Quantitative trait loci for meat quality traits in pigs considering imprinting and epistatic effects

Meat Science

Volumn 87, Issue 4, 2011, Pages 394-402

  Duthie, Carol Anne ^a   Simm, Geoff ^a   Doeschl Wilson, Andrea ^a   Kalm, Ernst ^b   Knap, Pieter W ^c   Roehe, Rainer ^a  

^a SCOTTISH AGRICULTURAL COLLEGE   (United Kingdom)

^b UNIVERSITY OF KIEL   (Germany)

^c PIC Germany   (Germany)

Author keywords

Epistasis; Imprinting; Meat quality; Pig; Quantitative trait loci

Indexed keywords

EPISTASIS; IMPRINTING; MEAT QUALITY; PIG; QUANTITATIVE TRAIT LOCUS;

ANIMALS; MEATS; REFLECTION;

PH EFFECTS;

ANIMAL; ARTICLE; GENETIC EPISTASIS; GENETICS; GENOME; GENOME IMPRINTING; GENOTYPE; MEAT; PHENOTYPE; QUANTITATIVE TRAIT LOCUS; STATISTICAL MODEL; SWINE;

ANIMALS; EPISTASIS, GENETIC; GENOME; GENOMIC IMPRINTING; GENOTYPE; LINEAR MODELS; MEAT; PHENOTYPE; QUANTITATIVE TRAIT LOCI; SUS SCROFA;

ANIMALIA; SUIDAE;

EID: 78651235536     PISSN: 03091740     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meatsci.2010.11.017     Document Type: Article

References (72)

1. Aaslyng M.D., Oksama M., Olsen E.V., Bejerholm C., Baltzer M., Andersen G., Bredie W.L.P., Byrne D.V., Gabrielsen G. The impact of sensory quality of pork on consumer preference. Meat Science 2007, 76:61-73.
2. Andersson L. Genetic dissection of phenotypic diversity in farm animals. Nature Reviews. Genetics 2001, 2:130-138.
3. Andersson L., Haley C.S., Ellegren H., Knott S.A., Johansson M., Andersson K., Andersson-eklund L., Edforslilja I., Fredholm M., Hansson I., Hakansson J., Lundstrom K. Genetic-mapping of quantitative trait loci for growth and fatness in pigs. Science 1994, 263:1771-1774.
4. Beeckmann P., Schroffel J., Moser G., Bartenschlager H., Reiner G., Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 1. Journal of Animal Breeding and Genetics 2003, 120:1-10.
5. Bidanel J.P. Estimation of crossbreeding parameters between Large White and Meishan porcine breeds.3. Dominance and epistatic components of heterosis on reproductive traits. Genetics, Selection, Evolution 1993, 25:263-281.
6. Bidanel J.P., Milan D., Iannuccelli N., Amigues Y., Boscher M.Y., Bourgeois F., Caritez J.C., Gruand J., Le Roy P., Lagant H., Quintanilla R., Renard C., Gellin J., Ollivier L., Chevalet C. Detection of quantitative trait loci for growth and fatness in pigs. Genetics, Selection, Evolution 2001, 33:289-309.
7. Carlborg O., Haley C.S. Epistasis: too often neglected in complex trait studies?. Nature Reviews. Genetics 2004, 5:618-625.
8. Carlborg O., Jacobsson L., Ahgren P., Siegel P., Andersson L. Epistasis and the release of genetic variation during long-term selection. Nature Genetics 2006, 38:418-420.
9. Cepica S., Reiner G., Bartenschlager H., Moser G., Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome X. Journal of Animal Breeding and Genetics 2003, 120:144-151.
10. Ciobanu D.C., Bastiaansen J.W.M., Lonergan S.M., Thomsen H., Dekkers J.C.M., Plastow G.S., Rothschild M.F. New alleles in calpastatin gene are associated with meat quality traits in pigs. Journal of Animal Science 2004, 82:2829-2839.
11. Clutter A.C., Brascamp E.W. Genetics of performance traits. The genetics of the pig 1998, 427-462. CAB International, UK. M.F. Rothschild, A. Ruvinsky (Eds.).
12. Cockerham C.C. An extension of the concept of partitioning hereditary variance for analysis of covariances among relatives when epistasis is present. Genetics 1954, 39:859-882.
13. de Koning D.J., Harlizius B., Rattink A.P., Groenen M.A.M., Brascamp E.W., van Arendonk J.A.M. Detection and characterization of quantitative trait loci for meat quality traits in pigs. Journal of Animal Science 2001, 79:2812-2819.
14. de Koning D.J., Janss L.L.G., Rattink A.P., van Oers P.A.M., de Vries B.J., Groenen M.A.M., van der Poel J.J., de Groot P.N., Brascamp E.W., van Arendonk J.A.M. Detection of quantitative trait loci for backfat thickness and intramuscular fat content in pigs (Sus scrofa). Genetics 1999, 152:1679-1690.
15. de Koning D.J., Rattink A.P., Harlizius B., Groenen M.A.M., Brascamp E.W., van Arendonk J.A.M. Detection and characterization of quantitative trait loci for growth and reproduction traits in pigs. Livestock Production Science 2001, 72:185-198.
16. de Koning D.J., Rattink A.P., Harlizius B., van Arendonk J.A.M., Brascamp E.W., Groenen M.A.M. Genome-wide scan for body composition in pigs reveals important role of imprinting. Proceedings of the National Academy of Sciences of the United States of America 2000, 97:7947-7950.
17. De Vries A.G., van der Wal P.G., Long T., Eikelenboom G., Merks J.W.M. Genetic parameters of pork quality and production traits in Yorkshire populations. Livestock Production Science 1994, 40:277-289.
18. Dekkers J.C.M., Hospital F. The use of molecular genetics in the improvement of agricultural populations. Nature Reviews. Genetics 2002, 3:22-32.
19. Duthie C., Simm G., Doeschl-Wilson A., Kalm E., Knap P.W., Roehe R. Quantitative trait loci for chemical body composition traits in pigs and their positional associations with body tissues, growth and feed intake. Animal Genetics 2008, 39:130-140.
20. 2 Duroc×Pietrain resource population: II. Carcass and meat quality traits. Journal of Animal Science 2008, 86:254-266.
21. Estelle J., Gil F., Vazquez J.M., Latorre R., Ramirez G., Barragan M.C., Folch J.M., Noguera J.L., Toro M.A., Perez-Enciso M. A QTL genome scan for porcine muscle fiber traits reveals overdominance and epistasis. Journal of Animal Science 2008, 86:3290-3299.
22. Fujii J., Otsu K., Zorzato F., Deleon S., Khanna V.K., Weiler J.E., Obrien P.J., Maclennan D.H. Identification of a mutation in porcine ryanodine receptor associated with malignant hyperthermia. Science 1991, 253:448-451.
23. Garnier J.P., Klont R., Plastow G. The potential impact of current animal research on the meat industry and consumer attitudes towards meat. Meat Science 2003, 63:79-88.
24. 2 families generated from Pietrain, Meishan and Wild Boar crosses. Journal of Animal Breeding and Genetics 2003, 120:363-393.
25. Georges M. Recent progress in livestock genomics and potential impact on breeding programs. Theriogenology 2001, 55:15-21.
26. Grindflek E., Szyda J., Liu Z.T., Lien S. Detection of quantitative trait loci for meat quality in a commercial slaughter pig cross. Mammalian Genome 2001, 12:299-304.
27. Hirooka H., de Koning D.J., van Arendonk J.A.M., Harlizius B., de Groot P.N., Bovenhuis H. Genome scan reveals new coat color loci in exotic pig cross. The Journal of Heredity 2002, 93:1-8.
28. Houston R.D., Haley C.S., Archibald A.L., Rance K.A. A QTL affecting daily feed intake maps to chromosome 2 in pigs. Mammalian Genome 2005, 16:464-470.
29. Jeon J.T., Carlborg O., Tornsten A., Giuffra E., Amarger V., Chardon P., Andersson-Eklund L., Andersson K., Hansson I., Lundstrom K., Andersson L. A paternally expressed QTL affecting skeletal and cardiac muscle mass in pigs maps to the IGF2 locus. Nature Genetics 1999, 21:157-158.
30. Kanis E., De Greef K.H., Hiemstra A., van Arendonk J.A.M. Breeding for societally important traits in pigs. Journal of Animal Science 2005, 83:948-957.
31. Karlsson A., Enfalt A.C., Essengustavsson B., Lundstrom K., Rydhmer L., Stern S. Muscle histochemical and biochemical-properties in relation to meat quality during selection for increased lean tissue-growth rate in pigs. Journal of Animal Science 1993, 71:930-938.
32. Klont R. Influence of ultimate pH on meat quality and consumer purchasing decisions. PIC 2005, www.thepigsite.com/articles/6/production-and-mgmt/1506/influence-of-ultimate-ph-on-meat-quality-and-consumer-purchasing-decisions [Accessed: June 2008].
33. Knapp P., Willam A., Solkner J. Genetic parameters for lean meat content and meat quality traits in different pig breeds. Livestock Production Science 1997, 52:69-73.
34. Landgraf S., Susenbeth A., Knap P.W., Looft H., Plastow G., Kalm E., Roehe R. Developments of carcass cuts, organs, body tissues and chemical body composition during growth of pigs. Animal Science 2006, 82:889-899.
35. Landgraf S., Susenbeth A., Knap P.W., Looft H., Plastow G.S., Kalm E., Roehe R. Allometric association between in vivo estimation of body composition during growth using deuterium dilution technique and chemical analysis of serial slaughtered pigs. Animal Science 2006, 82:223-231.
36. Lee S.S., Chen Y., Moran C., Cepica S., Reiner G., Bartenschlager H., Moser G., Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 2. Journal of Animal Breeding and Genetics 2003, 120:11-19.
37. Liu G., Jennen D.G.J., Tholen E., Juengst H., Kleinwachter T., Holker M., Tesfaye D., Un G., Schreinemachers H.J., Murani E., Ponsuksili S., Kim J.J., Schellander K., Wimmers K. A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics 2007, 38:241-252.
38. Malek M., Dekkers J.C.M., Lee H.K., Baas T.J., Prusa K., Huff-Lonergan E., Rothschild M.F. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig II. Meat and muscle composition. Mammalian Genome 2001, 12:637-645.
39. Malek M., Dekkers J.C.M., Lee H.K., Baas T.J., Rothschild M.F. A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig I. Growth and body composition. Mammalian Genome 2001, 12:630-636.
40. Milan D., Bidanel J.P., Iannuccelli N., Riquet J., Amigues Y., Gruand J., Le Roy P., Renard C., Chevalet C. Detection of quantitative trait loci for carcass composition traits in pigs. Genetics, Selection, Evolution 2002, 34:705-728.
41. Mohrmann M., Roehe R., Knap P.W., Looft H., Plastow G.S., Kalm E. Quantitative trait loci associated with AutoFOM grading characteristics, carcass cuts and chemical body composition during growth of Sus scrofa. Animal Genetics 2006, 37:435-443.
42. Mohrmann M., Roehe R., Susenbeth A., Baulain U., Knap P.W., Looft H., Plastow G.S., Kalm E. Association between body composition of growing pigs determined by magnetic resonance imaging, deuterium dilution technique and chemical analysis. Meat Science 2006, 72:518-531.
43. Nii M., Hayashi T., Mikawa S., Tani F., Niki A., Mori N., Uchida Y., Fujishima-Kanaya N., Komatsu M., Awata T. Quantitative trait loci mapping for meat quality and muscle fiber traits in a Japanese Wild Boar×Large White intercross. Journal of Animal Science 2005, 83:308-315.
44. Noguera J.L., Rodriguez M.C., Varona L., Tomas A., Munoz G., Ramirez O., Barragan C., Arque M., Bidanel J.P., Amills M., Ovilo C., Sanchez A. Epistasis is a fundamental component of the genetic architecture of prolificacy in pigs. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, 13-18 August 2006, Belo Horizonte, Brazil, (CD-ROM communication 11-06).
45. Oksbjerg N., Petersen J.S., Sorensen I.L., Henckel P., Vestergaard M., Ertbjerg P., Moller A.J., Bejerholm C., Stoier S. Long-term changes in performance and meat quality of Danish Landrace pigs: a study on a current compared with an unimproved genotype. Animal Science 2000, 71:81-92.
46. Otto G., Knap P.W., Roehe R., Looft H., Cavero D., Kalm E. Different approaches of estimating economical values for drip loss as lognormally distributed trait. Livestock Science 2007, 112:43-51.
47. Otto G., Roehe R., Looft H., Thoelking L., Henning M., Plastow G.S., Kalm E. Drip loss of case-ready meat and of premium cuts and their associations with earlier measured sample drip loss, meat quality and carcass traits in pigs. Meat Science 2006, 72:680-687.
48. Otto G., Roehe R., Looft H., Thoelking L., Kalm E. Comparison of different methods for determination of drip loss and their relationships to meat quality and carcass characteristics in pigs. Meat Science 2004, 68:401-409.
49. 2 pig population. Journal of Animal Science 2002, 80:2801-2808.
50. Paszek A.A., Wilkie P.J., Flickinger G.H., Miller L.M., Louis C.F., Rohrer G.A., Alexander L.J., Beattie C.W., Schook L.B. Interval mapping of carcass and meat quality traits in a divergent swine cross. Animal Biotechnology 2001, 12:155-165.
51. Perez-Enciso M., Clop A., Noguera J.L., Ovilo C., Coll A., Folch J.M., Babot D., Estany J., Oliver M.A., Diaz I., Sanchez A. A QTL on pig chromosome 4 affects fatty acid metabolism: evidence from an Iberian by Landrace intercross. Journal of Animal Science 2000, 78:2525-2531.
52. Perez-Enciso M., Misztal I. Qxpak: a versatile mixed model application for genetical genomics and QTL analyses. Bioinformatics 2004, 20:2792-2798.
53. Ponsuksili S., Chomdej S., Murani E., Blaser U., Schreinemachers H.J., Schellander K., Wimmers K. SNP detection and genetic mapping of porcine genes encoding enzymes in hepatic metabolic pathways and evaluation of linkage with carcass traits. Animal Genetics 2005, 36:477-483.
54. Rattink A.P., de Koning D.J., Faivre M., Harlizius B., van Arendonk J.A.M., Groenen M.A.M. Fine mapping and imprinting analysis for fatness trait QTLs in pigs. Mammalian Genome 2000, 11:656-661.
55. Rodriguez C., Tomas A., Alves E., Ramirez O., Arque M., Munoz G., Barragan C., Varona L., Silio L., Amills M., Noguera J.L. QTL mapping for teat number in an Iberian-by-Meishan pig intercross. Animal Genetics 2005, 36:490-496.
56. Roehe R., Plastow G.S., Knap P.W. Quantitative and molecular genetic determination of protein and fat deposition. Homo-Journal of Comparative Human Biology 2003, 54:119-131.
57. Rohrer G.A. Identification of quantitative trait loci affecting birth characters and accumulation of backfat and weight in a Meishan-White Composite resource population. Journal of Animal Science 2000, 78:2547-2553.
58. Rohrer G.A., Alexander L.J., Hu Z.L., Smith T.P.L., Keele J.W., Beattie C.W. A comprehensive map of the porcine genome. Genome Research 1996, 6:371-391.
59. Rohrer G.A., Keele J.W. Identification of quantitative trait loci affecting carcass composition in swine: I Fat deposition traits. Journal of Animal Science 1998, 76:2247-2254.
60. Rohrer G.A., Keele J.W. Identification of quantitative trait loci affecting carcass composition in swine: II Muscling and wholesale product yield traits. Journal of Animal Science 1998, 76:2255-2262.
61. 2 population. Animal Genetics 2005, 37:17-27.
62. 2 resource population. Journal of Animal Science 2003, 81:2938-2949.
63. Schwab C.R., Baas T.J., Stalder K.J., Mabry J.W. Effect of long-term selection for increased leanness on meat and eating quality traits in Duroc swine. Journal of Animal Science 2006, 84:1577-1583.
64. Sellier P. Genetics of meat and carcass traits. The genetics of the pig 1998, 463-510. CAB International, UK. M.F. Rothschild, A. Ruvinsky (Eds.).
65. Szyda J., Grindflek E., Wideroe I.S., Lien S. Search for linked QTL and genetic epistasis in swine with application of the false discovery rate. Proceedings of the 8th World Congress on Genetics Applied to Livestock Production, 13-18 August 2006 2006, Belo Horizonte, Brazil, (CD-ROM communication 20-02).
66. Thomsen H., Lee H.K., Rothschild M.F., Malek M., Dekkers J.C.M. Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine. Journal of Animal Science 2004, 82:2213-2228.
67. van Wijk H.J., Arts D.J.G., Matthews J.O., Webster M., Ducro B.J., Knol E.F. Genetic parameters for carcass composition and pork quality estimated in a commercial production chain. Journal of Animal Science 2005, 83:324-333.
68. van Wijk H.J., Dibbits B., Baron E.E., Brings A.D., Harlizius B., Groenen M.A.M., Knol E.F., Bovenhuis H. Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross. Journal of Animal Science 2006, 84:789-799.
69. Varona L., Ovilo C., Clop A., Noguera J.L., Perez-Enciso M., Coll A., Folch J.M., Barragan C., Toro M.A., Babot D., Sanchez A. QTL mapping for growth and carcass traits in an Iberian by Landrace pig intercross: additive, dominant and epistatic effects. Genetical Research 2002, 80:145-154.
70. Vidal O., Noguera J.L., Amills M., Varona L., Gil M., Jimenez N., Davalos G., Folch J.M., Sanchez A. Identification of carcass and meat quality quantitative trait loci in a Landrace pig population selected for growth and leanness. Journal of Animal Science 2005, 83:293-300.
71. Weller J.I. Historical Overview 2001, CABI Publishing, UK, In Quantitative Trait Loci Analysis in Animals.
72. Yue G., Stratil A., Kopecny M., Schroffelova D., Schroffel J., Hojny J., Cepica S., Davoli R., Zambonelli P., Brunsch C., Sternstein I., Moser G., Bartenschlager H., Reiner G., Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 6. Journal of Animal Breeding and Genetics 2003, 120:45-55.