Identification of proteomic biomarkers in M. Longissimus dorsi as potential predictors of pork quality

Meat Science

Volumn 95, Issue 3, 2013, Pages 679-687

  Te Pas, Marinus F W ^a   Kruijt, Leo ^a   Pierzchala, Mariusz ^b   Crump, Ronald E ^a   Boeren, Sjef ^a   Keuning, Els ^a   Hoving Bolink, Rita ^a   Hortós, Maria ^c   Gispert, Marina ^c   Arnau, Jacint ^c   Diestre, Alejandro ^d   Mulder, Herman A ^a  

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b INSTITUTE OF GENETICS AND ANIMAL BREEDING   (Poland)

^c IRTA   (Spain)

^d GENUS PLC   (United States)

Author keywords

Accuracy of prediction of traits; Biological mechanism; Meat quality; NanoLC FTMSMS; SELDI TOF

Indexed keywords

ACCURACY OF PREDICTION OF TRAITS; BIOLOGICAL MECHANISMS; MEAT QUALITY; NANOLC-FTMSMS; SELDI-TOF;

FORECASTING; PROTEINS;

MEATS;

BIOLOGICAL MARKER; MUSCLE PROTEIN; PROTEOME; WATER;

ANALYSIS; ANIMAL; FOOD QUALITY; MEAT; METABOLISM; PH; PROCEDURES; PROTEOMICS; SKELETAL MUSCLE; STANDARDS; SWINE; ACCURACY OF PREDICTION OF TRAITS; ARTICLE; BIOLOGICAL MECHANISM; MEAT QUALITY; METHODOLOGY; NANOLC-FTMSMS; SELDI-TOF; STANDARD;

ANIMALS; BIOLOGICAL MARKERS; FOOD QUALITY; HYDROGEN-ION CONCENTRATION; MEAT; MUSCLE PROTEINS; MUSCLE, SKELETAL; PROTEOME; PROTEOMICS; SWINE; WATER;

ACCURACY OF PREDICTION OF TRAITS; BIOLOGICAL MECHANISM; MEAT QUALITY; NANOLC-FTMSMS; SELDI-TOF;

EID: 84880327680     PISSN: 03091740     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.meatsci.2012.12.015     Document Type: Article

References (46)

1. Aaslyng M.D., Bejerholm C., Ertbjerg P., Bertram H.C., Andersen H.J. Cooking loss and juiciness of pork in relation to raw meat quality and cooking procedure. Food Quality and Preference 2003, 14:277-288.
2. Bayol S.A., Simbi B.H., Stickland N.C. A maternal cafeteria diet during gestation and lactation promotes adiposity and impairs skeletal muscle development and metabolism in rat offspring at weaning. The Journal of Physiology 2005, 567:951-961.
3. Becker B.A., Mayes H.F., Hahn G.L., Nienaber J.A., Jesse G.W., Anderson M.E., Heymann H., Hedrick H.B. Effect of fasting and transportation on various physiological parameters and meat quality of slaughter hogs. Journal of Animal Science 1989, 67:334-341.
4. Boersema P.J., Raijmakers R., Lemeer S., Mohammed S., Heck A.J.R. Multiplex peptide stable isotope dimethyl labeling for quantitative proteomics. Nature Protocols 2009, 4:484-494.
5. Calus M.P.L. Genomic breeding value prediction: Methods and procedures. Animal 2010, 4:157-164.
6. Calus M.P.L., Veerkamp R.F. Accuracy of breeding values when using and ignoring the polygenic effect in genomic breeding value estimation with a marker density of one SNP per cM. Journal of Animal Breeding and Genetics 2007, 124:362-368.
7. Chong I.-G., Jun C.-H. Performance of some variable selection methods when multicollinearity is present. Chemometrics and Intelligent Laboratory Systems 2005, 78:103-112.
8. Cox J., Mann M. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification. Nature Biotechnology 2008, 26s:1367-1372.
9. Cox J., Neuhauser N., Michalski A., Scheltema R.A., Olsen J.V., Mann M. Andromeda: A peptide search engine integrated into the MaxQuant environment. Journal of Proteome Research 2011, 10:1794-1805.
10. Damerval C., Maurice A., Josse J.M., de-Vienne D. Quantitative trait loci underlying gene product variation: A novel perspective for analyzing regulation of genome expression. Genetics 1994, 137:289-301.
11. Geladi P., Kowalski B.R. Partial least-squares regression: A tutorial. Analytica Chimica Acta 1986, 186:1-17.
12. Gispert M., Valero A., Oliver M.A., Diestre A. Problems related to lack of fat in pork carcasses. Eurocarne 1997, 61:27-32.
13. Goodsaid F., Frueh F. Biomarker qualification pilot process at the us food and drug administration. American Association Pharmaceutical Scientists Journal 2007, 9. Article 10 (http://www.aapsj.org).
14. Hasegawa K., Funatsu K. GA strategy for variable selection in QSAR studies: GAPLS and D-optimal designs for predictive QSAR model. Journal of Molecular Structure (THEOCHEM) 1998, 425:255-262.
15. Honikel K.O. Reference methods for the assessment of physical characteristics of meat. Meat Science 1998, 49:447-457.
16. Huff-Lonergan E., Baas T.J., Malek M., Dekkers J.C., Prusa K., Rothschild M.F. Correlations among selected pork quality traits. Journal of Animal Science 2002, 80:617-627.
17. Keane M.G., Allen P. Effects of production system intensity on performance, carcass composition and meat quality of beef cattle. Livestock Production Science 1998, 56:203-214.
18. Kwasiborski A., Sayd T., Chambon C., Santé-Lhoutellier V., Rocha D., Terlouw C. Pig Longissimus lumborum proteome: Part I. Effects of genetic background, rearing environment and gender. Meat Science 2008, 80:968-981.
19. Kwasiborski A., Sayd T., Chambon C., Santé-Lhoutellier V., Rocha D., Terlouw C. Pig Longissimus lumborum proteome: Part II: Relationships between protein content and meat quality. Meat Science 2008, 80:982-996.
20. Liu M.Y., Xydakis A.M., Hoogeveen R.C., Jones P.H., O'Brian Smith E., Nelson K.W., Ballantyne C.M. Multiplexed analysis of biomarkers related to obesity and the metabolic syndrome in human plasma, using the Luminex-100 system. Clinical Chemistry 2005, 51:1102-1109.
21. Lu J., Boeren S., de Vries S.C., van Valenberg H.J.F., Vervoort J., Hettinga K. Filter-aided sample preparation with dimethyl labeling to identify and quantify milk fat globule membrane proteins. Journal of Proteomics 2011, 74:34-43.
22. Mach N., Keuning E., Kruijt L., Hortós M., Arnau J., te Pas M.F.W. Comparative proteomic profiling of two muscles from five divergent pig breeds using SELDI-TOF proteomics technology. Journal of Animal Science 2010, 88:1522-1534.
23. Melody J.L., Lonergan S.M., Rowe L.J., Huiatt T.W., Mayes M.S., Huff-Lonergan E. Early postmortem biochemical factors influence tenderness and water-holding capacity of three porcine muscles. Journal of Animal Science 2004, 82:1195-1205.
24. Meuwissen T.H.E., Goddard M.E. The use of marker haplotypes in animal breeding schemes. Genetics Selection Evolution 1996, 28:161-176.
25. Müller M., Kersten S. Nutrigenomics: Goals and strategies. Nature Reviews Genetics 2003, 4:315-322.
26. NPB (National pork board) Pork quality standards 1999, Des Moines, IA, USA.
27. Paek S.H., Lee S.H., Cho J.H., Kim Y.S. Development of rapid one-step immunochromatographic assay. Nature Methods 2000, 22:53-60.
28. Pierzchala M., Pareek C.S., Lisowski P., Urbanski P., Goluch D., Czarnik U., Kamyczek M., Rozycki M., Cooper R.G., Kuryl J. Expression profile of porcine MYF5 and MYF6 genes in skeletal muscles of young growing gilts of five breeds at different ages, based on the most stable reference genes. Animal Science Papers and Reports 2011, 2011(29):231-246.
29. Pierzchala M., Pareek C.S., Urbanski P., Goluch D., Kamyczek M., Rozycki M., Smoczynski R., Horbanczuk J.O., Kuryl J. Study of the differential transcription in liver tissue of growth hormone receptor (GHR), insulin-like growth factor IGF1, IGF2 and IGF1-receptor genes at different postnatal developmental ages in pig breeds. Molecular Biology Reports 2011, 39:3055-3066.
30. Plackett R.L., Burman J.P. The design of optimum multifactorial experiments. Biometrika 1946, 33:305-325.
31. Sall J., Creighton L., Lehman A. JMP® start statistics: A guide to statistics and data analysis using jmp® 2007, SAS Institute Inc., Cary, NC. Fourth edition.
32. SAS release 9.3 2007, SAS Instute Inc., Cary, NC, USA.
33. Sellier P., Monin G. Genetics of pig meat quality: A review. Journal of Muscle Foods 1994, 5:187-219.
34. Sieczkowsk a H., Zybert A., Krzecio E., Antosik K., Kocwin-Podsiadla M., Pierzchala M., Urbanski P. The expression of genes PKM2 and CAST in the muscle tissue of pigs differentiated by glycolytic potential and drip loss, with reference to the genetic group. Meat Science 2010, 84:180-185.
35. Tanaka K., Matsumoto E., Higashimaki Y., Katagiri T., Sugimoto T., Seino S., Kaji H. Role of osteoglycin in the linkage between muscle and bone. Journal of Biological Chemistry 2012, 287:11616-11628.
36. Tarrant P.V. The effects of handling, transport, slaughter and chilling on meat quality and yield in pigs: A review. Irish Journal of Food Science and Technology 1989, 13:79-107.
37. Te Pas M.F.W., Hoekman A.J.W., Smits M.A. Biomarkers as management tools for the pork production chain industries. Journal on Chain and Network Science 2011, 11:155-166.
38. Te Pas M.F.W., Jansen J., Broekman K.C.J.A., Reimert H., Heuven H.C.M. Post mortem proteome degradation profiles of longissimus muscle in Yorkshire and Duroc pigs and its relationship with pork quality traits. Meat Science 2009, 83:744-751.
39. Te Pas M.F.W., Keuning E., Hulsegge B., Hoving-Bolink A.H., Evans G., Mulder H.A. Longissimus muscle transcriptome profiles related to carcass and meat quality traits in fresh meat Pietrain carcasses. Journal of Animal Science 2010, 88:4044-4055.
40. Te Pas M.F.W., Keuning E., van de Wiel D.J.M., Young J.F., Oksbjerg N., Kruijt L. Proteome profiles of Longissimus and Biceps femoris porcine muscles related to exercise and resting. Journal of Life Science 2011, 5:598-608.
41. Von Rohr P., Hofer A., Kunzi N. Economic values for meat quality traits in pigs. Journal of Animal Science 1999, 77:2633-2640.
42. Warriss P.D., Brown S.N. The relationships between initial pH, reflectance and exudation in pig muscle. Meat Science 1987, 20:65-74.
43. Wehrens R., Mevik B.-H. pls: Partial least squares regression (PLSR) and principal component regression (PCR). R package version 2.1-0 2007, http://mevik.net/work/software/pls.html.
44. Wisniewski J.R., Zougman A., Nagaraj N., Mann M. Universal sample preparation method for proteome analysis. Nature Methods 2009, 6:359-362.
45. Ye K., Hamada M. Critical values of the Lenth method for unreplicated factorial designs. Journal of Quality Technology 2000, 32:57-66.
46. Young J.F., Bertram H.C., Oksbjerg N. Rest before slaughter ameliorates pre-slaughter stress-induced increased drip los but not stress-induced increase in the toughness of pork. Meat Science 2009, 83:634-641.