, Genome Biology, 8: R165.

Tellam RL, 2007, ‘Capturing benefits from the bovine genome sequence’, Aust. J. Exp. Agric., 47: 1039-1050.

Zenger KR, Khatkar MS, Cavanagh JA, HawkenRJ, Raadsma HW, 2007, ‘Genome-wide genetic diversity of Holstein Friesian cattle reveals new insights into Australian and global population variability, including impact of selection’, Animal Genetics, 38: 7-14.

Dalrymple BP, 2005, ‘Harnessing the bovine genome sequence for the Australian cattle and sheep industries’, Aust. J. Exp. Agric., 45: 1011-1016.

Other papers

Becker D, Tetens J, Brunner A, Burstel D, Ganter M, Kijas J, for the ISGC and Drogemueller C, 2010, ‘Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 (PITX3) gene’, PLoS ONE, 5: e8689.

Cafe LM, McIntyre BL, Robinson DL, Geesink GH, Barendse W, Greenwood PL, 2010, ‘Production and processing studies on calpain-system gene markers for tenderness in Brahman cattle. 1. Growth, efficiency, temperament, and carcass characteristics’, J. Anim. Sci., 88: 3047-3058.

Cafe LM, McIntyre BL, Robinson DL, Geesink GH, Barendse W, Pethick DW, Thompson JM, Greenwood PL, 2010, ‘Production and processing studies on calpain-system gene markers for tenderness in Brahman cattle. 2. Objective meat quality’, J. Anim. Sci., 88: 3059-3069.

Magee DE, Park S, Scraggs E, Murphy AM, Doherty ML, Kijas J, for the International Sheep Genomics Consortium, MacHugh DE, 2010, ‘High fidelity of whole genome amplified sheep (Ovis aries) DNA using a high-density single nucleotide polymorphism array-based genotyping platform’, J. Anim. Sci., 88: 3183-3186.

Meadows JRS, Hiendleder S, Kijas JW, 2010, ‘Haplogroup relationships between domestic and wild sheep resolved using a mitogenome panel’, Heredity, In press.

Porto Neto LR, Bunch RJ, Harrison BE, Barendse W, 2010, ‘DNA variation in the gene ELTD1 is associated with tick burden in cattle’, Anim. Genet., 42: 50-55.

Porto Neto LR, Bunch RJ, Harrison BE, Prayaga KC, Barendse W, 2010, ‘Haplotypes that include the integrin alpha 11 gene are associated with tick burden in cattle’, BMC Genetics, 11: 55.

Sechi T, Coltman DW, Kijas JW, 2010, ‘Evaluation of 16 loci to examine the cross species utility of SNP arrays’, Animal Genetics, 41: 199-202.

Turner LB, Harrison BE, Bunch RJ, Neto LRP, Li YT, Barendse W, 2010, ‘A genome-wide association study of tick burden and milk composition in cattle’, Animal Production Science, 50: 235-245.

Chan EKF, Hawken R, Reverter A, 2009, ‘The combined effect of SNP marker and phenotype attributes in genome-wide association studies’, Animal Genetics, 40: 149-156.

Goldammer T, Brunner RM, Rebl A, Wu CH, Nomura K, Hadfield T, Gill C, Dalrymple BP, Womack JE, Cockett NE, 2009, ‘A high-resolution radiation hybrid map of sheep chromosome X and comparison with human and cattle’, Cytogenetic and Genome Research, 125: 40-45.

Goldammer T, Di Meo G, Luhken G, Drogemueller C, Wu C, Kijas J, Dalrymple B, Nicholas F, Maddox J, Iannuzii L, Cockett N, 2009, ‘Molecular cytogenetics and gene mapping in sheep (Ovis aries, 2n = 54)’, Cytogenetic and Genome Research, 126: 63-76.

Meadows JRS, Kijas JW, 2009, ‘Resequencing regions of the ovine Y chromosome in domestic and wild sheep reveals novel paternal haplotypes’, Animal Genetics, 40: 119-123.

Ratnakumar A, Barris W, McWilliam S, Brauning R, McEwan JC, Snelling WM, Dalrymple BP, 2009, ‘A multiway analysis for identifying high integrity bovine BACs’, BMC Genomics, 10: 46.

Tang DT, Glazov EA, McWilliam SM, Barris WC, Dalrymple BP, 2009, ‘Analysis of the complement and molecular evolution of tRNA genes in cow’, BMC Genomics, 10: 188.

Wu CH, Jin W, Nomura K, Goldammer T, Hadfield T, Dalrymple BP, McWilliam S, Maddox JF, Cockett NE, 2009, ‘A radiation hybrid comparative map of ovine chromosome 1 aligned to the virtual sheep genome’, Animal Genetics, 40: 435-455.

Drogemuller M, Tetens J, Dalrymple B, Goldammer T, Wu CH, Cockett NE, Leeb T, Drogemuller C, 2008, ‘A comparative radiation hybrid map of sheep chromosome 10′, Cytogenetic and Genome Research, 121: 35-40.

Glazov EA, McWilliam S, Barris WC, Dalrymple BP, 2008, ‘Origin, evolution, and biological role of miRNA cluster in DLK-DIO3 genomic region in placental mammals’, Molec. Biol. Evol., 25: 939-948.

McWilliam S, Maddox JF, Womack JE, Cockett NE, 2008, ‘A high resolution comparative radiation hybrid map of ovine chromosomal regions that are homologous to human chromosome 6 (HSA6)’, Animal Genetics, 39: 459-467.