Gene network analyses of first service conception in Brangus heifers: Use of genome and trait associations, hypothalamic-transcriptome information, and transcription factors1

Journal of Animal Science

Volumn 90, Issue 9, 2012, Pages 2894-2906

  Fortes, M R S ^a,b,c   Snelling, W M ^d   Reverter, A ^b,c   Nagaraj, S H ^b   Lehnert, S A ^b,c   Hawken, R J ^c,h   DeAtley, K L ^e   Peters, S O ^e,i   Silver, G A ^e   Rincon, G ^f   Medrano, J F ^f   Islas Trejo, A ^f   Thomas, M G ^e,g  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b CSIRO   (Australia)

^c Cooperative Research Centre for Beef Genetic Technologies ^*  (Australia)

^d U S MEAT ANIMAL RESEARCH CENTER   (United States)

^e NEW MEXICO STATE UNIVERSITY   (United States)

^f UNIVERSITY OF CALIFORNIA   (United States)

^g Department of Environmental and Radiological Health Sciences   (United States)

^h Cobb Vantress Inc ^*  (United States)

ⁱ Department of Obstetrics Gynecology   (United States)

Author keywords

Cattle; First service conception; Gene network; Genome wide association; Heifer

Indexed keywords

DNA; TRANSCRIPTION FACTOR; TRANSCRIPTOME;

ANIMAL; ARTICLE; BREEDING; CATTLE; FEMALE; FERTILITY; GENE EXPRESSION REGULATION; GENETICS; GENOME; GENOTYPE; HYPOTHALAMUS; METABOLISM; PHYSIOLOGY; PREGNANCY; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; CATTLE; DNA; FEMALE; FERTILITY; GENE EXPRESSION REGULATION; GENOME; GENOTYPE; HYPOTHALAMUS; POLYMORPHISM, SINGLE NUCLEOTIDE; PREGNANCY; PREGNANCY, ANIMAL; TRANSCRIPTION FACTORS; TRANSCRIPTOME;

EID: 84882689113     PISSN: 00218812     EISSN: 15253163     Source Type: Journal    
DOI: 10.2527/jas.2011-4601     Document Type: Article

References (88)

1. Ahmed, S. F., and C. Farquharson. 2010. Review: the effect of GH and IGF1 on linear growth and skeletal development and their modulation by SOCS proteins. J. Endocrinol. 206:249-259.
2. Anukulkitch, C., A. Rao, A. Pereria, J. McEwan, and I. J. Clarke. 2010. Expression of genes for appetite-regulating peptides in the hypothalamus of genetically selected lean and fat sheep. Neuroendocrinology 91:223-238.
3. Bader, G. D., and C. W. Hogue. 2003. An automated method for finding molecular complexes in large protein interaction networks. BMC Bioinformatics 4:2.
4. Barbási, A. B., and Z. N. Oltvai. 2004. Network biology: Understanding the cell's functional organization. Nat. Rev. 5:101-113.
5. Beauchemin, V. R., M. G. Thomas, D. E. Franke, and G. A. Silver. 2006. Evaluation of DNA polymorphisms involving growth hormone relative to growth and carcass characteristics in Brahman steers. Genet. Mol. Res. 5:438-447.
6. Bliss, S. P., A. M. Navratil, J. J. Xie, and M. S. Roberson. 2010. GnRH signaling, the gonadotrope and endocrine control of fertility. Front. Neuroendocrinol. 31:322-340.
7. Bolormaa, S., B. J. Hayes, R. J. Hawken, Y. Zhang, A. Reverter, and M. E. Goddard. 2011b. Detection of chromosome segments of zebu and taurine origin and their effect on beef production and growth. J. Anim Sci. 89:2050-2060.
8. Bolormaa, S., B. J. Hayes, K. Savin, R. Hawken, W. Barendse, P. F. Arthur, R. M. Herd, and M. E. Goddard. 2011a. Genomewide association studies for feedlot and growth traits in cattle. J. Anim. Sci. 89:1684-1697.
9. Bolormaa, S., L. R. Porto Neto, Y. D. Zhang, R. J. Bunch, B. E. Harrison, M. E. Goddard, and W. Barendes. 2011c. A genome wide association study of meat and carcass traits in Australian cattle. J. Anim. Sci. 89:2297-2309.
10. Brangus Herd Improvement Records. 2010. Accessed Jan. 1, 2010. http://www.int-Brangus.org.
11. Butte, A. J., A. Califano, S. Friend, T. Ideker, and E. Schadt. 2011. Integrative network-based association studies: Leveraging cell regulatory models in the post-GWAS era. Nat. Preced. doi:10.1038/npre.2011.5732.1
12. Cammack, K. M., M. G. Thomas, R. M. Enns. 2009. Review: Reproductive traits and their heritabilities in beef cattle. Prof. Anim. Sci. 25:517-528.
13. Canovas, A., G. Rincon, A. Islas-Trejo, S. Wickaramsinghe, and J. F. Medrano. 2010. SNP discovery in the bovine milk transcriptome using RNA-Seq technology. Mamm. Genome 21:592-598.
14. Caraux, G., and S. Pinloche. 2005. PermutMatrix: A graphical environment to arrange gene expression profiles in optimal linear order. Bioinformatics 21:1280-1281.
15. Clarkson, J., and A. E. Herbison. 2006. Development of GABA and glutamate signaling at the GnRH neuron in relation to puberty. Mol. Cell. Endocrinol. 254:32-38.
16. Colgrave, M. L., L. Xi, S. A. Lehnert, T. Flatscher-Bader, H. Wadensten, A. Nilsson, P. E. Andren, and G. Wijffels. 2011. Neuropeptide profiling of the bovine hypothalamus: thermal stabilization is an effective tool in inhibiting post-mortem degradation. Proteomics 11:1264-1276.
17. Day, M. L., and L. H. Anderson. 1998. Current concepts on the control of puberty in cattle. J. Anim. Sci. 76(Suppl. 3):1-15.
18. DeAtley, K. L., G. Rincon, C. R. Farber, J. F. Medrano, P. Luna-Nevarez, R. M. Enns, D. M. VanLeeuwen, G. A. Silver, and M. G. Thomas. 2011. Genetic analyses involving microsatellite ETH10 genotypes on bovine chromosome 5 and performance trait measures in Angus and Brahman-influenced cattle. J. Anim. Sci.89:2031-2041.
19. Dennis, G., B. T. Sherman, D. A. Hosack, J. Yang, W. Gao, H. C. Lane, and R. A. Lempicki. 2003. David: Database for annotation, visualization, and integrated discovery. Genome Biol. 4:3.
20. Doyle, S. P., B. L. Golden, R. D. Green, and J. S. Brinks. 2000. Additive genetic parameter estimates for heifer pregnancy and subsequent reproduction in Angus females. J. Anim. Sci. 78:2091-2098.
21. Dudley, E., F. Haabbler, and J. Thome. 2011. Profiling for novel proteomics biomarkers in neurodevelopmental disorders. Expert Rev. Proteomics 8:127-136.
22. Eden, E., R. Navon, I. Steinfeld, D. Lipson, and Z. Yakhini. 2009. Gorilla: A tool for discovery and visualization of enriched go terms in ranked gene lists. BMC Bioinformatics 10:7.
23. Elledge, R. 2009. Current concepts in research related to oncogenes implicated in salivary gland tumourigenesis: A review of literature. Oral Dis. 15:249-254.
24. Farber, C. R., P. M. Corva, and J. F. Medrano. 2006. Genome-wide isolation of growth and obesity QTL using mouse speed congenic strains. BMC Genomics 7:1-17.
25. Fortes, M. R. S., A. Reverter, S. H. Nagaraj, Y. Zhang, N. N. Jonsson, W. Barris, S. Lehnert, G. B. Boe-Hansen, and R. J. Hawken. 2011. A SNP-derived regulatory gene network underlying puberty in two tropical breeds of beef cattle. J. Anim. Sci. 89:1669-1683.
26. Fortes, M. R. S., A. Reverter, Y. Zhang, E. Collis, S. H. Nagaraj, N. N. Jonsson, W. Barris, and R. Hawken. 2010b. A new method for exploring genome-wide associations applied to cattle puberty. 9th World Congress on Genetics Applied to Livestock Production. German Society for Animal Science, Leipzig, Germany.
27. Fortes, M. R. S., A. Reverter, Y. Zhang, E. Collis, S. H. Nagaraj, N. N. Jonsson, K. C. Prayaga, W. Barris, and R. J. Hawken. 2010a. Association weight matrix for the genetic dissection of puberty in beef cattle. Proc. Natl. Acad. Sci. 107:13642-13647.
28. Furuse, C., L. Miguita, A. C. Garcia Rosa, A. Borges Soares, E. Ferreria Martinez, A. Altemani, and V. Cavalcanti de Araujo. 2010. Study of growth factors and receptors in carcinoma ex pleomorphic adenoma. J. Oral Pathol. Med. 39:540-547.
29. Garcia, M. R., M. Almstalden, S. W. Williams, R. L. Stanko, C. D. Morrison, D. H. Keisler, S. E. Nizielski, and G. L. Williams. 2002. Serum leptin and its adipose gene expression during pubertal development, the estrous cycle, and different seasons in cattle. J. Anim. Sci. 80:2158-2167.
30. Garcia-Gamez, E., A. Reverter, V. Whan, S. M. McWilliam, J. J. Arranz, and J. Kijas. 2011. Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in Merino sheep. PLoS One 6:e21158.
31. Gibbs, R. A., J. F. Taylor, C. P. Van Tassell, W. Barendse, K. A. Eversol, C. A. Gill, R. D. Green, D. L. Hamernik, S. M. Kappes, S. Lien, L. K. Matukumalli, J. C. McEwan, L. V. Nazareth, R. D. Schnabel, G. M. Weinstock, D. A. Wheeler, P. Ajmone-Marsan, P. J. Boettcher, A. R. Caetano, J. F. Garcia, O. Hanotte, P. Mariani, L. C. Skow, J. L. Williams, B. Diallo, L. Hailemariam, M. L. Martinez, C. A. Morris, L. O. C. Silva, R. J. Spellman, W. Mulatu, K. Y. Zhao, C. A. Abbey, M. Agaba, F.R. Araujo, R. J. Bunch, J. Burton, C. Gorni, H. Olivier, B. E. Harrison, B. Luff, M. A. Machado, J. Mwakaya, G. Plastow, W. Sim, T. Smith, T. S. Stonstegard, M. B. Thomas, A. Valentini, P. Williams, J. Womack, J. A. Wooliams, Y. Liu, X. Qin, K. C. Worley, C. Gao, H. Y. Jiang, S. S. Moore, Y. R. Ren, X. Z. Song, C. D. Bustamante, R. D. Hernandez, D. M. Muzny, S. Patil, A. S. Lucas, Q. Fu, M. P. Kent, R. Vega, A. Matukumalli, S. McWilliam, G. Sclep, K. Bryc, J. Choi, H. Gao, J. J. Grefenstette, B. Murdoch, A. Stella, R. Villa-Angulo, M. Wright, J. Aerts, O. Jann, R. Negrini, M. E. Goddard, B. J. Hayes, D. G. Bradley, M. B. da Silva, L. P. L. Lau, G. E. Liu, D. J. Lynn, F. Panzitta, and K. G. Dodds. 2009. Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324:528-532.
32. Goddard, M. E., and B. J. Hayes. 2009. Mapping genes for complex traits in domestic animals and their use in breeding programmes. Nat. Rev. Genet. 10:381-391.
33. Gutierrez, J. P., I. Alvarez, I. Fernandez, L. J. Royo, J. Dies, and F. Goyache. 2002. Genetic relationships between calving date, calving interval, age at first calving and type traits in beef cattle. Livest. Prod. Sci. 78:215.
34. Harhay, G. P., T. P. L. Smith, L. J. Alexander, C. D. Haudenschild, J. W. Keele, L. K. Matukamalli, S. G. Schroeder, C. P. Van Tassell, C. R. Gresham, S. M. Bridges, S. C. Burgess, T. S. Stonstegard. 2010. An atlas of bovine gene expression reveals novel distinctive tissue characteristics and evidence for improving genome annotation. Genome Biol. 11:R102.
35. Hawken, R. J., Y. D. Zhang, M. R. S. Fortes, E. Collis, W. C. Barris, N. J. Corbet, P. J. Williams, G. Fordyce, R. G. Holroyd, J. R. W. Walkey, W. Barendse, D. J. Johnston, K. C. Prayaga, B. Tier, A. Reverter, and S. A. Lehnert. 2012. Genome-wide association studies of female reproduction in tropically adapted beef cattle. J. Anim. Sci. 90:doi:10.2527/jas.2011-4410.
36. Hayes, B., and M. Goddard. 2010. Genome-wide association and genomic selection in animal breeding. Genome 53:876-883.
37. Huang, D.W., B. T. Sherman, and R. A. Lempicki. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc. 4:44-57.
38. Johnston, D. J., S. A. Barwick, N. J. Corbet, G. Fordyce, R. G. Holroyd, P. J. Williams, and H. M. Burrow. 2009. Genetics of heifer puberty in two tropical beef genotypes in northern Australia and associations with heifer- and steer-production traits. Anim. Prod. Sci. 49:399-412.
39. Karim, L., H. Takeda, L. Lin, T. Druet, J. A. C. Arias, D. Burain, N. Cambisano, S. R. Davis, F. Farnir, B. Grisart, B. L. Harris, M. D. Keehan, M. D. Littlejohn, R. J. Spelman, M. Georges, and W. Coppieters. 2011. Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nat. Genet. 43:405-413.
40. Lee, I., B. Lehner, T. Vavouri, J. Shi, A. G. Fraser, and E. M. Marcotte. 2010. Predicting genetic modifier loci using functional gene networks. Genome Res. 20:1143-1153.
41. Liu Y., X. Qin, X. Z. Song, H. Jiang, Y. Shen, K. J. Durbin, S. Lien, M. P. Kent, M. Sodeland, Y. Ren, L. Zhang, E. Sodergren, P. Havlak, K. C. Worley, G. M. Weinstock, and R. A. Gibbs. 2009. Bos taurus genome assembly. BMC Genomics 10:180.
42. Lopaschuk, G. D., J. R. Ussher, and J. S. Jaswal. 2010. Targeting intermediary metabolism in the hypothalamus as a mechanism to regulate appetite. Pharmacol. Rev. 62:237-264.
43. Luna-Nevarez P., D. W. Bailey, C. C. Bailey, D. M. VanLeeuwen, R. M. Enns, G. A. Silver, K. L. DeAtley, and M. G. Thomas. 2010. Growth characteristics, reproductive performance, and evaluation of their associative relationships in Brangus cattle managed in a Chihuahuan Desert production system. J. Anim. Sci. 88:1891-1904.
44. Luna-Nevarez, P., G. Rincon, J. F. Medrano, D. G. Riley, C. C. Chase, S. W. Coleman, D. M. VanLeeuwen, K. L. DeAtley, A. Ilsa-Trejo, G. A. Silver, and M. G. Thomas. 2011. Single nucleotide polymorphisms in the growth hormone-insulin like growth factor axis in straightbred and crossbred Angus, Brahman, and Romosinuano heifers: population genetic analyses and association of genotypes with reproductive phenotypes. J. Anim. Sci. 89:926-934.
45. Maere, S., K. Heymans, and M. Kuiper. 2005. BiNGO: A Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks. Bioinformatics 21:3448-3449.
46. Mamo, S., J. P. Mehta, P. McGettigan, T. Fair, T. E. Spencer, F. W. Bazer, and P. Lonergan. 2011. RNA sequencing reveals novel gene clusters in bovine conceptus associated with maternal recognition of pregnancy and implantation. Biol. Reprod. 85:1143-1151.
47. Marbach, D., R. J. Prill, T. Schaffter, C. Mattiussi, D. Floreano, and G. Stolovitzky. 2010. Revealing strengths and weakness of methods for gene network inference. Proc. Nat. Acad. Sci. 14:6286-6291.
48. Mardis, E. R. 2008. The impact of next-generation sequencing technology on genetics. Trends Genet. 24:133-141.
49. Matukumalli, L. K., C. T. Lawley, R. D. Schnabel, J. F. Taylor, M. F. Allan, M. P. Heaton, J. O'Connell, S. S. Moore, T. P. Smith, T. S. Sonstegard, and C. P. Van Tassell. 2009. Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4:e5350.
50. Meyer, K. 2007. Wombat-a tool for mixed model analyses in quantitative genetics by restricted maximum likelihood (REML). J. Zhejiang Univ. Sci. B. 8:815-821.
51. Mikawa, S., S. Sato, M. Nii, T. Morozumi, G. Yoshioka, N. Imaeda, T. Yamaguchi, T. Hayashi, and T. Awata. 2011. Identification of a second gene associated with variation in vertebral number in domestic pigs. BMC Genet. 12:5.
52. Miller, N. A., S. F. Kingsmore, A. Farmer, R. J. Langley, J. Mudge, J. A. Crow, A. J. Gonzalez1, F. D. Schilkey, R. J. Kim, J. Van Velkinburgh, G. D. May, C. F. Black, M. K. Myers, J. P. Utsey, N. S. Frost, D. J. Sugarbaker, R. Bueno, S. R. Gullans, S. M. Baxter, S. W. Day, and E. F. Retzel. 2008. Management of highthroughput DNA sequencing projects: Alpheus. J. Comput. Sci. Syst. Biol. 26:1-32.
53. Minick J.B., and D. E. Wilson. 2010. Calving day and age at first calving in Angus heifers. J. Anim. Sci. 88:1947-1956.
54. Mortazavi, A., B. A. Williams, K. McCue, L. Schaeffer, and B. Wold. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat. Meth. 5:621-628.
55. Mudge, J., N. A. Miller, I. Khrebutukova, I. E. Lindquist, G. D. May, J. J. Huntley, S. Luo, L. Zhang, J. C. van Velkinburgh, A. D. Farmer, S. Lewis, W. D. Beavis, F. D. Schilkey, S. M. Virk, C. F. Black, M. K. Myers, L. C. Mader, R. J. Langley, J. P. Utsey, R. W. Kim, R. C. Roberts, S. K. Khalsa, M. Garcia, W. Ambris-Griffith, R. Harlan, W. Czika, S. Martin, R. D. Wolfinger, N. I. Perrone-Bizzozero, G. P. Schroth, and S. F. Kingsmore. 2008. Genomic convergence analysis of Schizophrenia: mRNA sequencing reveals altered synaptic vesicular transport in postllum. PLoS ONE. 3:e3625.
56. Mueller, J. K., A. Dietzel, A. Lomniczi, A. Loche, K. Tefs, W. Kiess, T. Danne, S. R. Ojeda, and S. Heger. 2011. Transcriptional regulation of the human KISS1 gene. Mol. Cell. Endocrinol. 341:Epub ahead of print, doi:10.1016/j.mce.2011.04.025.
57. Narro, L. A., M. G. Thomas, G. A. Silver, K. J. Rozeboom, and D. H. Keisler. 2003. Body composition, leptin, and the leptin receptor and their relationship to the growth hormone (GH) axis in growing wethers treated with zeranol. Dom. Anim. Endocrinol. 24:243-255.
58. Nomura, D. K., M. M. Dix, and B. F. Cravatt. 2010. Activity-based protein profiling for biochemical pathway discovery in cancer. Nat. Rev. Cancer 10:630-638.
59. Ojeda, S. R., C. Dubay, A. Lomniczi, G. Kaidar, V. Matagne, U. S. Sandau, and G. A. Dissen. 2010a. Gene networks and the neuroendocrine regulation of puberty. Mol. Cell. Endocrinol. 324:3-11.
60. Ojeda, S. R., A. Lomniczi, U. Sandau, and V. Matagne. 2010b. New concepts on the control of the onset of puberty. Endocr. Dev. 17:44-51.
61. Prentice, L. M., X. d'Anglemont de Tassigny, S. McKinney, T. Ruiz de Algara, D. Yap, G. Turashvili, S. Poon, M. Sutcliffe, P. Allard, A. Burleigh, J. Fee, D. G. Huntsman, W. H. Colledge, and S. A. J. Aparicio. 2011. The testosterone-dependent and independent transcriptional networks in the hypothalamus of Gpr54 and Kiss1 knockout male mice are not fully equivalent. BMC Genomics 12:209.
62. Ravasi, T., H. Suzuki, C. V. Cannistraci, S. Katayama, V. B. Bajic, K. Tan, A. Akalin, S. Schmeier, M. Kanamori-Katayama, N. Bertin, P. Carninci, C. O. Daub, A. R. Forrest, J. Gough, S. Grimmond, J. H. Han, T. Hashimoto, W. Hide, O. Hofmann, H. Kawaji, A. Kubosaki, T. Lassmann, E. van Nimwegen, C. Ogawa, R. D. Teasdale, J. Tegner, B. Lenhard, S. A. Teichmann, T. Arakawa, N. Ninomiya, K. Murakami, M. Tagami, S. Fukuda, K. Imamura, C. Kai, R. Ishihara, Y. Kitazume, J. Kawai, D. A. Hume, T. Ideker, and Y. Hayashizaki. 2010. An atlas of combinatorial transcriptional regulation in mouse and man. Cell 140:744-752.
63. Reverter, A., and E. K. Chan. 2008. Combining partial correlation and an information theory approach to the reversed engineering of gene co-expression networks. Bioinformatics 24:2491-2497.
64. Ricardo-Gonzalez, R. R., A. R. Eagle, J. I. Odegaard, H. Jouihan, C. R. Morel, J. E. Heredia, L. Mukudan, D. Wu, R. M. Locksley, and A. Chawla. 2011. IL-4/STAT6 immune axis regulates peripheral nutrient metabolism and insulin sensitivity. Proc. Nat. Acad. Sci. 107:22617-22622.
65. Riley, D. G., C. C. Chase, S. W. Coleman, T. A. Olson, and R. D. Randel. 2010. Evaluation of tropically adapted straightbred and crossbred beef cattle: heifer age and size at first conception and characteristics of their first calves. J. Anim. Sci. 88:3173-3182.
66. Rincon, G., E. A. Farber, C. R. Farber, J. D. Nkrumah, and J. F. Medrano. 2009. Polymorphisms in the STAT6 gene and their association with carcass traits in feedlot cattle. Anim. Genet. 40:878-882.
67. Rodrigues, H. D., J. E. Kinder, and L. A. Fitzpatrick. 2002. Estradiol regulation of luteinizing hormone secretion in heifers of two breed types that reach puberty at different ages. Biol. Reprod. 66:603-609.
68. Roth, C. L., C. Mastronardi, A. Lomniczi, H. Wright, R. Cabrera, A. E. Mungenast, S. Heger, H. Jung, C. Dubay, and S. R. Ojeda. 2007. Expression of a tumor-related gene network increases in the mammalian hypothalamus at the time of female puberty. Neuroendocrinology 148:5147-5161.
69. Schadt, E. E. 2009. Molecular networks as sensors and drivers of common human diseases. Nature 46:218-223.
70. Schindler, C., and C. Plumlee. 2008. Interferons pen the JAK-STAT pathway. Semin. Cell Dev. Biol. 19:311-318.
71. Schneider, F. A., and D. M. Hallford. 1996. Use of a rapid progesterone radio-immunoassay to predict pregnancy and fetal numbers in ewes. Sheep and Goat Res. J. 12:33-38.
72. Shannon P, A. Markiel, O. Ozier, N. S. Baliga, J. T. Wang, D. Ramage, N. Amin, B. Schwikowski, and T. Ideker. 2003. Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res. 13:2498-2504.
73. Shirley, K. L., M. G. Thomas, D. H. Keisler, D. M. Hallford, D. M. Montrose, G. A. Silver, and M. D. Garcia. 2006. Case study: A Chihuahuan Desert Brangus breeding program: feed efficiency, metabolic hormones, and puberty in heifers sired by bulls with different expected progeny differences for growth and scrotal circumference. Prof. Anim. Sci. 22:48-58.
74. Snelling, W. M., M. F. Allan, J. W. Keele, L. A. Kuehn, T. McDaneld, T. P. L. Smith, T. S. Sonstegard, R. M. Thallman, and G. L. Bennett. 2010. Genome-wide association study of growth in crossbred beef cattle. J. Anim. Sci. 88:837-848.
75. Snelling, W. M., R. A. Cushman, M. R. S. Fortes, A. Reverter, G. L. Bennett, J. W. Keele, L. A. Kuehn, T. G. McDaneld, R. M. Thallman, and M. G. Thomas. 2012. How SNP chips will advance our knowledge of factors controlling puberty and aid in selecting replacement females. J. Anim. Sci. 90:doi:10.2527/jas.2011-4581
76. Soma, Y., Y. Uemoto, S. Sato, T. Shibata, H. Kadowaki, E. Kobayashi, and K. Suzuki. 2010. Genome wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits with a Duroc purebred population. J. Anim. Sci. 89:601-608.
77. Tanaka, S., T. Kodama, T. Nonaka, H. Toyoda, M. Arai, M. Fukazawa, Y. Honda, M. Honda, and E. Mignot. 2010. Transcriptional regulation of the hypocretin/orexin gene by NR6A1. Biochem. Biophys. Res. Comm. 403:178-183.
78. Thomas, M. G., M. Almstalden, D. M. Hallford, G. A. Silver, M. D. Garcia, D. H. Keisler, and G. L. Williams. 2009. Dynamics of GHRH in third-ventricle cerebrospinal fluid of cattle: relationship with serum concentrations of GH and response to appetite regulating peptides. Dom. Anim. Endocrinol. 37:196-205.
79. Thomas, M. G., R. M. Enns, K. L. Shirley, M. D. Garcia, A. J. Garrett, and G. A. Silver. 2007. Association of DNA polymorphism in growth hormone and its traditional regulators with growth carcass traits in two populations of Brangus bulls. Genet. Mol. Res. 6:222-237.
80. Thrift, F. A., J. O. Sanders, M. A. Brown, A. H. Brown, A. D. Herring, D. G. Riley, S. M. DeRouen, J. W. Holloway, W. E. Wyatt, R. C. Vann, C. C. Chase, D. E. Franke, L. V. Cundiff, and J. F. Baker. 2010. Review: preweaning, postweaning, and carcass trait comparisons for progeny sired by subtropically adapted beef sire breeds at various U. S. locations. Prof. Anim. Sci. 26:451-473.
81. Tyler, A. L., F. W. Asselbergs, S. M. Williams, and J. H. Moore. 2009. Shadows of complexity: What biological networks reveal about epistasis and pleiotropy. Bioessays 31:220-227.
82. Van Dyck, F., J. DeClercq, C. V. Braem, and W. J. Van de Ven. 2007. PLAG1, the prototype of the PLAG gene family: Versatility in tumour development (review). Int. J. Oncol. 30:765-774.
83. Van Eenennaam, A. L., J. H. J. Van der Werf, and M. E. Goddard. 2011. The value of using DNA markers for beef bull selection in the seedstock sector. J. Anim. Sci. 89:307-320.
84. Van Tassell, C. P., T. P. L. Smith, L. K. Matukamalli, J. F. Taylor, R. D. Schnabel, C. T. Lawley, C. D. Haudenschild, S. S. Moore, W. C. Warren, and T. S. Stonstegard. 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nature Meth. 5:247-252.
85. Vaquerizas, J. M., S. K. Kummerfeld, S. A. Teichmann, and N. M. Luscombe. 2009. A census of human transcription factors: function, expression and evolution. Nat. Rev. Gen. 10:252-263.
86. Vilborg, A., M. T. Wilhelm, and K. G. Wiman. 2010. Regulation of tumor suppressor p53 at the RNA level. J. Mol. Med. 88:645-652.
87. Wang, M., B. Yu, K. Westerlind, R. Strange, G. Khan, D. Patil, K. Boeneman, and L. Hilakivi-Clarke. 2009b. Prepubertal and physical activity up-regulates estrogen receptor β, BRCA1 and p53 mRNA expression in the rat mammary gland. Breast Cancer Res. Treat. 115:213-220.
88. Wang, Z., M. Gerstein, and M. Synder. 2009a. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 10:57-63.