Whole Genome Association Studies of Residual Feed Intake and Related Traits in the Pig

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Onteru, Suneel K ^a   Gorbach, Danielle M ^a   Young, Jennifer M ^a   Garrick, Dorian J ^a   Dekkers, Jack C M ^a   Rothschild, Max F ^a  

^a IOWA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

INSULIN; LEPTIN;

ACOXL GENE; AEBP1 GENE; ANTHROPOMETRIC PARAMETERS; ARTICLE; BAYES THEOREM; BODY FAT; CDKAL GENE; COMPUTER PROGRAM; FALSE POSITIVE RESULT; FOOD INTAKE; GENE; GENE CONTROL; GENE FREQUENCY; GENE MAPPING; GENETIC ASSOCIATION; GENETIC LINE; GENETIC SELECTION; GENETIC TRAIT; GLP1R GENE; GPR81 GENE; HAPLOTYPE; INSULIN RELEASE; KLHL31 GENE; LOIN MUSCLE AREA; MC4R GENE; NONHUMAN; PGM1 GENE; PROBABILITY; QUANTITATIVE TRAIT LOCUS; RESIDUAL FEED INTAKE; SGMS1 GENE; SINGLE NUCLEOTIDE POLYMORPHISM; SWINE; TGFB1 GENE; WEIGHT GAIN; ADIPOSE TISSUE; ANATOMY AND HISTOLOGY; ANIMAL; BODY WEIGHT; GENETICS; GENOME-WIDE ASSOCIATION STUDY; GROWTH, DEVELOPMENT AND AGING; METABOLISM; MUSCLE; PHENOTYPE; PIG;

ANIMALIA; SUIDAE;

ADIPOSE TISSUE; ANIMALS; BODY WEIGHT; GENE FREQUENCY; GENOME-WIDE ASSOCIATION STUDY; MUSCLES; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SUS SCROFA;

EID: 84879470635     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0061756     Document Type: Article

References (69)

1. Boggess M (2009) A pork industry perspective. Pig Genome III Conference, Hinxton, UK, Nov. 2-4.
2. Cai W, Casey DS, Dekkers JCM, (2008) Selection response and genetic parameters for residual feed intake in Yorkshire swine. J Anim Sci 86: 287-298.
3. Gilbert H, Bidanel JP, Gruand J, Caritez JC, Billon Y, et al. (2007) Genetic parameters for residual feed intake in growing pigs, with emphasis on genetic relationships with carcass and meat quality traits. J Anim Sci 85: 3182-3188.
4. Hoque MA, Suzuki K, (2009) Genetics of residual feed intake in cattle and pigs: A Review. Asian-Aust. J Anim Sci 22: 747-755.
5. Hoque MA, Kadowaki H, Shibata T, Oikawa T, Suzuki K, (2007) Genetic parameters for measures of the efficiency of gain of boars and the genetic relationships with its component traits in Duroc pigs. J Anim Sci 85: 1873-1879.
6. Johnson ZB, Chewning JJ, Nugent RA, (1999) Genetic parameter for production traits and measures of residual feed intake in Large White swine. J Anim Sci 77: 1679-1685.
7. Mrode RA, Kennedy BW, (1993) Genetic variation in measures of food efficiency in pigs and their genetic relationships with growth rate and backfat. Anim Prod 56: 225-232.
8. Nguyen NH, McPhee CP, Wade CM, (2005) Responses in residual feed intake in lines of Large White pigs selected for growth rate on restricted feeding (measured on ad libitum individual feeding). J Anim Breed Genet 122: 264-270.
9. Von Flede A, Roehe R, Looft H, Kalm E, (1996) Genetic association between feed intake and feed intake behaviour at different stages of growth of group-housed boars. Livest Prod Sci 47: 11-22.
10. Young JM, Cai W, Dekkers JCM, (2011) Effect of selection for residual feed intake on feeding behavior and daily feed intake patterns in Yorkshire swine. J Anim Sci 89: 639-647.
11. Onteru SK, Fan B, Nikkilä MT, Garrick DJ, Stalder KJ, et al. (2011) Whole-genome association analyses for lifetime reproductive traits in the pig. J Anim Sci 89: 988-995.
12. Onteru SK, Fan B, Du ZQ, Garrick DJ, Stalder KJ, et al. (2012) A whole-genome association study for pig reproductive traits. Anim Genet 43: 18-26.
13. Fan B, Onteru SK, Du ZQ, Garrick DJ, Stalder KJ, et al. (2011) Genome-wide association study identifies loci for body composition and structural soundness traits in pigs. PLoS ONE 6: e14726.
14. Sherman EL, Nkrumah JD, Moore SS, (2010) Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J Anim Sci 88: 16-22.
15. Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W, et al. (2007) A validated whole-genome association study of efficient food conversion in cattle. Genetics 176: 1893-1905.
16. Rolf MM, Taylor JF, Schnabel RD, McKay SD, McClure MC, et al. (2011) Genome-wide association analysis for feed efficiency in Angus cattle. Anim Genet 43: 367-374.
17. Nkrumah JD, Sherman EL, Li C, Marques E, Crews DH, et al. (2007) Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle. J Anim Sci 85: 3170-3181.
18. Bolormaa S, Hayes BJ, Savin K, Hawken R, Barendse W, et al. (2011) Genome-wide association studies for feedlot and growth traits in cattle. J Anim Sci 89: 1684-1697.
19. Mujibi FDN, Nkrumah JD, Durunna ON, Stothard P, Mah J, et al. (2011) Accuracy of genomic breeding values for residual feed intake in crossbred beef cattle. J Anim Sci 89: 3353-3361.
20. Casey DS, Stern HS, Dekkers JCM, (2005) Identifying errors and factors associated with errors in data from electronic swine feeders. J Anim Sci 83: 969-982.
21. R Development Core Team (2011) R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. ISBN 3-900051-07-0. Available: http://www.R-project.org/. Accessed 2012 Nov 5.
22. Bejamini Y, Hochberg Y, (1995) Controlling the false discovery rate: a practical and powerful approach for multiple testing. J R Statist Soc B 57: 287-300.
23. Meuwissen THE, Hayes BJ, Goddard ME, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
24. Fernando RL, Garrick DJ (2008) GenSel-User manual for a portfolio of genomic selection related analyses. Animal Breeding and Genetics, Iowa State University, Ames. Available: http://bigs.ansci.iastate.edu/bigsgui/login.html. Accessed 2012 Sept 15.
25. Habier D, Fernando RL, Kizilkaya K, Garrick DJ, (2011) Extension of the Bayesian alphabet for genomic selection. BMC Bioinformatics 23: 186.
26. Saatchi M, Garrick DJ, Fernando RL, Boddicker N (2012) Comparison of different Bayesian methods for QTL mapping in Hereford beef cattle using 1 Mb windows. Plant and Animal Genome Conference XX, Jan 14-18, San Diego, CA. P0552.
27. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81: 559-575 http://pngu.mgh.harvard.edu/purcell/plink/ (Accessed 2012 November 5th).
28. Lee KT, Byun MJ, Kang KS, Park EW, Lee SH, et al. (2011) Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study. PLoS One 6: e16356.
29. Barret JC, Fry B, Maller J, Daly MJ, (2005) Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 21: 263-265 http://www.broad.mit.edu/mpg/haploview/ (Accessed 2012 October 15th.
30. Stephens M, Scheet P, (2005) Accounting for decay of linkage disequilibrium in haplotype inference and missing data imputation. Am J Hum Genet 76: 449-462.
31. Stephens M, Smith NJ, Donnelly P, (2001) A new statistical method for haplotype reconstruction from population data. Am J Hum Genet 68: 978-989.
32. Zeng J (2011) Genomic selection of purebred animals for crossbred performance under dominance. A master's thesis submitted to Iowa State University.
33. Okamoto K, Iwasaki N, Doi K, Noiri E, Iwamoto Y, et al. (2012) Inhibition of glucose-stimulated insulin secretion by KCNJ15, a newly identified susceptibility gene for type 2 diabetes. Diabetes 61: 1734-1741.
34. Kobayashi T, Zadravec D, Jacobsson A, (2007) ELOVL2 over expression enhances triacylglycerol synthesis in 3T3-L1 and F442A cells. FEBS Letters 581: 3157-3163.
35. Friedman JM, Halaas JL, (1998) Leptin and the regulation of body weight in mammals. Nature 395: 763-770.
36. Schwartz MW, Woods SC, Porte D Jr, Seeley RJ, Baskin DG, (2000) Central nervous system control of food intake. Nature 404: 661-671.
37. Woods SC, Lutz TA, Geary N, Langhans W, (2006) Pancreatic signals controlling food intake; insulin, glucagon and amylin. Phil Trans R Soc B 361: 1219-1235.
38. Li Q, Luo C, Löhr CV, Dashwood RH, (2011) Activator protein-2a functions as a master regulator of multiple transcription factors in the mouse liver. Hepatol Res 41: 776-783.
39. Girard C, Duprat F, Terrenoire C, Tinel N, Fosset M, et al. (2001) Genomic and functional characteristics of novel pancreatic 2P domain K(+) channels. Biochem Biophys Res Commun 282: 249-256.
40. Drucker DJ, Philippe J, Mojsov S, Chicko WL, Habener JF, (1987) Glucagon-like peptide I stimulates insulin gene expression and increases cyclic AMP levels in a rat islet cell line. Proc Nati Acad Sci USA 84: 3434-3438.
41. Ohara-Imaizumi M, Yoshida M, Aoyagi K, Saito T, Okamura T, et al. (2010) Deletion of CDKAL1 affects mitochondrial ATP generation and first-phase insulin exocytosis. PLoS One 5: e15553.
42. Le NT, Le FN, Louveau I, Gilbert H, Gondret F, (2012) Metabolic changes and tissue responses to selection on residual feed intake in growing pigs. J Anim Sci [Epub ahead of print].
43. Yuzaki M, (2008) Cbln and C1q family proteins: new transneuronal cytokines. Cell Mol Life Sci 65: 1698-705.
44. Yano M, Watanabe K, Yamamoto T, Ikeda K, Senokuchi T, et al. (2011) Mitochondrial dysfunction and increased reactive oxygen species impair insulin secretion in sphingomyelin synthase 1-null mice. J Biol Chem 286: 3992-4002.
45. Strowski MZ, Kaczmarek P, Mergler S, Wiedenmann B, Domin D, et al. (2009) Insulinostatic activity of cerebellin-Evidence from in vivo and in vitro studies in rats. Regul Pept 157 (2009): 19-24.
46. Sherman EL, Nkrumah JD, Moore SS, (2010) Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J Anim Sci 88: 16-22.
47. Pal A, Barber TM, Van de Bunt M, Rudge SA, Zhang Q, et al. (2012) PTEN mutations as a cause of constitutive insulin sensitivity and obesity. N Engl J Med 367: 1002-1011.
48. Townsend KL, Suzuki R, Huang TL, Jing E, Schulz TJ, et al. (2012) Bone morphogenic protein 7 (BMP7) reverses obesity and regulates appetite through a central mTOR pathway. FASEB J 26: 2187-2196.
49. Begriche K, Marston OJ, Rossi J, Burke LK, McDonald P, et al. (2012) Melanocortin-3 receptors are involved in adaptation to restricted feeding. Genes Brain Behav 11: 291-302.
50. Kim KS, Larsen N, Short T, Plastow G, Rothschild MF, (2000) A missense variant of the porcine melanocortin-4 receptor (MC4R) gene is associated with fatness, growth, and feed intake traits. Mamm Genome 11: 131-135.
51. Piorkowska K, Tyra M, Rogoz M, Ropka-Molik K, Oczkowicz M, (2010) Association of the melanocortin-4 receptor (MC4R) with feed intake, growth, fatness and carcass composition in pigs raised in Poland. Meat Sci 85: 297-301.
52. Seeley RJ, Yagaloff KA, Fisher SL, Burn P, Thiele TE, et al. (1997) Melanocortin receptors in leptin effects. Nature 390: 349.
53. Obici S, Feng Z, Tan J, Liu L, Karkanias G, et al. (2001) Central melanocortin receptors regulate insulin action. J Clin. Invest 108: 1079-1085.
54. Flock GB, Cao X, Maziarz M, Drucker DJ, (2012) Activation of enteroendocrine membrane progesterone receptors promotes incretin secretion and improves glucose tolerance in mice. Diabetes [Epub ahead of print].
55. Van den Maagdenberg K, Stinckens A, Claeys E, Seynaeve M, Clinquart A, et al. (2007) The Asp298Asn missense mutation in the porcine melanocortin-4 receptor (MC4R) gene can be used to affect growth and carcass traits without an effect on meat quality. Animal 1: 1089-1098.
56. Kim KS, Lee JJ, Shin HY, Choi BH, Lee CK, et al. (2006) Association of melanocortin 4 receptor (MC4R) and high mobility group AT-hook 1 (HMGA1) polymorphisms with pig growth and fat deposition traits. Anim Genet 37: 419-421.
57. Davoli R, Braglia S, Valastro V, Annarratone C, Comella M, et al. (2012) Analysis of MC4R polymorphism in Italian Large White and Italian Duroc pigs: Association with carcass traits. Meat Sci 90: 887-892.
58. Liu W, Yan M, Liu Y, Wang R, Li C, et al. (2010) Olfactomedin 4 down-regulates innate immunity against Helicobactor pylori infection. Proc Natl Acad Sci USA 107: 11056-11061.
59. Bradfield JP, Taal HR, Timpson NJ, Scherag A, Lecoeur C, et al. (2012) A genome-wide association meta-analysis identified new childhood obesity loci. Nature Genet 44: 526-531.
60. Kim HR, Ingham PW, (2009) The extracellular matrix protein TGFBI promotes myofibril bundling and muscle fibre growth in the Zebrafish embryo. Dev Dyn 238: 56-65.
61. Lin CS, Hsu CW, (2005) Differentially transcribed genes in skeletal muscle of Duroc and Taoyuan pigs. J Anim Sci 83: 2075-2086.
62. Cai TQ, Ren N, Jin L, Cheng K, Kash S, et al. (2008) Role of GPR81 in lactate-mediated reduction of adipose lipolysis. Biochem and Biophys Res Commun 377: 987-991.
63. Takeuchi K, Reue K, (2009) Biochemistry, physiology, and genetics of GPAT, AGPAT, and lipin enzymes in triglyceride synthesis. Am J Physiol Endocrinol Metab 296: E1195-E1209.
64. Clemente-Postigo M, Queipo-Ortun MI, Fernandez-Garcia D, Gomez-Huelgas R, Tinahones FJ, et al. (2011) Adipose tissue gene expression of factors related to lipid processing in obesity. PLoS One 6: e24783.
65. Damon M, Louveau I, Lefaucheur L, Lebret B, Vincent A, et al. (2006) Number of intramuscular adipocytes and fatty acid binding protein-4 content are significant indicators of intramuscular fat level in crossbred Large White×Duroc pigs. J Anim Sci 84: 1083-1092.
66. Abou-Elhamd A, Cooper O, Münsterberg A, (2009) Klhl31 is associated with skeletal myogenesis and its expression is regulated by myogenic signals and Myf-5. Mech Dev 126: 852-862.
67. Jung YC, Rothschild MF, Flanagan MP, Warner CM, Christian LL, (1989) Association of restriction fragment length polymorphisms of swine leucocyte antigen class I genes and production traits in Duroc and Hampshire boars. Anim Genet 20: 79-91.
68. Hoff PD, (2009) A First Course in Bayesian Statistical Methods. New York, Springer Press. 5p.
69. Meuwissen TH, Hayes BJ, Goddard ME, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.