Publications

2009

Decker JE, Pires JC, Conant GC, McKay SD, Heaton MP, Vilkki J, Seabury CM, Caetano AR, Johnson GS, Brenneman RA, Hanotte O, Eggert LS, Wiener P, Kim J-J, Kim K-S, Sonstegard TS, Van Tassell CP, Neibergs HL, Chen K, Cooper A, McEwan JC, Brauning R, Coutinho LL, Babar ME, Wilson GA, McClure MC, Rolf MM, Kim J-W, Schnabel RD, Taylor JF. High‐Throughput Phylogenomics: From Ancient DNA to Signatures of Human Animal Husbandry. In review at Proc Natl Acad Sci USA.Decker_PNAS_2009.pdf - Decker_PNAS_S_2009.pdf
(Complete data: Decker_PNAS_2009_data.zip).

Ramos AM, Crooijmans RPMA, Amaral AJ, Archibald AL, Beever JE, Bendixen C, Dehais P, Hansen MS, Hedegaard J, Hu ZL, Kerstens HH, Law AS, Megens HJ, Milan D, Nonneman DJ, Rohrer GA, Rothschild MF, Smith TP, Schnabel RD, Van Tassell CP, Taylor JF, Wiedmann RJ, Schook LB and Groenen MAM. 2009 Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS ONE. 4(8): e6524. (Ramos_PLoS_One_2009.pdf)

McClure MC, McKay SD, Schnabel RD, Taylor JF. 2009. Extraction of DNA from FTA® cards for use on the Illumina iSelect BeadChip. BMC Research 2:107 (McClure_BMC_Research_2009.pdf).

The Bovine Genome Sequencing and Analysis Consortium. The Genome Sequence of Taurine Cattle: a window to ruminant biology and evolution. Science 324: 522-528. (Bovine_Genome_Sequencing_and_Analysis_Consortium_Science_2009.pdf).

The Bovine HapMap Consortium. 2009. Genome Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds. Science 324:528-532. (Bovine_HapMap_Consortium_Science_2009.pdf)

Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan M, Heaton MP, O’ Connell JR, Sonstegard TS, Smith TPL, Moore SS, Van Tassell CP. 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4:4 e5350. (Matukumalli_PLoS_ONE_2009.pdf)

Wiggans GR, Sonstegard TS, VanRaden PM, Matukumalli LK, Schnabel RD, Taylor JF, Schenkel FS, Van Tassell CP.2009 Selection of single nucleotide polymorphisms and genotype quality for genomic prediction of genetic merit of dairy cattle. J. Dairy Sci. 92: 3431-3436. (Wiggins_J_Dairy_Sci_2009.pdf)

Awano T, GS Johnson, CM Wade, ML Katz, GC Johnson, JF Taylor, M Perloski, T Biagi, S Long, PA March, NJ Olby, S Khan, DP O’Brien, K Lindblad-Toh and JR Coates. 2009. Genome-wide association analysis reveals a SOD1 mutation in canine degenerative myelopathy that resembles amyotrophic lateral sclerosis. Proc Natl. Acad. Sci. USA. 106:2794-2799 (Awano_PNAS_2009.pdf).

Settles M, Zanella R, McKay SD, Schnabel RD, Taylor JF, Fyock T, Whitlock R, Schukken Y, Van Kessel J, Karns J, Hovingh E, Smith J, Neibergs H. A whole genome association analysis identifies loci associated with Mycobacterium avium subsp. Paratuberculosis infection status in US Holstein cattle. Anim. Genet. In press. (Settles_ANGEN_2009.pdf)

Cole JB, VanRaden PM, O'Connell JR, Van Tassell CP, Sonstegard TS, Schnabel RD, Taylor JF and Wiggans GR. 2009. Distribution and Location of Genetic Effects for Dairy Traits. J. Dairy Sci. 92 2931-2946. (Cole_J_Dairy_Sci_2009.pdf)

VanRaden PM, Van Tassell CP, Wiggans GR, Sonstegard TS, Schnabel RD, Taylor JF and Schenkel F. 2009. INVITED REVIEW: Reliability of genomic predictions for North American Holstein bulls. J. Dairy Sci. 92:16-24. (VanRaden_J_Dairy_Sci_2009.pdf)

2008

Carleton SM, DJ McBride, WL Carson, CE Huntington, KL Twenter, KM Rolwes, CT Winkelmann, JS Morris, JF Taylor and CL Phillips. 2008. Role of genetic background in determining phenotypic severity throughout postnatal development and at peak bone mass in Col1a2 deficient mice (oim). Bone 42:681-694. (Carleton_Bone_2008.pdf)

Marques E, Schnabel RD, Stothard P, Kolbehdar D, Wang Z, Taylor JF and Moore SS.  2008. High density linkage disequilibrium maps of bovine chromosome 14 in Holstein and Angus cattle. BMC Genetics 9:45. (Marques_BMC_Genetics_2008.pdf)

Prasad A, Schnabel RD, McKay SD, Murdoch B, Stothard P, Wang Z, Taylor JF and Moore SS. Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle. Anim. Genet. 39, 597-605. (Prasad_Anim_Genet_2008.pdf)

McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Dias Neto E, GillCA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF and Moore SS. 2008. An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC-Genetics 9:37. (McKay_BMC_Genetics_2008.pdf)

Khatkar MS, Nicholas FW, Collins A, Zenger KR, Cavanagh JAL, Barris W, Schnabel RD, Taylor JF and Raadsma HW. 2008. Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics 9:187. (Khatkar_BMC_Genomics_2008.pdf)

Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenchild CD, Moore SS, Warren WC and Sonstegard TS. 2008. Simultaneous SNP discovery and allele frequency estimation by high throughput sequencing of reduced representation genomic libraries. Nature Methods. 5:247-252 cover article. (Van_Tassell_Nature_Methods_2008.pdf)

2007

Chen Xuhua, Johnson GS, Schnabel RD, Taylor JF, Johnson GC, Parker HG, Patterson EE, Katz ML, Awano T, Khan S and O,Brien DP. 2007. A neonatal encephalopathy with seizures in standard poodle dogs with a missense mutation in the canine ortholog of ATF2. Neurogenetics 9:41-49. (Chen_Neurogenetics_2007.pdf)

Sellner EM, Kim J-W, McClure MC, Taylor KH, Schnabel RD and Taylor JF. 2007. Board-invited review: Applications of genomic information in livestock. J. Anim. Sci. 85:3148-3158. (Sellner_J_Anim_Sci_2007.pdf)

Snelling WM, Chiu R, Schein JE, Hobbs M, Abbey CA, Adelson DL, Bennett GL, Bosdet IE, Boussaha M, Brauning R, Caetano AR, Costa MM, Crawford AM, Dalrymple BP, Eggen A, Everts-van der Wind A, Floriot S, Gautier M, Gill CA, Green RD, Holt R, Jones SJM, Kappes SM, Keele JW, de Jong PJ, Larkin DM, Lewin HA, McEwan JC, McKay S, McWilliam S, Marra MA, Mathewson CA, Matukumalli LK, Moore SS, Murdoch B, Nicholas F, Osoegawa K, Roy A, Salih H, Schibler L, Schnabel RD, Silveri L, Skow LC, Smith TPL, Sonstegard TS, Taylor J, Tellam R, Van Tassell CP, Williams JL, Womack JE, Wye NH, Yang G and Zhao S. 2007. A physical map of the bovine genome. Genome Biol. 8:R165. (Snelling_Genome_Biol_2007.pdf)

McKay SD, Schnabel RD, Murdoch BM, Matukumalli LK, Aerts J, Coppieters W, Crews D, Neto ED, Georges M, Gill CA, Gao C, Mannen H, Wang Z, Van Tassell CP, Williams JL, Taylor JF and Moore SS. 2007. Whole genome linkage disequilibrium maps in multiple breeds of cattle. BMC Genet. 8:74. (McKay_BMC_Genetics_2007.pdf)

McKay SD, Schnabel RD, Murdoch BM, Aerts J, Gill CA, Gao C, Li C, Matukumalli LK, Wang Z, Van Tassell CP, Williams JL, Taylor JF and Moore SS. 2007. High-throughput genotyping facilitates rapid construction of whole genome radiation hybrid and linkage maps. Anim. Genet. 38:120-125. (McKay_Anim_Genet_2007.pdf)

Cooley P, C Seifer, KH Taylor and JF Taylor. 2007. Including genotype information in health surveys. Comput. Human Behav. 23: 2345-2354. (Cooley_Computers_Human_Behavior_2007.pdf)

2006

O’Brien DP, Chen X, Johnson GS, Khan S, Awano T, Schnabel RD, Taylor JF. 2006 Standard poodle neonatal encephalopathy locus maps to canine chromosome 36. J. Vet. Intern. Med. 20:734-734. (OBrien_J_Vet_Intern_Med_2006.pdf)

Wunderlich KR, CA Abbey, DR Clayton, Y Song, J Schein, M Georges, W Coupieters, DL Adelson, JF Taylor, SL Davis and CA Gill. 2006. A 2.5 Mb Angus, Longhorn and horned Hereford BAC contig and STS map of the polled critical interval on bovine chromosome one. Anim. Genet. 37:592-4. (Wunderlich_ANGEN_2006.pdf)

Stolowski GD, BE Baird, RK Miller, JW Savell, AR Sams, JF Taylor, JO Sanders and SB Smith. 2006. Factors influencing the variation in tenderness of seven major beef muscles from three Angus and Brahman breed crosses. Meat Sci. 73:475–483. (Stolowski_Meat_Sci_2006.pdf)

King DA, WW Morgan, RK Miller, JO Sanders, DK Lunt, JF Taylor, CA Gill and JW Savell. 2006. Carcass merit between and among family groups of Bos indicus crossbred steers and heifers. Meat Sci. 72:496-502.( King_Meat_Sci_2006.pdf)

Awano T, ML Katz, DP O’Brien, JF Taylor, J Evans, S Khan, I Sohar, P Lobel and GS Johnson. 2006. A mutation in the cathepsin D gene (CTSD) in American Bulldogs with neuronal ceroid lipofuscinosis. Mol. Genet. Metab. 87:341-48. (Awano_Mol_Gen_Metab_2006.pdf)

Morsci NS, Schnabel RD and Taylor JF. (2006) Association analysis of Adiponectin and Somatostatin polymorphisms on BTA1 with growth and carcass traits in Angus Cattle. Anim. Genet. 37:554-562 View Document

Taylor KH, Taylor JF, White SN and Womack JE (2006) Identification of genetic variation and putative regulatory regions in bovine CARD15 Mamm. Genome 17:892-901 View Document

Di Meo GP, Gallagher D, Perucatti A, Wu X, Incarnato D, Mohammadi G, Taylor JF and Iannuzzi L.(2006) FISH-mapping of type I loci to BTA2, BBU2q, OAR2q and CHI2 and comparative mapping to HSA2q. Anim. Genet. 37:293-307 View Document

Awano T, Katz ML, O'brien DP, Sohar I, Lobel P, Coates JR, Khan S, Johnson GC, Giger U, Johnson GS. (2006) A frame shift mutation in canine TPP1 (the ortholog of human CLN2) in a juvenile Dachshund with neuronal ceroid lipofuscinosis.
Mol Genet Metab. 87:341-348 View Document

Connor EE, Ashwell MS, Schnabel RD and Williams JL. (2006) Comparative mapping of bovine chromosome 27 with human chromosome 8 near a dairy form QTL in cattle. Cytogenet. Genome Res. 112:98-102. View Document

2005

Cooley P, KH Taylor, W Czika, C Seifer and JF Taylor. 2005. Confirming a biomarker for Wegener’s Granulomatosis by association analysis. Eur. J. Immunogenet. 32:237–243.

Cargill EJ, Famula TR, Schnabel RD, Strain GM, Murphy KE. (2005) The color of a Dalmation's spots: Linkage evidence to support the Tyrp 1 gene. BMC Vet. Res. 1:1-3. View Document

Halbert ND, Ward TJ, Taylor JF, Schnabel RD and Derr JN. (2005) Conservation genomics: Disequilibrium mapping of domestic cattle genomic segments in North American bison populations. Mol. Ecol. 14:2343-62. View Document (296 KB)

O'Brien DP, Johnson GS, Schnabel RD, Kahn S, Coates JR, Johnson GC and Taylor JF. (2005) Genetic mapping of the canine multiple system degeneration and ectodermal dysplasia loci. Journal of Heredity Advance Access published on June 15, 2005, DOI 10.1093/jhered/esi086. View Document (509 KB)

Schnabel RD, Sonstegard TS, Taylor JF and Ashwell MS. (2005) Whole Genome Scan to Detect QTL for Milk Production, Conformation and Functional Traits in Two U.S. Holstein Families. Anim, Genet. 36, 408-416 View Document (184 KB)

Robert D. Schnabel, Jong-Joo Kim, Melissa S. Ashwell, Tad S. Sonstegard, Erin E. Connor, Curtis P, Van Tassel and Jeremy F. Taylor (2005). Fine-mapping milk production quantities trait loci on BTA6: Analysis of the bovine opsteopontin gene. Proc. Nat. Acad. Sci. USA 102: 6896-6901. View Document (460 KB), View Supplimental Document (900 KB)

2004

Cargill EJ, Schnabel RD and Murphy KE. (2004) Assignment of canine MSS1 microsatellite markers to chromosomes by linkage. DNA Sequence 15:209-212. View Document (71 KB)

De Donato M, RA Brenneman, DM Stelly, JE Womack and JF Taylor. 2004. A methodological approach for the construction of a radiation hybrid map of bovine chromosome 5. Genet. Mol. Biol. 27:22-32. View Document (208 KB)

2003

Schnabel RD, JF Taylor and JN Derr. 2003. Development of a linkage map and QTL scan for growth traits in North American bison. Cytogenet. Genome Res. 102:59-64. View Document (146 KB)

De Donato M, DS Gallagher, C Lehn, C Gill and JF Taylor. 2003. Molecular cytogenetic assignment of genes to bovine chromosome 5. Genet. Mol. Res. 2:260-270. View Document (602 KB)

2002

Kim J-J, F Farnir, J Savell and JF Taylor. 2003. Detection of QTL for growth and beef carcass fatness traits in a cross between Bos taurus (Angus) and Bos indicus (Brahman) cattle. J. Anim. Sci. 81:1933-1942. View Document (1.43 MB)

Antoniou E, D Gallagher, J Taylor, S Davis, J Womack and M Grosz. 2002. A comparative map of bovine chromosome 25 with human chromosomes 7 and 16. Cytogenet. Genome Res. 97:128-32.

Kim J-J, SK Davis and JF Taylor. 2002. Application of non-parametric bootstrap methods to estimate confidence intervals for QTL location in a beef cattle QTL experimental population. Genet. Res.79:259-263. View Document (268 KB)

2001

De Donato M, DS Gallagher, SK Davis, DM Stelly and JF Taylor. 2001.The assignment of PRKCI to bovine chromosome 1q34->q36 by FISH suggests a new assignment to human chromosome 3. Cytogenet. Cell Genet.95:79-81.

Matthee CA, Burzlaff JD, Taylor JF and Davis SK 2001. Mining the mammalian genome for artiodactyl systematics. Syst. Biol. 50:367-390.

Sonstegard TS; W Barendse, GL Bennett, GA Brockmann, S Davis, C Droegemuller, E Kalm, SM Kappes, C Kuhn, Y Li, M Schwerin, J Taylor, H Thomsen, CP Van Tassell and CC Yeh. 2001. Consensus and comprehensive linkage maps of the bovine sex chromosomes. Anim Genet. 32:115-7. View Document (227 KB)

Ward TJ, LC Skow, DS Gallagher, RD Schnabel, CA Nall, CE Kolenda, SK Davis, JF Taylor and JN Derr. 2001. Differential intogression of uniparentally inherited markers in bison populations with hybrid ancestries. Anim. Genet.32:89-91. View Document (54 KB)

SEQ CHAPTER \h \r 1McShane R.D., D.S. Gallagher, H. Newkirk, J.F. Taylor, J.D. Burzlaff, S.K. Davis and L.C. Skow. 2001. Physical localization and order of genes in the class I region of the bovine MHC.Anim Genet. 32:235-9. View Document (160 KB)

2000

Schnabel RD, Ward TJ, and Derr JN. (2000) Validation of 15 Microsatellites for Parentage Testing in North American Bison, Bison bison L. and Domestic Cattle. Anim Genet. 31, 360-366. View Document (121 KB)

Wu X, SK Davis, SLF Davis, DS Gallagher, Y Song, RA Brenneman, C-C Yeh and JF Taylor. 2000. Assignment of laminin B1 polypeptide (LAMB1) and 2, 3 bisphosphoglycerate mutase (BPGM) to the physical and genetic maps of BTA4. Anim. Genet. 31:282-283. View Document (480 KB)

1999

Gallagher DS, SK Davis, M De Donato, JD Burzlaff, JE Womack, AT Kumamoto and JF Taylor 1999. Applications of chromosomal FISH in the Bovidae with emphases on physical mapping in domestic cattle and comparative cytogenetic analyses of the tribe Bovini. Anim. Biotech.10:105-8.

Iannuzzi L, DS Gallagher, GP DiMeo, Y Yang, JE Womack, SK Davis and JF Taylor. 1999.Comparative FISH-mapping of six expressed gene loci to river buffalo and sheep chromosomes. Cytogenet. Cell Genet.84:161-163.

Larsen NJ, H Hayes, M Bishop, SK Davis, JF Taylor and BW Kirkpatrick. 1999. A comparative linkage and physical map of bovine chromosome 24 with human chromosome 18. Mamm. Genome 10:482-487. View Document (214 KB)

Riquet J, W Coppieters, N Cambisano, JJ Arranz, P Berzi, SK Davis, B Grisart, F Farnir, L Karim, M Mni, P Simon, JF Taylor, P Vanmanshoven, D Wagenaar, JE Womack and M Georges. 1999. Fine-mapping of quantitative trait loci by identity by descent in outbred populations: application to milk production in dairy cattle. Proc. Natl. Acad. Sci. USA 96:9252-7. View Document (519 KB)

Gill CA, SK Davis, JF Taylor, NE Cockett and CDK Bottema. 1999. Construction and characterization of an ovine bacterial artificial chromosome library. Mamm. Genome.10:1108-1111. View Document (129 KB)

De Donato M, DS Gallagher, SK Davis, Y Ji, JD Burzlaff, DM Stelly, JE Womack and JF Taylor. 1999. Physical assignment of microsatellite-containing BACs to bovine chromosomes. Cytogenet. Cell Genet. 87:59-61.

Gallagher DS, J Schlapfer, JD Burzlaff, JE Womack, DM Stelly, SK Davis and JF Taylor. 1999. Cytogenetic alignment of the bovine chromosome 13 genome map by fluorescence in-situ hybridization of human chromosome 10 and 20 comparative markers. Chromosome Res. 7:115-119. View Document (83 KB)

Taylor JF, A Eggen, A Aleyasin, SM Armitage, W Barendse, JE Beever, MD Bishop, RA Brenneman, BM Burns, SK Davis, K Elo, B Harlizius, SM Kappes, JW Keele, SJ Kemp, BW Kirkpatrick, HA Lewin, RZ Ma, RA McGraw, D Pomp, RT Stone, Y Sugimoto, AJ Teale, D Vaiman, J Vilkki, JL Williams, C-C Yeh and MC Zanotti. 1998. Report of the first workshop on the genetic map of bovine chromosome 1. Anim. Genet. 29:228-235.

Taylor JF, LL Coutinho, KL Herring, DS Gallagher, RA Brenneman, N Burney, JO Sanders, JW Turner, SB Smith, RK Miller, JW Savell and SK Davis. 1998. Candidate gene analysis of GH1 for effects on growth and carcass composition of cattle. Anim. Genet. 29:194-201. View Document (437 KB)

Gallagher DS, Y-P Yang, JD Burzlaff, JE Womack, DM Stelly, SK Davis and JF Taylor. 1998. Physical assignment of six type I anchor loci to bovine chromosome 19 by fluorescence in situ hybridization. Anim. Genet. 29:130-134. View Document (196 KB)

Rocha JL, JO Sanders, DM Cherbonnier, TJ Lawlor and JF Taylor. 1998. Trait-based analysis in dairy cattle using blood group polymorphisms. J. Dairy Sci. 81:1681-1689. View Document (127 KB)

Rocha JL, JO Sanders, DM Cherbonnier, TJ Lawlor and JF Taylor. 1998. Blood groups and milk and type traits in dairy cattle: After forty years of research. J. Dairy Sci. 81:1663-1680. View Document (68 KB)

Schlapfer J, DS Gallagher, JD Burzlaff, SK Davis, JF Taylor and JE Womack. 1997. Physical mapping of the Endothelin Receptor Type B to bovine chromosome 12. Mamm. Genome 8:380-381. View Document (1.57 MB)

Taylor JF, E Lutaaya, JO Sanders, JW Turner and SK Davis. 1997. A medium density microsatellite map of BTA10: Reassignment of INRA69. Anim. Genet. 28:360-362. View Document (214 KB)

Sun HS, L Cai, SK Davis, JF Taylor, LK Doud, MD Bishop, H Hayes, W Barendse, D Vaiman, RA McGraw, T Hirano, Y Sugimoto and BW Kirkpatrick. 1997. Comparative linkage mapping of human chromosome 13 and bovine chromosome 12. Genomics 39:47-54.

Reyes-Valdes MH, Y Ji, CF Crane, JF Taylor, MN Islam-Faridi, HJ Price and DM Stelly. 1996. ISH-facilitated analysis of meiotic bivalent pairing. Genome 39:784-792.

Skow LC, SN Snaples, SK Davis, JF Taylor, B Huang and DS Gallagher. 1996. Localization of bovine lymphocyte antigen (BoLA) DYA and class I loci to different regions of chromosome 23. Mamm. Genome 7:388-389. View Document (84 KB)

Brenneman RA, SK Davis, JO Sanders, BM Burns, TC Wheeler, JW Turner and JF Taylor. 1996. The polled locus maps to BTA1 in a Bos indicus x Bos taurus cross. J. Hered. 87:156-161.

Yeh CC, JF Taylor, DS Gallagher, JO Sanders, JW Turner and SK Davis. 1996. Genetic and physical mapping of the bovine X chromosome. Genomics 32:245-252.

Engel SR, RA Linn, JF Taylor and SK Davis. 1996. Conservation of microsatellite loci across species--implications for population studies in different taxa. J. Mammal. 77:504-518.

Cai L, JF Taylor, RA Wing, DS Gallagher, S-S Woo and SK Davis. 1995. Construction and characterization of a bovine bacterial artificial chromosome library. Genomics 29:413-425.

Rohrer GA, JF Taylor, JO Sanders and RM Thallman. 1994. Evaluation of line and breed of cytoplasm effects on performance of purebred Brangus cattle. J. Anim. Sci.72:2798-2803. View Document (621 KB)

Taylor JF, B Abbitt, JP Walter, SK Davis, JT Jaques and RF Ochoa. 1993. Estimation of genotype distributions and posterior genotype probabilities for β-Mannosidosis in Salers cattle. Genetics 135:855-868. View Document (1.75 MB)

Rocha JL, JF Baker, JE Womack, JO Sanders and JF Taylor. 1992. Statistical associations between restriction fragment length polymorphisms and quantitative traits in beef cattle. J. Anim. Sci.70:3360-3370. View Document (1.06 MB)

Ehiobu NG, ME Goddard and JF Taylor. 1990. Prediction of heterosis in crosses between inbred lines of Drosophila melanogaster. Theor. Appl. Genet. 80:321-325.

Ehiobu NG, ME Goddard and JF Taylor. 1989. Effect of rate of inbreeding on inbreeding depression in Drosophila melanogaster. Theor. Appl. Genet.77:123-127.

Stoddart JA and JF Taylor. 1988. Genotypic diversity: estimation and prediction in samples. Genetics 118:705-711. View Document (611 KB)