Etherton TD: Somatotropic function: The somatomedin hypothesis revisited. J Anim Sci. 2004, 82 (13_suppl): E239-244.
PubMed
Google Scholar
Lucy MC, Verkerk GA, Whyte BE, Macdonald KA, Burton L, Cursons RT, Roche JR, Holmes CW: Somatotropic axis components and nutrient partitioning in genetically diverse dairy cows managed under different feed allowances in a pasture system. J Dairy Sci. 2009, 92 (2): 526-539. 10.3168/jds.2008-1421.
Article
CAS
PubMed
Google Scholar
Lucy MC: Functional differences in the growth hormone and insulin-like growth factor axis in cattle and pigs: implications for post-partum nutrition and reproduction. Reprod Domest Anim. 2008, 43 (Suppl 2): 31-39.
Article
PubMed
Google Scholar
Mullen MP, Berry DP, Howard DJ, Diskin MG, Lynch CO, Giblin L, Kenny DA, Magee DA, Meade KG, Waters SM: Single nucleotide polymorphisms in the insulin-like growth factor 1 (IGF-1) gene are associated with performance in Holstein-Friesian dairy cattle. Frontiers in Genetics. 2011, 2: 3-
Article
PubMed Central
PubMed
Google Scholar
Mullen MP, Berry DP, Howard DJ, Diskin MG, Lynch CO, Berkowicz EW, Magee DA, MacHugh DE, Waters SM: Associations between novel single nucleotide polymorphisms in the Bos taurus growth hormone gene and performance traits in Holstein-Friesian dairy cattle. J Dairy Sci. 2010, 93 (12): 5959-5969. 10.3168/jds.2010-3385.
Article
CAS
PubMed
Google Scholar
Viitala S, Szyda J, Blott S, Schulman N, Lidauer M, Maki-Tanila A, Georges M, Vilkki J: The Role of the Bovine Growth Hormone Receptor and Prolactin Receptor Genes in Milk, Fat and Protein Production in Finnish Ayrshire Dairy Cattle. Genetics. 2006, 173 (4): 2151-2164. 10.1534/genetics.105.046730.
Article
PubMed Central
CAS
PubMed
Google Scholar
Waters SM, McCabe MS, Howard DJ, Giblin L, Magee DA, MacHugh DE, Berry DP: Associations between newly discovered polymorphisms in the Bos taurus growth hormone receptor gene and performance traits in Holstein-Friesian dairy cattle. Anim Genet. 2011, 42: 39-49. 10.1111/j.1365-2052.2010.02087.x.
Article
CAS
PubMed
Google Scholar
Blott S, Kim JJ, Moisio S, Schmidt-Kuntzel A, Cornet A, Berzi P, Cambisano N, Ford C, Grisart B, Johnson D: Molecular dissection of a quantitative trait locus: a phenylalanine-to-tyrosine substitution in the transmembrane domain of the bovine growth hormone receptor is associated with a major effect on milk yield and composition. Genetics. 2003, 163 (1): 253-266.
PubMed Central
CAS
PubMed
Google Scholar
Allan MF, Kuehn LA, Cushman RA, Snelling WM, Echternkamp SE, Thallman RM: Confirmation of quantitative trait loci using a low-density single nucleotide polymorphism map for twinning and ovulation rate on bovine chromosome 5. J Anim Sci. 2009, 87 (1): 46-56.
Article
CAS
PubMed
Google Scholar
Kim ES, Shi X, Cobanoglu O, Weigel K, Berger PJ, Kirkpatrick BW: Refined mapping of twinning-rate quantitative trait loci on bovine chromosome 5 and analysis of insulin-like growth factor-1 as a positional candidate gene. J Anim Sci. 2009, 87 (3): 835-843.
Article
CAS
PubMed
Google Scholar
Sahana G, Guldbrandtsen B, Bendixen C, Lund MS: Genome-wide association mapping for female fertility traits in Danish and Swedish Holstein cattle. Anim Genet. 2010, 41 (6): 579-588. 10.1111/j.1365-2052.2010.02064.x.
Article
CAS
PubMed
Google Scholar
McCarthy MI, Abecasis GR, Cardon LR, Goldstein DB, Little J, Ioannidis JPA, Hirschhorn JN: Genome-wide association studies for complex traits: consensus, uncertainty and challenges. Nature Review Genetics. 2008, 9 (5): 356-369. 10.1038/nrg2344.
Article
CAS
Google Scholar
Frazer KA, Murray SS, Schork NJ, Topol EJ: Human genetic variation and its contribution to complex traits. Nature Review Genetics. 2009, 10 (4): 241-251.
Article
CAS
Google Scholar
Goddard ME, Hayes BJ: Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nature Review Genetics. 2009, 10 (6): 381-391. 10.1038/nrg2575.
Article
CAS
Google Scholar
Manolio TA, Collins FS, Cox NJ, Goldstein DB, Hindorff LA, Hunter DJ, McCarthy MI, Ramos EM, Cardon LR, Chakravarti A: Finding the missing heritability of complex diseases. Nature. 2009, 461 (7265): 747-753. 10.1038/nature08494.
Article
PubMed Central
CAS
PubMed
Google Scholar
Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW BA, Hardenbol P, Leal SM, Pasternak S, Wheeler DA WT, Yu F, Yang H, Zeng C, Gao Y, Hu H, Li C LW, Liu S, Pan H, Tang X, Wang J, Wang W, Yu J, Zhang B, Zhang Q ZH, Zhao H, Zhou J, Gabriel SB, Barry R: A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007, 449 (7164): 851-861. 10.1038/nature06258.
Article
CAS
PubMed
Google Scholar
VanRaden PM, Olson KM, Null DJ, Hutchison JL: Harmful recessive effects on fertility detected by absence of homozygous haplotypes. J Dairy Sci. 2011, 94 (12): 6153-6161. 10.3168/jds.2011-4624.
Article
CAS
PubMed
Google Scholar
Mackay TFC, Stone EA, Ayroles JF: The genetics of quantitative traits: challenges and prospects. Nature Review Genetics. 2009, 10 (8): 565-577. 10.1038/nrg2612.
Article
CAS
Google Scholar
Davey JW, Hohenlohe PA, Etter PD, Boone JQ, Catchen JM, Blaxter ML: Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nature Review Genetics. 2011, 12 (7): 499-510. 10.1038/nrg3012.
Article
CAS
Google Scholar
Gnirke A: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009, 27: 182-189. 10.1038/nbt.1523.
Article
PubMed Central
CAS
PubMed
Google Scholar
Summerer D: Enabling technologies of genomic-scale sequence enrichment for targeted high-throughput sequencing. Genomics. 2009, 94 (6): 363-368. 10.1016/j.ygeno.2009.08.012.
Article
CAS
PubMed
Google Scholar
Hedges DJ, Guettouche T, Yang S, Bademci G, Diaz A, Andersen A, Hulme WF, Linker S, Mehta A, Edwards YJK: Comparison of Three Targeted Enrichment Strategies on the SOLiD Sequencing Platform. PLoS ONE. 2011, 6 (4): e18595-10.1371/journal.pone.0018595.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nejentsev S, Walker N, Riches D, Egholm M, Todd JA: Rare Variants of IFIH1, a Gene Implicated in Antiviral Responses, Protect Against Type 1 Diabetes. Science. 2009, 324 (5925): 387-389. 10.1126/science.1167728.
Article
PubMed Central
CAS
PubMed
Google Scholar
Calvo SE, Tucker EJ, Compton AG, Kirby DM, Crawford G, Burtt NP, Rivas M, Guiducci C, Bruno DL, Goldberger OA: High-throughput, pooled sequencing identifies mutations in NUBPL and FOXRED1 in human complex I deficiency. Nat Genet. 2010, 42 (10): 851-858. 10.1038/ng.659.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Durbin R: Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics. 2009, 25 (14): 1754-1760. 10.1093/bioinformatics/btp324.
Article
PubMed Central
CAS
PubMed
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. Bioinformatics. 2009, 25 (16): 2078-2079. 10.1093/bioinformatics/btp352.
Article
PubMed Central
PubMed
Google Scholar
McKenna A: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010, 20: 1297-1303. 10.1101/gr.107524.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Flicek P, Birney E: Sense from sequence reads: methods for alignment and assembly. Nat Methods. 2009, 6: S6-S12. 10.1038/nmeth.1376.
Article
CAS
PubMed
Google Scholar
DePristo MA: A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genet. 2011
Google Scholar
Flicek P, Amode MR, Barrell D, Beal K, Brent S, Chen Y, Clapham P, Coates G, Fairley S, Fitzgerald S: Ensembl 2011. Nucl Acids Res. 2011, D800-806. 39 Database
Berkowicz EW, Magee DA, Berry DP, Sikora KM, Howard DJ, Mullen MP, Evans RD, Spillane C, MacHugh DE: Single nucleotide polymorphisms in the imprinted bovine insulin-like growth factor 2 receptor gene (IGF2R) are associated with body size traits in Irish Holstein-Friesian cattle. Anim Genet. 2011, 78 (1): 1-8.
CAS
Google Scholar
Berkowicz EW, Magee DA, Sikora KM, Berry DP, Howard DJ, Mullen MP, Evans RD, Spillane C, Machugh DE: Single nucleotide polymorphisms at the imprinted bovine insulin-like growth factor 2 (IGF2) locus are associated with dairy performance in Irish Holstein-Friesian cattle. J Dairy Res. 2011, 1: 1-8.
Article
Google Scholar
Quandt K, Frech K, Karas H, Wingender E, Werner T: MatInd and MatInspector: new fast and versatile tools for detection of consensus matches in nucleotide sequence data. Nucleic Acids Res. 1995, 23 (23): 4878-4884. 10.1093/nar/23.23.4878.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rusinov V, Baev V, Minkov IN, Tabler M: MicroInspector: a web tool for detection of miRNA binding sites in an RNA sequence. Nucleic Acids Res. 2005, 33 (suppl_2): W696-700.
Article
PubMed Central
CAS
PubMed
Google Scholar
Benjamini Y, Hochberg Y: Controlling the false discovery rate: a practical and powerful approach to multiple testing. Journal of the Royal Statistical Society, series B. 1995, 57 (1): 289-300.
Google Scholar
Bansal V, Tewhey R, LeProust EM, Schork NJ: Efficient and Cost Effective Population Resequencing by Pooling and In-Solution Hybridization. PLoS ONE. 2011, 6 (3): e18353-10.1371/journal.pone.0018353.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nielsen R, Paul JS, Albrechtsen A, Song YS: Genotype and SNP calling from next-generation sequencing data. Nature Review Genetics. 2011, 12 (6): 443-451. 10.1038/nrg2986.
Article
CAS
Google Scholar
Altmann A, Weber P, Quast C, Rex-Haffner M, Binder EB, Müller-Myhsok B: vipR: variant identification in pooled DNA using R. Bioinformatics. 2011, 27 (13): i77-i84. 10.1093/bioinformatics/btr205.
Article
PubMed Central
CAS
PubMed
Google Scholar
McIntyre L, Lopiano K, Morse A, Amin V, Oberg A, Young L, Nuzhdin S: RNA-seq: technical variability and sampling. BMC Genomics. 2011, 12 (1): 293-10.1186/1471-2164-12-293.
Article
PubMed Central
CAS
PubMed
Google Scholar
Mamanova L, Coffey AJ, Scott CE, Kozarewa I, Turner EH, Kumar A, Howard E, Shendure J, Turner DJ: Target-enrichment strategies for next-generation sequencing. Nat Methods. 2010, 7 (2): 111-118. 10.1038/nmeth.1419.
Article
CAS
PubMed
Google Scholar
Maricic T, Whitten M, Pääbo S: Multiplexed DNA Sequence Capture of Mitochondrial Genomes Using PCR Products. PLoS ONE. 2010, 5 (11): e14004-10.1371/journal.pone.0014004.
Article
PubMed Central
PubMed
Google Scholar
Kim SY: Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol. 2010, 34: 479-491. 10.1002/gepi.20501.
Article
PubMed
Google Scholar
Day INM: dbSNP in the detail and copy number complexities. Hum Mutat. 2010, 31 (1): 2-4. 10.1002/humu.21149.
Article
CAS
PubMed
Google Scholar
Weller JI, Ron M: Invited review: Quantitative trait nucleotide determination in the era of genomic selection. J Dairy Sci. 2011, 94 (3): 1082-1090. 10.3168/jds.2010-3793.
Article
CAS
PubMed
Google Scholar
Ron M, Weller JI: From QTL to QTN identification in livestock--winning by points rather than knock-out: a review. Anim Genet. 2007, 38 (5): 429-439. 10.1111/j.1365-2052.2007.01640.x.
Article
CAS
PubMed
Google Scholar
Ge W, Davis ME, Hines HC, Irvin KM, Simmen RC: Association of a genetic marker with blood serum insulin-like growth factor-I concentration and growth traits in Angus cattle. J Anim Sci. 2001, 79 (7): 1757-1762.
CAS
PubMed
Google Scholar
Ge W, Davis ME, Hines HC, Irvin KM, Simmen RCM: Association of single nucleotide polymorphisms in the growth hormone and growth hormone receptor genes with blood serum insulin-like growth factor I concentration and growth traits in Angus cattle. J Anim Sci. 2003, 81 (3): 641-648.
CAS
PubMed
Google Scholar
Pereira AP, Alencar MMd, Oliveira HNd, Regitano LCdA: Association of GH and IGF-1 polymorphisms with growth traits in a synthetic beef cattle breed. Genetics and Molecular Biology. 2005, 28: 230-236. 10.1590/S1415-47572005000200009.
Article
CAS
Google Scholar
Thomas MG, Enns RM, Shirley KL, Garcia MD, Garrett AJ, Silver GA: Associations of DNA polymorphisms in growth hormone and its transcriptional regulators with growth and carcass traits in two populations of Brangus bulls. Genet Mol Res. 2007, 6 (1): 222-237.
CAS
PubMed
Google Scholar
Maj A, Snochowski M, Siadkowska E, Rowinska B, Lisowski P, Robakowska-Hyzorek D, Oprzadek J, Grochowska R, Kochman K, Zwierzchowski L: Polymorphism in genes of growth hormone receptor (GHR) and insulin-like growth factor-1 (IGF1) and its association with both the IGF1 expression in liver and its level in blood in Polish Holstein-Friesian cattle. Neuro Endocrinology Letters. 2008, 29 (6): 981-989.
CAS
PubMed
Google Scholar
Islam KK, Vinsky M, Crews RE, Okine E, Moore SS, Crews DH, Li C: Association analyses of a SNP in the promoter of IGF1 with fat deposition and carcass merit traits in hybrid, Angus and Charolais beef cattle. Anim Genet. 2009, 40 (5): 766-769. 10.1111/j.1365-2052.2009.01912.x.
Article
CAS
PubMed
Google Scholar
Berry DP, Kearney JF, Twomey K, Cromie AR, Evans RD: Revision of the Fertility and Health Genetic Evaluations for Irish Holstein-Friesian Dairy Cattle. In Proceedings of the 9th World Congress on Genetics Applied to Livestock production: 1st - 6th August, 2010 1st - 6th August, 2010; Leipzig, Germany. 2010
Google Scholar
Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M: A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature. 2003, 425 (6960): 832-836. 10.1038/nature02064.
Article
CAS
PubMed
Google Scholar
Farnir F, Coppieters W, Arranz JJ, Berzi P, Cambisano N, Grisart B, Karim L, Marcq F, Moreau L, Mni M: Extensive genome-wide linkage disequilibrium in cattle. Genome Res. 2000, 10 (2): 220-227. 10.1101/gr.10.2.220.
Article
CAS
PubMed
Google Scholar
Tenesa A, Knott SA, Ward D, Smith D, Williams JL, Visscher PM: Estimation of linkage disequilibrium in a sample of the United Kingdom dairy cattle population using unphased genotypes. J Anim Sci. 2003, 81 (3): 617-623.
CAS
PubMed
Google Scholar
Khatkar M, Nicholas F, Collins A, Zenger K, Cavanagh J, Barris W, Schnabel R, Taylor J, Raadsma H: Extent of genome-wide linkage disequilibrium in Australian Holstein-Friesian cattle based on a high-density SNP panel. BMC Genomics. 2008, 9 (1): 187-10.1186/1471-2164-9-187.
Article
PubMed Central
PubMed
Google Scholar
Waters SM, Berry DP, Mullen MP: Polymorphisms in genes of the somatotrophic axis are independently associated with milk production, udder health, survival and animal size in Holstein Friesian Dairy cattle. Journal of Animal Breeing and Genetics. 2011, doi:101111/j1439-0388201100938x,
Google Scholar
Fisher RA: The correlation between relatives on the supposition of mendelian inheritance. Transactions of the Royal Society of Edinburgh. 1918, 52: 399-433.
Article
Google Scholar
Drogemuller C, Tetens J, Sigurdsson S, Gentile A, Testoni S, Lindblad-Toh K, Leeb T: Identification of the Bovine Arachnomelia Mutation by Massively Parallel Sequencing Implicates Sulfite Oxidase (SUOX) in Bone Development. PLoS Genet. 2010, 6 (8): e1001079-10.1371/journal.pgen.1001079.
Article
PubMed Central
PubMed
Google Scholar
Kim SY, Li Y, Guo Y, Li R, Holmkvist J, Hansen T, Pedersen O, Wang J, Nielsen R: Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol. 2010, 34 (5): 479-491. 10.1002/gepi.20501.
Article
PubMed
Google Scholar
Van Tassell CP, Smith TPL, Matukumalli LK, Taylor JF, Schnabel RD, Lawley CT, Haudenschild CD, Moore SS, Warren WC, Sonstegard TS: SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat Methods. 2008, 5 (3): 247-252. 10.1038/nmeth.1185.
Article
CAS
PubMed
Google Scholar
Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA: Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res. 2010, 20 (4): 537-545. 10.1101/gr.100040.109.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ingman M, Gyllensten U: SNP frequency estimation using massively parallel sequencing of pooled DNA. Eur J Hum Genet. 2008, 17 (3): 383-386.
Article
PubMed Central
PubMed
Google Scholar