Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs

BMC Genetics

Volumn 15, Issue , 2014, Pages

  Do, Duy N ^a   Ostersen, Tage ^b   Strathe, Anders B ^a,b   Mark, Thomas ^a   Jensen, Just ^c   Kadarmideen, Haja N ^a  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b Pig Research Centre   (Denmark)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

Backfat; GWAS; Pathways; Pigs; Residual feed intake; Systems genetics

Indexed keywords

ANIMAL; ANIMAL FOOD; BODY FAT DISTRIBUTION; EATING; GENE LINKAGE DISEQUILIBRIUM; GENETIC ASSOCIATION; GENETICS; GENOTYPE; HAPLOTYPE; MALE; MEAT; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; SINGLE NUCLEOTIDE POLYMORPHISM; STATISTICAL MODEL; SWINE; SYSTEMS BIOLOGY; WEIGHT GAIN;

ANIMAL FEED; ANIMALS; BODY FAT DISTRIBUTION; EATING; GENETIC ASSOCIATION STUDIES; GENOTYPE; HAPLOTYPES; LINEAR MODELS; LINKAGE DISEQUILIBRIUM; MALE; MEAT; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SUS SCROFA; SYSTEMS BIOLOGY; WEIGHT GAIN;

EID: 84894280861     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-15-27     Document Type: Article

References (75)

1. Cai W, Casey DS, Dekkers JCM. Selection response and genetic parameters for residual feed intake in Yorkshire swine. J Anim Sci 2008, 86(2):287-298.
2. Kennedy B, Van der Werf J, Meuwissen T. Genetic and statistical properties of residual feed intake. J Anim Sci 1993, 71(12):3239-3250.
3. Gilbert H, Bidanel JP, Gruand J, Caritez JC, Billon Y, Guillouet P, Lagant H, Noblet J, Sellier P. Genetic parameters for residual feed intake in growing pigs, with emphasis on genetic relationships with carcass and meat quality traits. J Anim Sci 2007, 85(12):3182-3188.
4. Saintilan R, Mérour I, Brossard L, Tribout T, Dourmad JY, Sellier P, Bidanel J, van Milgen J, Gilbert H. Genetics of residual feed intake in growing pigs: relationships with production traits, and nitrogen and phosphorus excretion traits. J Anim Sci 2013, 91(6):2542-2554.
5. Muro-Reyes A, Gutierrez-Banuelos H, Diaz-Garcia LH, Gutierrez-Pina FJ, Escareno-Sanchez LM, Banuelos-Valenzuela R, Medina-Flores CA, Corral Luna A. Potential environmental benefits of residual feed intake as strategy to mitigate methane emissions in sheep. J Anim Vet Adv 2011, 10(12):1551-1556.
6. Carberry CA, Kenny DA, Han S, McCabe MS, Waters SM. Effect of phenotypic residual feed intake and dietary forage content on the rumen microbial community of beef cattle. Appl Environ Microbiol 2012, 78(14):4949-4958.
7. Do DN, Strathe AB, Jensen J, Mark T, Kadarmideen HN. Genetic parameters for different measures of feed efficiency and related traits in boars of three pig breeds. J Anim Sci 2013, 91(9):4069-4079.
8. Kadarmideen HN. Genetical systems biology in livestock: application to gonadotrophin releasing hormone and reproduction. IET Syst Biol 2008, 2(6):423-441.
9. Kadarmideen HN, von Rohr P, Janss LL. From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding. Mamm Genome 2006, 17(6):548-564.
10. Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W, Thomas MB. A validated whole-genome association study of efficient food conversion in cattle. Genetics 2007, 176(3):1893-1905.
11. Sherman E, Nkrumah J, Moore S. Whole genome single nucleotide polymorphism associations with feed intake and feed efficiency in beef cattle. J Anim Sci 2010, 88(1):16-22.
12. Rolf M, Taylor J, Schnabel R, McKay S, McClure M, Northcutt S, Kerley M, Weaber R. Genome-wide association analysis for feed efficiency in Angus cattle. Anim Genet 2012, 43(4):367-374.
13. Lindholm-Perry A, Kuehn L, Smith T, Ferrell C, Jenkins T, Freetly H, Snelling W. A region on BTA14 that includes the positional candidate genes LYPLA1, XKR4 and TMEM68 is associated with feed intake and growth phenotypes in cattle1. Anim Genet 2012, 43(2):216-219.
14. Karisa BK, Thomson J, Wang Z, Stothard P, Moore SS, Plastow GS. Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle. J Anim Sci 2013, 91(8):3502-3513.
15. Sherman EL, Nkrumah JD, Li C, Bartusiak R, Murdoch B, Moore SS. Fine mapping quantitative trait loci for feed intake and feed efficiency in beef cattle. J Anim Sci 2009, 87(1):37-45.
16. Sherman EL, Nkrumah JD, Murdoch BM, Moore SS. Identification of polymorphisms influencing feed intake and efficiency in beef cattle. Anim Genet 2008, 39(3):225-231.
17. Lindholm-Perry AK, Kuehn LA, Snelling WM, Smith TPL, Ferrell CL, Jenkins TG, Andy King D, Shackelford SD, Wheeler TL, Freetly HC. Genetic markers on BTA14 predictive for residual feed intake in beef steers and their effects on carcass and meat quality traits. Anim Genet 2012, 43(5):599-603.
18. Lu D, Miller S, Sargolzaei M, Kelly M, Vander Voort G, Caldwell T, Wang Z, Plastow G, Moore S. Genome-wide association analyses for growth and feed efficiency traits in beef cattle. J Anim Sci 2013, 91(8):3612-3633.
19. Yao C, Spurlock DM, Armentano LE, Page CD, VandeHaar MJ, Bickhart DM, Weigel KA. Random Forests approach for identifying additive and epistatic single nucleotide polymorphisms associated with residual feed intake in dairy cattle. J Dairy Sci 2013, 90(10):6716-6729.
20. Chen Y, Gondro C, Quinn K, Herd RM, Parnell PF, Vanselow B. Global gene expression profiling reveals genes expressed differentially in cattle with high and low residual feed intake. Anim Genet 2011, 42(5):475-490.
21. Gilbert H, Riquet J, Gruand J, Billon Y, Fève K, Sellier P, Noblet J, Bidanel JP. Detecting QTL for feed intake traits and other performance traits in growing pigs in a Piétrain-Large White backcross. Anim 2010, 4(08):1308-1318.
22. Fan B, Lkhagvadorj S, Cai W, Young J, Smith RM, Dekkers JCM, Huff-Lonergan E, Lonergan SM, Rothschild MF. Identification of genetic markers associated with residual feed intake and meat quality traits in the pig. Meat Sci 2010, 84(4):645-650.
23. Lkhagvadorj S, Qu L, Cai W, Couture OP, Barb CR, Hausman GJ, Nettleton D, Anderson LL, Dekkers JC, Tuggle CK. Gene expression profiling of the short-term adaptive response to acute caloric restriction in liver and adipose tissues of pigs differing in feed efficiency. Am J Physiol Regul Integr Comp Physiol 2010, 298(2):R494-507.
24. Onteru SK, Gorbach DM, Young JM, Garrick DJ, Dekkers JCM, Rothschild MF. Whole genome association studies of residual feed intake and related traits in the pig. PLoS ONE 2013, 8(6):e61756.
25. Jiao S, Cassady J, Maltecca C, Gray K, Holl J. Whole-genome association analysis for feed efficiency traits in Duroc pigs 2013, Indiana, Abstract no. 124, Proceedings of the ADSA-ASAS Joint Annual Meetings: The American Dairy Science Association, July, 08-12, 2013.
26. Sahana G, Kadlecová V, Hornshøj H, Nielsen B, Christensen OF. A genome-wide association scan in pig identifies novel regions associated with feed efficiency trait. J Anim Sci 2013, 91(3):1041-1050.
27. Gunsett G, Gunsett FC. Linear index selection to improve traits defined as ratios. J Anim Sci 1984, 59:1185-1193.
28. Henderson CR. Applications of Linear Models in Animal Breeding 1984, Guelph, Ontario, Canada: University of Guelph.
29. Garrick DJ, Taylor JF, Fernando RL. Deregressing estimated breeding values and weighting information for genomic regression analyses. Genet Sel Evol 2009, 41.
30. Ostersen T, Christensen OF, Henryon M, Nielsen B, Su G, Madsen P. Deregressed EBV as the response variable yield more reliable genomic predictions than traditional EBV in pure-bred pigs. Genet Sel Evol 2011, 43:38.
31. Do DN, Strathe AB, Ostersen T, Jensen J, Mark T, Kadarmideen HN. Genome-wide association study reveals genetic architecture of eating behavior in pigs and its implications for humans obesity by comparative mapping. PLoS ONE 2013, 8(8):e71509.
32. Madsen P, Sørensen P, Su G, Damgaard LH, Thomsen H, Labouriau R. DMU-a package for analyzing multivariate mixed models. 8th World Congress on Genetics Applied to Livestock Production 2006, 247.
33. Duggal P, Gillanders E, Holmes T, Bailey-Wilson J. Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies. BMC Genomics 2008, 9(1):516.
34. Consortium WTCC. Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447(7145):661-678.
35. Barrett JC, Fry B, Maller J, Daly MJ. Haploview: analysis and visualization of LD and haplotype maps. Bioinformatics 2005, 21(2):263-265.
36. Gabriel SB, Schaffner SF, Nguyen H, Moore JM, Roy J, Blumenstiel B, Higgins J, DeFelice M, Lochner A, Faggart M, et al. The structure of haplotype blocks in the human genome. Science 2002, 296(5576):2225-2229.
37. R Development Team R: A language and environment for statistical computing 2008, Vienna, Austria: R Foundation for Statistical Computing, R Development Team.
38. Huang DW, Sherman BT, Lempicki RA. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 2009, 4(1):44-57.
39. Nkrumah JD, Sherman EL, Li C, Marques E, Crews DH, Bartusiak R, Murdoch B, Wang Z, Basarab JA, Moore SS. Primary genome scan to identify putative quantitative trait loci for feedlot growth rate, feed intake, and feed efficiency of beef cattle. J Anim Sci 2007, 85(12):3170-3181.
40. Chibon F, Mariani O, Derre J, Mairal A, Coindre JM, Guillou L, Sastre X, Pedeutour F, Aurias A. ASK1 (MAP3K5) as a potential therapeutic target in malignant fibrous histiocytomas with 12q14-q15 and 6q23 amplifications. Genes Chromosomes Cancer 2004, 40(1):32-37.
41. Matsuzawa A, Nishitoh H, Tobiume K, Takeda K, Ichijo H. Physiological roles of ASK1-mediated signal transduction in oxidative stress- and endoplasmic reticulum stress-induced apoptosis: advanced findings from ASK1 knockout mice. Antioxid Redox Signal 2002, 4(3):415-425.
42. Hayes MR, Leichner TM, Zhao SR, Lee GS, Chowansky A, Zimmer D, De Jonghe BC, Kanoski SE, Grill HJ, Bence KK. Intracellular signals mediating the food intake-suppressive effects of hindbrain glucagon-like peptide-1 receptor activation. Cell Metab 2011, 13(3):320-330.
43. Kyriakis JM, Avruch J. Mammalian mitogen-activated protein kinase signal transduction pathways activated by stress and inflammation. Physiol Rev 2001, 81(2):807-869.
44. Mogensen MS, Scheibye-Alsing K, Karlskov-Mortensen P, Proschowsky HF, Jensen VF, Bak M, Tommerup N, Kadarmideen HN, Fredholm M. Validation of genome-wide intervertebral disk calcification associations in Dachshund and further investigation of the chromosome 12 susceptibility locus. Front Genet 2012, 3.
45. Cardon LR, Abecasis GR. Using haplotype blocks to map human complex trait loci. Trends Genet 2003, 19(3):135-140.
46. Braverman N, Steel G, Obie C, Moser A, Moser H, Gould SJ, Valle D. Human PEX7 encodes the peroxisomal PTS2 receptor and is responsible for rhizomelic chondrodysplasia punctata. Nat Genet 1997, 15(4):369-376.
47. Arning L, Monté D, Hansen W, Wieczorek S, Jagiello P, Akkad D, Andrich J, Kraus P, Saft C, Epplen J. ASK1 and MAP2K6 as modifiers of age at onset in Huntington's disease. J Mol Med 2008, 86(4):485-490.
48. Li J-L, Hayden MR, Almqvist EW, Brinkman RR, Durr A, Dodé C, Morrison PJ, Suchowersky O, Ross CA, Margolis RL, et al. A genome scan for modifiers of Age at onset in huntington disease: the HD MAPS study. Am J Hum Genet 2003, 73(3):682-687.
49. Wyszynski D, Baldwin C, Cleves M, Amirault Y, Nolan V, Farrell J, Bisbee A, Kutlar A, Farrer L, Steinberg M. Polymorphisms near a chromosome 6q QTL area are associated with modulation of fetal hemoglobin levels in sickle cell anemia. Cell Mol Biol (Noisy-le-grand) 2004, 50(1):23.
50. Hansen KR, Resta R, Webb CF, Thompson LF. Isolation and characterization of the promoter of the human 5'-nucleotidase (CD73)-encoding gene. Gene 1995, 167(1-2):307-312.
51. Fuerst PG, Bruce F, Tian M, Wei W, Elstrott J, Feller MB, Erskine L, Singer JH, Burgess RW. DSCAM and DSCAML1 function in self-avoidance in multiple cell types in the developing mouse retina. Neuron 2009, 64(4):484-497.
52. Garrett AM, Tadenev ALD, Burgess RW. DSCAMs: restoring balance to developmental forces. Front Mol Neurosci 2012, 5:e. 00086.
53. Yang X, Aoki Y, Li X, Sakamoto O, Hiratsuka M, Kure S, Taheri S, Christensen E, Inui K, Kubota M, et al. Structure of human holocarboxylase synthetase gene and mutation spectrum of holocarboxylase synthetase deficiency. Hum Genet 2001, 109(5):526-534.
54. Houston RD, Haley CS, Archibald AL, Rance KA. A QTL affecting daily feed intake maps to Chromosome 2 in pigs. Mamm Genome 2005, 16(6):464-470.
55. Dragos-Wendrich M, Stratil A, Hojny J, Moser G, Bartenschlager H, Reiner G, Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 18. J Anim Breed Genet 2003, 120:138-143.
56. Langberg EC, Seed Ahmed M, Efendic S, Gu HF, Ostenson CG. Genetic association of adrenergic receptor alpha 2A with obesity and type 2 diabetes. Obesity (Silver Spring) 2013, 21(8):1720-1725.
57. Papathanasopoulos A, Camilleri M, Carlson PJ, Vella A, Nord SJ, Burton DD, Odunsi ST, Zinsmeister AR. A preliminary candidate genotype-intermediate phenotype study of satiation and gastric motor function in obesity. Obesity (Silver Spring) 2010, 18(6):1201-1211.
58. Yuzaki M. Cbln and C1q family proteins: new transneuronal cytokines. Cell Mol Life Sci 2008, 65(11):1698-1705.
59. Strowski MZ, Kaczmarek P, Mergler S, Wiedenmann B, Domin D, Szwajkowski P, Wojciechowicz T, Skrzypski M, Szczepankiewicz D, Szkudelski T, et al. Insulinostatic activity of cerebellin-evidence from in vivo and in vitro studies in rats. Regul Pept 2009, 157(1-3):19-24.
60. Bidanel JP, Milan D, Iannuccelli N, Amigues Y, Boscher MY, Bourgeois F, Caritez JC, Gruand J, Le Roy P, Lagant H, et al. Detection of quantitative trait loci for growth and fatness in pigs. Genetics, selection, evolution GSE 2001, 33(3):289-309.
61. Ruckert C, Bennewitz J. Joint QTL analysis of three connected F2-crosses in pigs. Genetics, selection, evolution GSE 2010, 42:40.
62. Duran RV, Hall MN. Regulation of TOR by small GTPases. EMBO reports 2012, 13(2):121-128.
63. Dufour CR, Levasseur M-P, Pham NHH, Eichner LJ, Wilson BJ, Charest-Marcotte A, Duguay D, Poirier-Héon J-F, Cermakian N, Giguère V. Genomic convergence among ERRα, PROX1, and BMAL1 in the control of metabolic clock outputs. PLoS Genet 2011, 7(6):e1002143.
64. Okumura N, Matsumoto T, Hayashi T, Hirose K, Fukawa K, Itou T, Uenishi H, Mikawa S, Awata T. Genomic regions affecting backfat thickness and cannon bone circumference identified by genome-wide association study in a Duroc pig population. Anim Genet 2013, 44(4):454-457.
65. Pond WG, Mersmann HJ. Genetically diverse pig models in nutrition research related to lipoprotein and cholesterol metabolism. Advances in swine in biomedical research, Volume 2 1997, 843-863. Springer, Tumbleson ME, Schook LB.
66. Cánovas A, Quintanilla R, Gallardo D, Díaz I, Noguera JL, Ramírez O, Pena RN. Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme. Anim 2010, 4(02):224-233.
67. Zakharova E, Boukina TM. Gene symbol: GALC. Disease: krabbe disease. Hum Gen 2008, 124(3):299.
68. Herd RM, Arthur PF. Physiological basis for residual feed intake. J Anim Sci 2009, 87(14):E64-E71.
69. Nagasaki K, Iida T, Sato H, Ogawa Y, Kikuchi T, Saitoh A, Ogata T, Fukami M. PRKAR1A mutation affecting cAMP-mediated G protein-coupled receptor signaling in a patient with acrodysostosis and hormone resistance. J Clin Endocrinol Metab 2012, 97(9):E1808-1813.
70. Malek M, Marklund S, Dyer C, Matteri R, Rothschild M. Linkage and physical mapping of the porcine prepro-orexin gene. Mamm Genome 2000, 11(4):342-343.
71. Chen Y, Arthur P, Barchia I, Quinn K, Parnell P, Herd R. Using gene expression information obtained by quantitative real-time PCR to evaluate Angus bulls divergently selected for feed efficiency. Anim Prod Sci 2012, 52(11):1058-1067.
72. Colditz I. Some mechanisms regulating nutrient utilisation in livestock during immune activation: an overview. Anim Prod Sci 2004, 44(5):453-457.
73. Lampe PD, Lau AF. The effects of connexin phosphorylation on gap junctional communication. Int J Biochem Cell Biol 2004, 36(7):1171-1186.
74. Hamill RM, McBryan J, McGee C, Mullen AM, Sweeney T, Talbot A, Cairns MT, Davey GC. Functional analysis of muscle gene expression profiles associated with tenderness and intramuscular fat content in pork. Meat Sci 2012, 92(4):440-450.
75. Wang K, Li M, Hakonarson H. Analysing biological pathways in genome-wide association studies. Nat Rev Genet 2010, 11(12):843-854.