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Profiling of the yak skeletal muscle tissue gene expression and comparison with the domestic cattle by genome array

Published online by Cambridge University Press:  14 November 2013

H. B. Wang ,
L. S. Zan  and
Y. Y. Zhang
H. B. Wang
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China National Beef Cattle Improvement Centre, Yangling, Shaanxi 712100, China
L. S. Zan*
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China National Beef Cattle Improvement Centre, Yangling, Shaanxi 712100, China
Y. Y. Zhang
Affiliation:
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
*
†E-mail: zanlinsen@163.com
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Abstract

Of all the mammals of the world, the yak lives at the highest altitude area of more than 3000 m. Comparison between yak and cattle of the low-altitude areas will be informative in studying animal adaptation to higher altitudes. To investigate the molecular mechanism involved in meat quality differences between the two Chinese special varieties Qinghai yak and Qinchuan cattle, 12 chemical–physical characteristics of the longissimus dorsi muscle related to meat quality were compared at the age of 36 months, and the gene expression profiles were constructed by utilizing the bovine genome array. Significant analysis of microarrays was used to identify the differentially expressed genes. Gene ontology and pathway analysis were performed by a free Web-based Molecular Annotation System 2.0. The results reveal ~11 000 probes representing about 10 000 genes that were detected in both the Qinghai yak and Qinchuan cattle. A total of 1922 genes were shown to be differentially expressed, 633 probes were upregulated and 1259 probes were downregulated in the muscle tissue of Qinghai yak that were mainly involved in ubiquitin-mediated proteolysis, muscle growth regulation, glucose metabolism, immune response and so on. Quantitative real-time PCR (qRT-PCR) was performed to validate some differentially expressed genes identified by microarray. Further analysis implied that animals living at a high altitude may supply energy by more active protein catabolism and glycolysis compared with those living in the plain areas. Our results establish the groundwork for further studies on yaks’ meat quality and will be beneficial in improving the yaks’ breeding by molecular biotechnology.

Keywords

Qinghai yakQinchuan cattleskeletal muscle tissuesgene expression profile
Type
Full Paper
Information
animal , Volume 8 , Issue 1 , January 2014 , pp. 28 - 35
Copyright
Copyright © The Animal Consortium 2013 

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References

Association of Official Analytical Chemist 1984. Official methods of analysis, 18th edition. AOAC, Arlington, VA, USA.Google Scholar
Bourneuf, E, Hérault, F, Chicault, C, Carré, W, Assaf, S, Monnier, A, Mottier, S, Lagarrigue, S, Douaire, M, Mosser, J and Diot, C 2006. Microarray analysis of differential gene expression in the liver of lean and fat chickens. Gene 372, 162–170.Google Scholar
Buchanan, FC, Fitzsimmons, CJ, Van Kessel, AG, Thue, TD, Winkelman-Sim, DC and Schmutz, S 2002. Association of a missense mutation in the bovine gene with carcass fat content and leptin mRNA levels. Genetics Selection Evolution 34, 105–116.Google Scholar
Casas, E, White, SN, Riley, DG, Smith, TP, Brenneman, RA, Olson, TA, Johnson, DD, Coleman, SW, Bennett, GL and Chase, CC Jr 2005. Assessment of single nucleotide polymorphisms in genes residing on chromosomes 14 and 29 for association with carcass composition traits in Bos indicus cattle. Journal of Animal Science 83, 13–19.Google Scholar
Chesney, J, Mitchell, R, Benigni, F, Bacher, M, Spiegel, L, Al-Abed, Y, Han, JH, Metz, C and Bucala, R 1999. An inducible gene product for 6-phosphofructo-2-kinase with an AU-rich instability element: role in tumor cell glycolysis and the Warburg effect. Proceedings of the National Academy of Sciences 96, 3047–3052.Google Scholar
Ciechanover, A, Orian, A and Schwartz, AL 2000. Ubiquitin-mediated proteolysis: biological regulation via destruction. Bioessays 22, 442–451.Google Scholar
Clarke, NF, Ilkovski, B, Cooper, S, Valova, VA, Robinson, PJ, Nonaka, I, Feng, JJ, Marston, S and North, K 2007. The pathogenesis of ACTA1-related congenital fiber type disproportion. Animals of Neurology 61, 552–561.Google Scholar
Destefanis, G, Brugiapaglia, A, Barge, MT and Lazzaroni, C 2003. Effect of castration on meat quality in Piemontese cattle. Meat Science 64, 215–218.Google Scholar
Failla, S, Gigli, S, Gaddini, A, Signorelli, F, Saňudo, C, Panea, B, Olleta, JL, Monsón, F, Hocquette, JF, Jailler, R, Albertí, P, Ertbjerg, P, Christiansen, M, Nue, GR and Williams, JL 2004. Physical quality of several European beef breeds: preliminary results. Proceeding of the 50th International Congress of Meat Science and Technology, Helsinki, Finland, August 8 to 13.Google Scholar
Hocquette, JF, Gondret, F, Baéza, E, Médale, F, Jurie, C and Pethick, DW 2010. Intramuscular fat content in meat-producing animals: development genetic and nutritional control and identification of putative markers. Animal 4, 303–319.Google Scholar
Huffman, KL, Miller, MF, Hoover, LC, Wu, CK, Brittin, HC and Ramsey, CB 1996. Effect of beef tenderness on consumer satisfaction with steaks consumed in the home and restaurant. Journal of Animal Science 74, 91–97.Google Scholar
Lagonigro, R, Wiener, P, Pilla, F, Woolliams, JA and Williams, JL 2003. A new mutation in the coding region of the bovine leptin genes associated with feed intake. Animal Genetics 34, 371–374.Google Scholar
Li, C and Wong, WH 2001a. Model-based analysis of oligonucleotide arrays: expression index computation and outlier detection. Proceedings of the National Academy of Sciences 98, 31–36.Google Scholar
Li, C and Wong, WH 2001b. Model-based analysis of oligonucleotide arrays: model validation, design issues and standard error application. Genome Biology 2, 1–32.Google Scholar
Li, X, Zhong, S and Wong, WH 2005. Reliable prediction of transcription factor binding sites by phylogenetic verification. Proceedings of the National Academy of Sciences 102, 16945–16950.Google Scholar
Luciano, G, Monahan, FJ, Vasta, V, Biondi, L, Lanza, M and Priolo, A 2009. Dietary tannins improve lamb meat colour stability. Meat Science 81, 120–125.Google Scholar
Lundström, K and Malmfors, G 1985. Variation in light scattering and water holding capacity along the porcine longissimus dorsi muscle. Meat Science 15, 203–215.Google Scholar
Meyuhas, O and Perry, RP 1980. Construction and identification of cDNA clones for mouse ribosomal proteins: application for the study of r-protein gene expression. Gene 10, 113–129.Google Scholar
Miller, MF, Carr, MA, Ramsey, CB, Crockett, KL and Hoover, LC 2001. Consumer thresholds for establishing the value of beef tenderness. Journal of Animal Science 79, 3062–3068.Google Scholar
Minchenko, O, Opentanova, I, Minchenko, D, Ogura, T and Esumi, H 2004. Hypoxia induces transcription of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase-4 gene via hypoxia- inducible factor-1alpha activation. FEBS Letters 576, 14–20.Google Scholar
Otto, G, Roehe, R, Looft, H, Thoelking, L, Henning, M, Plastow, GS and Kalm, E 2006. 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 72, 680–687.Google Scholar
Page, BT, Casas, E, Heaton, MP, Cullen, NG, Hyndman, DL, Morris, CA, Crawford, AM, Wheeler, TL, Koohmaraie, M, Keele, JW and Smith, TP 2002. Evaluation of single-nucleotide polymorphisms in CAPN1 for association with meat tenderness in cattle. Journal of Animal Science 80, 3077–3085.Google Scholar
Page, BT, Casas, E, Quaas, RL, Thallman, RM, Wheeler, TL, Shackelford, SD, Koohmaraie, M, White, SN, Bennett, GL, Keele, JW, Dikemean, ME and Smith, TP 2004. Association of markers in the bovine CAPN1 gene with meat tenderness in large crossbred populations that sample influential industry sires. Journal of Animal Science 82, 3474–3481.Google Scholar
Platter, WJ, Tatum, JD, Belk, KE, Chapman, PL, Scanga, JA and Smith, GC 2003. Relationships of consumer sensory ratings, marbling score, and shear force value to consumer acceptance of beef strip loin steaks. Journal of Animal Science 81, 2741–2750.Google Scholar
Qiu, Q, Zhang, G, Ma, T, Qian, W, Wang, J, Ye, Z, Cao, C, Hu, Q, Kim, J, Larkin, DM, Auvil, L, Capitanu, B, Ma, J, Lewin, HA, Qian, X, Lang, Y, Zhou, R, Wang, L, Wang, K, Xia, J, Liao, S, Pan, S, Lu, X, Hou, H, Wang, Y, Zang, X, Yin, Y, Ma, H, Zhang, J, Wang, Z, Zhang, Y, Zhang, D, Yonezawa, T, Hasegawa, M, Zhong, Y, Liu, W, Zhang, Y, Huang, Z, Zhang, S, Long, R, Yang, H, Wang, J, Lenstra, JA, Cooper, DN, Wu, Y, Wang, J, Shi, P, Wang, J and Liu, J 2012. The yak genome and adaptation to life at high altitude. Nature Genetics 44, 946–949.Google Scholar
Sakakibara, R, Kato, M, Okamura, N, Nakagawa, T, Komada, Y, Tominaga, N, Shimojo, M and Fukasawa, M 1997. Characterization of a human placental fructose-6-phosphate, 2-kinase/fructose-2, 6-bisphosphatase. The Journal of Biochemistry 122, 122–128.Google Scholar
Smerdu, V, Karsch-Mizrachi, I, Campione, M, Leinwand, L and Schiaffino, S 1994. Type IIx myosin heavy chain transcripts are expressed in type IIb fibers of human skeletal muscle. The American Journal of Physiology 267, C1723–C1728.Google Scholar
Strous, GJ and Govers, R 1999. The ubiquitin-proteasome system and endocytosis. Journal of Cell Science 112, 1417–1423.Google Scholar
Tajsharghi, H, Thornell, LE, Darin, N, Martinsson, T, Kyllerman, M, Wahlström, J and Oldfors, A 2002. Myosin heavy chain IIa gene mutation E706K is pathogenic and its expression increases with age. Neurology 58, 780–786.Google Scholar
Tajsharghi, H, Darin, N, Rekabdar, E, Kyllerman, M, Wahlström, J, Martinsson, T and Oldfors, A 2005. Mutations and sequence variation in the human myosin heavy chain IIa gene (MYH2). European Journal of Human Genetics 13, 617–622.Google Scholar
Thaller, G, Kühn, C, Winter, A, Ewald, G, Bellmann, O, Wegner, J, Zühlke, H and Fries, R 2003. DGAT1, a new positional and functional candidate gene for intramuscular fat deposition in cattle. Animal Genetics 34, 354–357.Google Scholar
Wang, HB, Li, H, Wang, QG, Zhang, XY, Wang, SZ, Wang, YX and Wang, XP 2007. Profiling of chicken adipose tissue gene expression by genome array. BMC Genomics 27, 193.Google Scholar
Webb, EC and O’Neill, HA 2008. The animal fat paradox and meat quality. Meat Science 80, 28–36.Google Scholar
Wood, JD, Enser, M, Fisher, AV, Nute, GR, Sheard, PR, Richardson, RI, Hughes, SI and Whittington, FM 2008. Fat deposition, fatty acid composition and meat quality: a review. Meat Science 78, 343–358.Google Scholar
Zhang, QW, Yu, HX, Jing, HX, Li, L, Wei, Q, Niu, HL, Xue, Q and Liang, Lin 2013. Adaptation mechanism of developmental yak to hypoxia base on skeletal muscle mitochondria ultrastructure. Acta Veterinaria et Zootechnica Sinica 44, 447–452.Google Scholar
Zhang, Y, Zan, L and Wang, H 2011. Screening candidate genes related to tenderness trait in Qinchuan cattle by genome array. Molecular Biology Reports 38, 2007–2014.Google Scholar
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