MEHMET ULAŞ ÇINAR, Huitao FAN, Christiane NEUHOFF, Christine GROßE-BRINKHAUS

eQTL Analysis and association of MYF6 mRNA expression with meat quality traits in pigs

Bu çalışmanın amacı literatürde herculin ve myogenic factor 4 (MRF4) olarak ta bilinen domuz MYF6 (myogenic factor 6) geninin et kalite özellikleri ile ilişkisi belirlenmesi ve transkripsiyon seviyesinde gen ifadesinin kontrölünün QTL (eQTL) yöntemiyle incelenmesidir. Bu amaçla, Duroc × Pietrain F2 deneysel populasyonu (DuPi; n = 313) asosiyasyon ve eQTL analizleri icin kullanılmıştır. MYF6 geninin mRNA düzeyleri Longissimus dorsi kas dokusu hücrelerinde asosiyasyon ve eQTL analizi icin qRT-PCR kullanılarak ölçülmüştür. MYF6 genin mRNA düzeyi iletkenlik24L (P

Anahtar Kelimeler:

domuz eti, domuz, kantitatif karakter lokusları, transkripsiyon, gen ifadesi, genler, genetik analizler, et kalitesi, elçi RNA

MYF6 mRNA ifadesinin domuzlarda et kalitesi ile ilişkisi ve eQTL analizi

The aim of this research was to measure mRNA expression of porcine MYF6 (myogenic factor 6, also known in the medical literature as herculin and myogenic regulatory factor 4, MRF4) and to perform association study with meat quality traits as well as to unravel the transcriptional regulation of this gene by expression QTL (eQTL) study. For this purpose, Duroc × Pietrain F2 resource population (DuPi; n = 313) were used for association and eQTL study. The mRNA levels in Longissimus dorsi muscle tissue of MYF6 gene were evaluated by using qRT-PCR to identify association between gene expression and meat quality traits as well as to analyse eQTL. The mRNA expression of MYF6 associated with conductivity24L (P<0.01) and pH24L (P<0.1). Expression of MYF6 gene was higher in animals with high pH and conductivity of muscle. Linkage analysis using GridQTL revealed 4 trans-regulated eQTL on four porcine autosomes. Significant eQTL [P<0.01, CW (chromosome-wide)] were found for MYF6 on SSC2. A suggestive eQTL (P<0.05, CW) was identified on SSC8. These results revealed that gene expression of MYF6 associated with the meat quality traits and this gene could be potential functional candidate gene for meat quality traits in pigs. However, the analysis of eQTL also suggested that additional genes encoding for transcription factors (TF) could be considered, via fine-mapping underlying the eQTL peaks, in order to understand interaction among these genes.

Keywords:

pigmeat, pigs, quantitative trait loci, transcription, gene expression, genes, genetic analysis, meat quality, messenger RNA,

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1. Davoli R, Fontanesi L, Cagnazzo M, Scotti E, Buttazzoni L, Yerle M, Russo V: Identification of SNPs, mapping and analysis of allele frequencies in two candidate genes for meat production traits: The porcine myosin heavy chain 2B (MYH4) and the skeletal muscle myosin regulatory light chain 2 (HUMMLC2B). Animal Genet, 34 (3): 221-225, 2003.
2. Fontanesi L, Colombo M, Tognazzi L, Scotti E, Buttazzoni L, Dall’Olio S, Davoli R, Russo V: The porcine TBC1D1 gene: Mapping, SNP identification, and association study with meat, carcass and production traits in Italian heavy pigs. Mol Biol Rep, 38 (2): 1425-1431, 2011.
3. Srikanchai T, Murani E, Phatsara C, Schwerin M, Schellander K, Wimmers K, Ponsuksili S: Association of ZYX polymorphisms with carcass and meat quality traits in commercial pigs. Meat Sci, 84 (1): 159-164, 2010.
4. Rothschild MF, Fan B, Lkhagvadorj S, Cai W, Young J, Smith RM, Dekkers JCM, Huff-Lonergan E, Lonergan SM: Identification of genetic markers associated with residual feed intake and meat quality traits in the pig. Meat Sci, 84 (4): 645-650, 2010.
5. Maak S, Neumann K, Swalve HH: Identification and analysis of putative regulatory sequences for the MYF5/MYF6 locus in different vertebrate species. Gene, 379, 141-147, 2006.
6. Wyszynska-Koko J, Kuryl J: Porcine MYF6 gene: sequence, homology analysis, and variation in the promoter region. Anim Biotech, 15 (2): 159-173, 2004.
7. Bober E, Lyons GE, Braun T, Cossu G, Buckingham M, Arnold HH: The muscle regulatory gene, Myf-6, has a biphasic pattern of expression during early mouse development. J Cell Biol, 113 (6): 1255-1265, 1991.
8. Fan H, Cinar MU, Phatsara C, Tesfaye D, Tholen E, Looft C, Schellander K: Molecular mechanism underlying the differential MYF6 expression in postnatal skeletal muscle of Duroc and Pietrain breeds. Gene, 2011.
9. Hinterberger TJ, Sassoon DA, Rhodes SJ, Konieczny SF: Expression of the muscle regulatory factor MRF4 during somite and skeletal myofiber development. Dev Biol, 147 (1): 144-156, 1991.
10. Lowe DA, Lund T, Alway SE: Hypertrophy-stimulated myogenic regulatory factor mRNA increases are attenuated in fast muscle of aged quails. Am J Physiol, 275 (1 Pt 1): C155-162, 1998.
11. Kassar-Duchossoy L, Gayraud-Morel B, Gomes D, Rocancourt D, Buckingham M, Shinin V, Tajbakhsh S: Mrf4 determines skeletal muscle identity in Myf5: Myod double-mutant mice. Nature, 431 (7007): 466-471, 2004.
12. Buonanno A, Apone L, Morasso MI, Beers R, Brenner HR, Eftimie R: The myod family of myogenic factors is regulated by electrical-activity - Isolation and characterization of a mouse Myf-5 Cdna. Nucleic Acids Res, 20 (3): 539-544, 1992.
13. Carvajal JJ, Rigby PWJ: Regulation of gene expression in vertebrate skeletal muscle. Exp Cell Res, 316 (18): 3014-3018, 2010.
14. Pas MFWT, Harders FL, Soumillion A, Born L, Buist W, Meuwissen THE: Genetic variation at the porcine MYF-5 gene locus. Lack of association with meat production traits. Mamm Genome, 10 (2): 123-127, 1999.
15. Vykoukalova Z, Knoll A, Dvorak J, Rohrer GA, Cepica S: Linkage and radiation hybrid mapping of the porcine MYF6 gene to chromosome 5. Animal Genet, 34 (3): 238-240, 2003.
16. Ropka-Molik K, Eckert R, Piorkowska K: The expression pattern of myogenic regulatory factors MyoD, Myf6 and Pax7 in postnatal porcine skeletal muscles. Gene Exp Patt, 11 (1-2): 79-83, 2011.
17. Gandolfi G, Cinar MU, Ponsuksili S, Wimmers K, Tesfaye D, Looft C, Jungst H, Tholen E, Phatsara C, Schellander K: Association of PPARGC1A and CAPNS1 gene polymorphisms and expression with meat quality traits in pigs. Meat Sci, 89 (4): 478-485, 2011.
18. Kayan A, Cinar MU, Uddin MJ, Phatsara C, Wimmers K, Ponsuksili S, Tesfaye D, Looft C, Juengst H, T holen E, Schellander K: Polymorphism and expression of the porcine Tenascin C gene associated with meat and carcass quality. Meat Sci, 89 (1): 76-83, 2011.
19. Jansen RC, Nap JP: Genetical genomics: The added value from segregation. Trends Genet, 17 (7): 388-391, 2001.
20. Liu G, Jennen DGJ, Tholen E, Juengst H, Kleinwachter T, Holker M, Tesfaye D, Un G, Schreinemachers HJ, Murani E, Schellander K, Wimmers K: A genome scan reveals QTL for growth, fatness, leanness and meat quality in a Duroc-Pietrain resource population. Animal Genet, 38 (3): 241-252, 2007.
21. ZDS: Richtlinie für die Stationsprüfung auf Mastleistung, Schlachtkörperwert und Fleischbeschaffenheit beim Schwein. Zentralverband der Deutschen Schweineproduktion eV, Ausschussfür Leistungsprüfung und Zuchtwertschätzung, Bonn, 2003.
22. Grosse-Brinkhaus C, Phatsara C, Tholen E, Schellander K, Jonas ES: Finemapping of QTL for meat quality traits on porcine chromosome 1. Zuchtungskunde, 81 (1): 63-68, 2009.
23. Seaton G, Grunchec JA, White I, Allen J, De Koning DJ, Wei W, Berry D, Haley C, Knott S: GridQTL: A Grid Portal for QTL Mapping of Compute Intensive Datasets. In: Proceedings of the 8th World Congress on Genetics Applied to Livestock Production: August 13-18 2006; Belo Horizonte, Brazil, 2006.
24. Churchill GA, Doerge RW: Empirical threshold values for quantitative trait mapping. Genetics, 138, 963-971, 1994.
25. Uemoto Y, Soma Y, Sato S, Shibata T, Kadowaki H, Katoh K, Kobayashi E, Suzuki K: Mapping QTL for fat area ratios and serum leptin concentrations in a Duroc purebred population. Anim Sci J, doi: 10.1111/j.1740-0929.2011.00951.x, 2011.
26. Cagnazzo M, te Pas MF, Priem J, de Wit AA, Pool MH, Davoli R, Russo V: Comparison of prenatal muscle tissue expression profiles of two pig breeds differing in muscle characteristics. J Anim Sci, 84 (1): 1-10, 2006.
27. Pownall ME, Gustafsson MK, Emerson CP Jr: Myogenic regulatory factors and the specification of muscle progenitors in vertebrate embryos. Annu Rev Cell Dev Biol, 18, 747-783, 2002.
28. Miner JH, Wold B: Herculin, a fourth member of the MyoD family of myogenic regulatory genes. Proc Natl Acad Sci USA, 87 (3): 1089-1093, 1990.
29. Wyszynska-Koko J, Pierzchala M, Flisikowski K, Kamyczek M, Rozycki M, Kuryl J: Polymorphisms in coding and regulatory regions of the porcine MYF6 and MYOG genes and expression of the MYF6 gene in m. longissimus dorsi versus productive traits in pigs. J Appl Genet, 47 (2): 131-138, 2006.
30. Essén-Gustavsson B, Karlström K, Lundström K: Muscle fibre characteristics and metabolic response at slaughter in pigs of different halothane genotypes and their relation to meat quality. Meat Sci, 31 (1): 1-11, 1992.
31. Liu M, Peng J, Xu DQ, Zheng R, Li FE, Li JL, Zuo B, Lei MG, Xiong YZ, Deng CY: Association of MYF5 and MYOD1 Gene polymorphisms and meat quality traits in Large White x Meishan F2 Pig Populations. Biochem Genet, 46 (11-12): 720-732, 2008.
32. te Pas MF, Verburg FJ, Gerritsen CL, de Greef KH: Messenger ribonucleic acid expression of the MyoD gene family in muscle tissue at slaughter in relation to selection for porcine growth rate. J Anim Sci, 78 (1): 69-77, 2000.
33. Robakowska-Hyzorek D, Oprzadek J, Zelazowska B, Olbromski R, Zwierzchowski L: Effect of the g.-723G -> T polymorphism in the bovine myogenic factor 5 (Myf5) gene promoter region on gene transcript level in the longissimus dorsi muscle and on meat traits of Polish Holstein-Friesian Cattle. Biochem Genet, 48 (5-6): 450-464, 2010.
34. Yin HD, Zhang ZC, Lan X, Zhao XL, Wang Y, Zhu Q: Association of MyF5, MyF6 and MyOG gene polymorphisms with carcass traits in Chinese Meat Type Quality chicken populations. J Anim Vet Adv, 10 (6): 704-708, 2011.
35. Michaelson JJ, Loguercio S, Beyer A: Detection and interpretation of expression quantitative trait loci (eQTL). Methods, 48 (3): 265-276, 2009.
36. Morley M, Molony CM, Weber TM, Devlin JL, Ewens KG, Spielman RS, Cheung VG: Genetic analysis of genome-wide variation in human gene expression. Nature, 430 (7001): 743-747, 2004.
37. Ponsuksili S, Murani E, Phatsara C, Schwerin M, Schellander K, Wimmers K: Expression quantitative trait loci analysis of genes in porcine muscle by quantitative real-time RT-PCR compared to microarray data. Heredity, 105 (3): 309-317, 2010.
38. Stranger BE, Forrest MS, Clark AG, Minichiello MJ, Deutsch S, Lyle R, Hunt S, Kahl B, Antonarakis SE, Tavare S: Genome-wide associations of gene expression variation in humans. PLoS Genet, 1 (6): e78, 2005.
39. Wimmers K, Ponsuksili S, Murani E, Schwerin M, Schellander K: Identification of expression QTL (eQTL) of genes expressed in porcine M. longissimus dorsi and associated with meat quality traits. BMC Genomics, 11 (1): 572, DOI: 10.1186/1471-2164-11-572.
40. Soma Y, Uemoto Y, Sato S, Shibata T, Kadowaki H, Kobayashi E, Suzuki K: Genome-wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits within a Duroc purebred population. J Anim Sci, 89 (3): 601-608, 2011.
41. Van Ooijen JW: LOD significance thresholds for QTL analysis in experimental populations of diploid species Heredity, 83, 613-624, 1999.
42. Ponsuksili S, Jonas E, Murani E, Phatsara C, Srikanchai T, Walz C, Schwerin M, Schellander K, Wimmers K: Trait correlated expression combined with expression QTL analysis reveals biological pathways and candidate genes affecting water holding capacity of muscle. BMC Genomics, 9, 367, doi:10.1186/1471-2164-9-367, 2008.
43. Bystrykh L, Weersing E, Dontje B, Sutton S, Pletcher MT, Wiltshire T, Su AI, Vellenga E, Wang J, Manly KF: Uncovering regulatory pathways that affect hematopoietic stem cell function using ‘genetical genomics’. Nat Genet, 37 (3): 225-232, 2005.
44. Carvajal JJ, Cox D, Summerbell D, Rigby PWJ: Control of the expression of the Mrf4 and Myf5 genes: A BAC transgenic approach. Inter J Dev Biol, 45, S139-S140, 2001.
45. Black BL, Martin JF, Olson EN: The mouse Mrf4 promoter is trans-activated directly and indirectly by muscle-specific transcription factors. J Biol Chem, 270 (7): 2889-2892, 1995.
46. Georges M, Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N: A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature, 425 (6960): 832-836, 2003.
47. Alzhanov DT, Rotwein P, McInerney SF: Long range interactions regulate Igf2 gene transcription during skeletal muscle differentiation. J Biol Chem, 285 (50): 38969-38977, 2010.
48. Gibson G, Weir B: The quantitative genetics of transcription. Trends Genet, 21 (11): 616-623, 2005.
49. Petretto E, Mangion J, Dickens NJ, Cook SA, Kumaran MK, Lu H, Fischer J, Maatz H, Kren V, Pravenec M: Heritability and tissue specificity of expression quantitative trait loci. PLoS Genet, 2 (10): e172, 2006.
50. Lee SS, Chen Y, Moran C, Cepica S, Reiner G, Bartenschlager H, Moser G, Geldermann H: Linkage and QTL mapping for Sus scrofa chromosome 2. J Anim Breed Genet, 120, 11-19, 2003.