Transcriptome analysis to identify differential gene expression affecting meat quality in heavy Italian pigs

Animal Genetics

Volumn 42, Issue 2, 2011, Pages 161-171

  Gorni, C ^a   Garino, C ^a,b,d   Iacuaniello, S ^a,b   Castiglioni, B ^c   Stella, A ^a,c   Restelli, G L ^b   Pagnacco, G ^b   Mariani, P ^a  

^a PARCO TECNOLOGICO PADANO   (Italy)

^b UNIVERSITY OF MILAN   (Italy)

^c CNR Consiglio Nazionale delle Ricerche   (Italy)

^d UNIVERSITY OF EASTERN PIEDMONT   (Italy)

Author keywords

Heavy pig; Meat quality; Skeletal muscle; Suppression subtractive hybridization

Indexed keywords

PIERIS BRASSICAE; SUIDAE;

TRANSCRIPTOME;

ANALYSIS; ANIMAL; CHROMOSOME MAP; DNA SEQUENCE; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENETICS; GENOME; MALE; MEAT; METABOLISM; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROCEDURES; SINGLE NUCLEOTIDE POLYMORPHISM; SKELETAL MUSCLE; SPECIES DIFFERENCE; SUBTRACTIVE HYBRIDIZATION; SWINE; VETERINARY;

ANIMALS; BASE SEQUENCE; CHROMOSOME MAPPING; FEMALE; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION; GENE LIBRARY; GENOME; MALE; MEAT; MOLECULAR SEQUENCE DATA; MUSCLE, SKELETAL; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SEQUENCE ANALYSIS, DNA; SPECIES SPECIFICITY; SUBTRACTIVE HYBRIDIZATION TECHNIQUES; SWINE; TRANSCRIPTOME;

EID: 79952591582     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2010.02098.x     Document Type: Article

References (71)

1. Altschul S.F., Gish W., Miller W., Myers E.W. & Lipman D.J. (1990) Basic local alignment search tool. Journal of Molecular Biology 215, 403-10.
2. Bai Q., McGillivray C., da Costa N., Dornan S., Evans G., Stear M.J. & Chang K.C. (2003) Development of a porcine skeletal muscle cDNA microarray: analysis of differential transcript expression in phenotypically distinct muscles. BMC Genomics 4, 8.
3. Beeckmann P., Schroffel J., Moser G., Bartenschlager H., Reiner G. & Geldermann H. (2003) Linkage and QTL mapping for Sus scrofa chromosome 3. Journal of Animal Breeding and Genetics 120, 20-7. (Pubitemid 38463650)
4. Bozzo C., Spolaore B., Toniolo L., Stevens L., Bastide B., Cieniewski-Bernard C., Fontana A., Mounier Y. & Reggiani C. (2005) Nerve influence on myosin light chain phosphorylation in slow and fast skeletal muscles. The FEBS Journal 272, 5771-85.
5. Cagnazzo M., te Pas M.F., Priem J., de Wit A.A., Pool M.H., Davoli R. & Russo V. (2006) Comparison of prenatal muscle tissue expression profiles of two pig breeds differing in muscle characteristics. Journal of Animal Science 84, 1-10.
6. Cao W., Epstein C., Liu H. et al. (2004) Comparing gene discovery from Affymetrix GeneChip microarrays and Clontech PCR-select cDNA subtraction: a case study. BMC Genomics 5, 26.
7. Cepica S., Bartenschlager H. & Geldermann H. (2007) Mapping of QTL on chromosome X for fat deposition, muscling and growth traits in a wild boar x Meishan F2 family using a high-density gene map. Animal Genetics 38, 634.
8. Chang K.C., Da Costa N., Blackley R., Southwood O., Evans G., Plastow G., Wood J.D. & Richardson R.I. (2003) Relationships of myosin heavy chain fibre types to meat quality traits in traditional and modern pigs. Meat Science 64, 93-103.
9. Davoli R. & Braglia S. (2008) Molecular approaches in pig breeding to improve meat quality. Briefings in Functional Genomics and Proteomics 6, 313-321.
10. Davoli R., Fontanesi L., Zambonelli P. et al. (2002) Isolation of porcine expressed sequence tags for the construction of a first genomic transcript map of the skeletal muscle in pig. Animal Genetics 33, 3-18. (Pubitemid 34137596)
11. Department for Environment Food and Rural Affairs (DEFRA). National Statistics 2006. www.statistics.gov.uk.
12. Dekkers J.C.M. (2004) Commercial application of marker-and gene-assisted selection in livestock: strategies and lessons. Journal of Animal Science 82, E313.
13. Diatchenko L., Lau Y.F., Campbell A.P. et al. (1996) Suppression subtractive hybridization: a method for generating differentially regulated or tissue-specific cDNA probes and libraries. Proceedings of the National Academy of Sciences of the United States of America 93, 6025-30. (Pubitemid 26190796)
14. Dragos-Wendrich M., Moser G., Bartenschlager H., Reiner G. & Geldermann H. (2003) Linkage and QTL mapping for Sus scrofa chromosome 11. Journal of Animal Breeding and Genetics 120, 89-94. (Pubitemid 38463657)
15. Edwards D.B., Ernst C.W., Raney N.E., Doumit M.E., Hoge M.D. & Bates R.O. (2008) Quantitative trait locus mapping in an F2 Duroc x Pietrain resource population: II. Carcass and meat quality traits. Journal of Animal Science 86, 254-66. (Pubitemid 351229747)
16. Eikelenboom G. & van den Bergh S.G. (1973) Mitochondrial metabolism in stress-susceptible pigs. Journal of Animal Science 37, 692-6.
17. Evans G.J., Giuffra E., Sanchez A., Kerje S., Davalos G., Vidal O., Illan S., Noguera J.L., Varona L. & Velander I. (2003) Identification of quantitative trait loci for production traits in commercial pig populations. Genetics 164, 621.
18. Fernandez A.I., Alves E., Fernandez A., de Pedro E., Lopez-Garcia M.A., Ovilo C., Rodriguez M.C. & Silio L. (2008) Mitochondrial genome polymorphisms associated with longissimus muscle composition in Iberian pigs. Journal of Animal Science 86, 1283-90. (Pubitemid 351860776)
19. Harmegnies N., Davin F., De Smet S., Buys N., Georges M. & Coppieters W. (2006) Results of a whole-genome quantitative trait locus scan for growth, carcass composition and meat quality in a porcine four-way cross. Animal Genetics 37, 543-53. (Pubitemid 44789656)
20. Hellemans J., Mortier G., De Paepe A., Speleman F. & Vandesompele J. (2007) qBase relative quantification framework and software for management and automated analysis of real-time quantitative PCR data. Genome biology 8, R19.
21. Hu Z.L. & Reecy J.M. (2007) Animal QTLdb: beyond a repository. A public platform for QTL comparisons and integration with diverse types of structural genomic information. Mammalian Genome 18, 1-4.
22. Hu H., Wang J., Zhu R., Guo J. & Wu Y. (2008) Effect of myosin heavy chain composition of muscles on meat quality in Laiwu pigs and Duroc. Science in China. Series C, Life Sciences 51, 127-32. (Pubitemid 351199323)
23. Huang X. (1994) On global sequence alignment. Computer Applications in the Biosciences 10, 227-35.
24. Jansen E.J., Holthuis J.C., McGrouther C., Burbach J.P. & Martens G.J. (1998) Intracellular trafficking of the vacuolar H+-ATPase accessory subunit Ac45. Journal of Cell Science 111(Pt 20), 2999-3006. (Pubitemid 28517388)
25. Kanehisa M. & Goto S. (2000) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Research 28, 27-30. (Pubitemid 30047706)
26. Karlskov-Mortensen P., Bruun C.S., Braunschweig M.H., Sawera M., Markljung E., Enfält A.C., Hedebro-Velander I., Josell Å., Lindahl G. & Lundström K. (2006) Genome-wide identification of quantitative trait loci in a cross between Hampshire and Landrace I: carcass traits. Animal Genetics 37, 156-62.
27. Katoch S.S. & Soni A. (1999) Changes in myosin ATPase activity in skeletal muscles of rat during cold stress. Indian Journal of Biochemistry and Biophysics 36, 204-6. (Pubitemid 129486078)
28. Kim J.J., Rothschild M.F., Beever J., Rodriguez-Zas S. & Dekkers J.C. (2005a) Joint analysis of two breed cross populations in pigs to improve detection and characterization of quantitative trait loci. Journal of Animal Science 83, 1229-40.
29. Kim J.J., Zhao H., Thomsen H., Rothschild M.F. & Dekkers J.C. (2005b) Combined line-cross and half-sib QTL analysis of crosses between outbred lines. Genetical Research 85, 235-48. (Pubitemid 41264230)
30. Kim C.W., Hong Y.H., Yun S.I. et al. (2006a) Use of microsatellite markers to detect quantitative trait loci in Yorkshire pigs. The Journal of Reproduction and Development 52, 229-37.
31. Kim T.H., Kim N.S., Lim D. et al. (2006b) Generation and analysis of large-scale expressed sequence tags (ESTs) from a full-length enriched cDNA library of porcine backfat tissue. BMC Genomics 7, 36.
32. de Koning D.J., Harlizius B., Rattink A.P., Groenen M.A., Brascamp E.W. & van Arendonk J.A. (2001) Detection and characterization of quantitative trait loci for meat quality traits in pigs. Journal of Animal Science 79, 2812-9. (Pubitemid 33721431)
33. de Koning D.J., Pong-Wong R., Varona L., Evans G.J., Giuffra E., Sanchez A., Plastow G., Noguera J.L., Andersson L. & Haley C.S. (2003) Full pedigree quantitative trait locus analysis in commercial pigs using variance components. Journal of Animal Science 81, 2155.
34. Küchenmeister U., Nürnberg K., Fiedler I., Kuhn G., Nürnberg G. & Ender K. (1999) Cell injury and meat quality of pig in the time period post mortem from two genotypes susceptible or resistant to malignant hyperthermia. European Food Research and Technology 209, 97-103.
35. Lee S.S., Chen Y., Moran C., Cepica S., Reiner G., Bartenschlager H., Moser G. & Geldermann H. (2003) Linkage and QTL mapping for Sus scrofa chromosome 2. Journal of Animal Breeding and Genetics 120, 11-9. (Pubitemid 38463649)
36. Liu G., Jennen D.G., Tholen E. et al. (2007) A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genetics 38, 241-52. (Pubitemid 46848872)
37. Liu G., Kim J.J., Jonas E., Wimmers K., Ponsuksili S., Murani E., Phatsara C., Tholen E., Juengst H. & Tesfaye D. (2008) Combined line-cross and half-sib QTL analysis in Duroc-Pietrain population. Mammalian Genome 19, 429-38.
38. Lobjois V., Liaubet L., SanCristobal M., Glenisson J., Feve K., Rallieres J., Le Roy P., Milan D., Cherel P. & Hatey F. (2008) A muscle transcriptome analysis identifies positional candidate genes for a complex trait in pig. Animal Genetics 39, 147-62. (Pubitemid 351441682)
39. Luo G.F., Yu T.Y., Wen X.H., Li Y. & Yang G.S. (2008) Alteration of mitochondrial oxidative capacity during porcine preadipocyte differentiation and in response to leptin. Molecular and Cellular Biochemistry 307, 83-91. (Pubitemid 350238650)
40. Mains R.E., Alam M.R., Johnson R.C., Darlington D.N., Back N., Hand T.A. & Eipper B.A. (1999) Kalirin, a multifunctional PAM COOH-terminal domain interactor protein, affects cytoskeletal organization and ACTH secretion from AtT-20 cells. Journal of Biological Chemistry 274, 2929-37. (Pubitemid 29075380)
41. Malek M., Dekkers J.C., Lee H.K., Baas T.J., Prusa K., Huff-Lonergan E. & Rothschild M.F. (2001a) A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. II. Meat and muscle composition. Mammalian Genome 12, 637-45.
42. Malek M., Dekkers J.C., Lee H.K., Baas T.J. & Rothschild M.F. (2001b) A molecular genome scan analysis to identify chromosomal regions influencing economic traits in the pig. I. Growth and body composition. Mammalian Genome 12, 630-6. (Pubitemid 32675531)
43. Milan D., Hawken R., Cabau C. et al. (2000a) IMpRH server: an RH mapping server available on the Web. Bioinformatics 16, 558-9.
44. Milan D., Jeon J.T., Looft C., Amarger V., Robic A., Thelander M., Rogel-Gaillard C., Paul S., Iannuccelli N. & Rask L. (2000b) A mutation in PRKAG3 associated with excess glycogen content in pig skeletal muscle. Science 288, 1248.
45. Milan D., Bidanel J.P., Iannuccelli N., Riquet J., Amigues Y., Gruand J., Le Roy P., Renard C. & Chevalet C. (2002) Detection of quantitative trait loci for carcass composition traits in pigs. Genetics, Selection, Evolution 34, 705-28.
46. Nezer C., Moreau L., Wagenaar D. & Georges M. (2002) Results of a whole genome scan targeting QTL for growth and carcass traits in a Pietrain x Large White intercross. Genetics, Selection, Evolution 34, 371-87.
47. Olsen J.V., Blagoev B., Gnad F., Macek B., Kumar C., Mortensen P. & Mann M. (2006) Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. Cell 127, 635-48. (Pubitemid 44647421)
48. Ovilo C., Clop A., Noguera J.L. et al. (2002) Quantitative trait locus mapping for meat quality traits in an Iberian x Landrace F2 pig population. Journal of Animal Science 80, 2801-8. (Pubitemid 41132931)
49. Ponsuksili S., Jonas E., Murani E., Phatsara C., Srikanchai T., Walz C., Schwerin M., Schellander K. & Wimmers K. (2008) Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics 9, 367.
50. Ramirez C.D. & Padron R. (2004) Familial hypertrophic cardiomyopathy: genes, mutations and animal models. A review. Investigacion Clinica 45, 69-99.
51. Rogatcheva M.B., Chen K., Larkin D.M., Meyers S.N., Marron B.M., He W., Schook L.B. & Beever J.E. (2008) Piggy-BACing the human genome I: constructing a porcine BAC physical map through comparative genomics. Animal Biotechnology 19, 28-42. (Pubitemid 351170649)
52. Rohrer G.A., Thallman R.M., Shackelford S., Wheeler T. & Koohmaraie M. (2006) A genome scan for loci affecting pork quality in a Duroc-Landrace F population. Animal Genetics 37, 17-27. (Pubitemid 43381848)
53. Rosenvold K. & Andersen H.J. (2003) Factors of significance for pork quality - a review. Meat Science 64, 219-37.
54. Rothschild M.F., Hu Z.L. & Jiang Z. (2007) Advances in QTL mapping in pigs. International Journal of Biological Sciences 3, 192-7. (Pubitemid 46280055)
55. Russo V. (1986) Selezione e incrocio per il miglioramento quantiqualitativo della produzione suinicola. Suinicoltura 27, 28.
56. Sellier P. (1998) Genetics of meat and carcass traits. In. The Genetics of the Pig (Ed. by Rothschild M.F., Ruvinsky A.), pp. 463-493, CAB International, Cambridge (GBR).
57. Shmueli O., Horn-Saban S., Chalifa-Caspi V., Shmoish M., Ophir R., Benjamin-Rodrig H., Safran M., Domany E. & Lancet D. (2003) GeneNote: whole genome expression profiles in normal human tissues. Comptes Rendus Biologies 326, 1067-72. (Pubitemid 38016462)
58. Thomsen H., Lee H.K., Rothschild M.F., Malek M. & Dekkers J.C.M. (2004) Characterization of quantitative trait loci for growth and meat quality in a cross between commercial breeds of swine. Journal of Animal Science 82, 2213.
59. Toniolo L., Patruno M., Maccatrozzo L., Pellegrino M.A., Canepari M., Rossi R., D'Antona G., Bottinelli R., Reggiani C. & Mascarello F. (2004) Fast fibres in a large animal: fibre types, contractile properties and myosin expression in pig skeletal muscles. Journal of Experimental Biology 207, 1875-86. (Pubitemid 38826061)
60. Van Laere A.S., Nguyen M., Braunschweig M., Nezer C., Collette C., Moreau L., Archibald A.L., Haley C.S., Buys N. & Tally M. (2003) A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature 425, 832-6. (Pubitemid 37351466)
61. Vandesompele J., De Preter K., Pattyn F., Poppe B., Van Roy N., De Paepe A. & Speleman F. (2002) Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome biology 3, research 0034.1-0034.11.
62. van Wijk H.J., Dibbits B., Baron E.E., Brings A.D., Harlizius B., Groenen M.A., Knol E.F. & Bovenhuis H. (2006) Identification of quantitative trait loci for carcass composition and pork quality traits in a commercial finishing cross. Journal of Animal Science 84, 789-99. (Pubitemid 44405637)
63. Wimmers K., Fiedler I., Hardge T., Murani E., Schellander K. & Ponsuksili S. (2006) QTL for microstructural and biophysical muscle properties and body composition in pigs. BMC Genetics 7, 15.
64. Worby C.A. & Dixon J.E. (2002) Sorting out the cellular functions of sorting nexins. Nature Reviews. Molecular Cell Biology 3, 919-31. (Pubitemid 35477370)
65. Wyllie C.J., Sargent C.A. & Affara N.A. (2008) Identifying and locating genes of possible commercial and biological importance within the pig mitochondrial genome. Proceedings of XVI Plant and Animal Genome Conference, San Diego, USA., P569.
66. Xu D.Q., Zhang Y.B., Xiong Y.Z., Gui J.F., Jiang S.W. & Su Y.H. (2003) Construction of forward and reverse subtracted cDNA libraries between muscle tissue of Meishan and Landrace pigs. Yi Chuan Xue Bao 30, 668-72.
67. Yanai I., Benjamin H., Shmoish M., Chalifa-Caspi V., Shklar M., Ophir R., Bar-Even A., Horn-Saban S., Safran M. & Domany E. (2005) Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21, 650-9. (Pubitemid 40424791)
68. Yao J., Coussens P.M., Saama P., Suchyta S. & Ernst C.W. (2002) Generation of expressed sequence tags from a normalized porcine skeletal muscle cDNA library. Animal Biotechnology 13, 211-22. (Pubitemid 135705598)
69. Yerle M., Pinton P., Robic A. et al. (1998) Construction of a whole-genome radiation hybrid panel for high-resolution gene mapping in pigs. Cytogenetics and Cell Genetics 82, 182-8. (Pubitemid 29002460)
70. Yue G., Schroffel J., Moser G., Bartenschlager H., Reiner G. & Geldermann H. (2003) Linkage and QTL mapping for Sus scrofa chromosome 12. Journal of Animal Breeding and Genetics 120, 95-102. (Pubitemid 38463658)
71. Zheng B., Tang T., Tang N., Kudlicka K., Ohtsubo K., Ma P., Marth J.D., Farquhar M.G. & Lehtonen E. (2006) Essential role of RGS-PX1/sorting nexin 13 in mouse development and regulation of endocytosis dynamics. Proceedings of the National Academy of Sciences 103, 16776.