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http://dx.doi.org/10.5713/ajas.2013.13199

Reference Gene Screening for Analyzing Gene Expression Across Goat Tissue  

Zhanga, Yu (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Zhang, Xiao-Dong (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Liu, Xing (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Li, Yun-Sheng (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Ding, Jian-Ping (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Zhang, Xiao-Rong (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Zhang, Yun-Hai (Anhui Provincial Laboratory for Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, College of Animal Science and Technology, Anhui Agricultural University)
Publication Information
Asian-Australasian Journal of Animal Sciences / v.26, no.12, 2013 , pp. 1665-1671 More about this Journal
Abstract
Real-time quantitative PCR (qRT-PCR) is one of the important methods for investigating the changes in mRNA expression levels in cells and tissues. Selection of the proper reference genes is very important when calibrating the results of real-time quantitative PCR. Studies on the selection of reference genes in goat tissues are limited, despite the economic importance of their meat and dairy products. We used real-time quantitative PCR to detect the expression levels of eight reference gene candidates (18S, TBP, HMBS, YWHAZ, ACTB, HPRT1, GAPDH and EEF1A2) in ten tissues types sourced from Boer goats. The optimal reference gene combination was selected according to the results determined by geNorm, NormFinder and Bestkeeper software packages. The analyses showed that tissue is an important variability factor in genes expression stability. When all tissues were considered, 18S, TBP and HMBS is the optimal reference combination for calibrating quantitative PCR analysis of gene expression from goat tissues. Dividing data set by tissues, ACTB was the most stable in stomach, small intestine and ovary, 18S in heart and spleen, HMBS in uterus and lung, TBP in liver, HPRT1 in kidney and GAPDH in muscle. Overall, this study provided valuable information about the goat reference genes that can be used in order to perform a proper normalisation when relative quantification by qRT-PCR studies is undertaken.
Keywords
Reference Gene; Expression Stability; Tissue; Goat;
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1 Chi, X., R. Hu, Q. Yang, X. Zhang, L. Pan, N. Chen, M. Chen, Z. Yang, T. Wang, Y. He, and S. Yu. 2012. Validation of reference genes for gene expression studies in peanut by quantitative real-time RT-PCR. Mol. Genet. Genomics 287:167-176.   DOI   ScienceOn
2 Dabek, J., J. Ligus, and J. Szota. 2010. Oligonucleotide microarray and QRT-PCR study of adhesion protein gene expression in acute coronary syndrome patients. Inflammation 33:398-407.   DOI   ScienceOn
3 Domby, E., T. Engle, and H. Han. 2010. The relationship of tissue copper concentrations and genes involved in copper homeostasis in the cow, pig, and goat. J. Dairy Sci 93:403-404.
4 Dubeuf, J. P., P. Morand-Fehr, and R. Rubino. 2004. Situation, changes and future of goat industry around the world. Small Rumin. Res. 51:165-173.   DOI   ScienceOn
5 Fleige, S. and M. W. Pfaffl. 2006. RNA integrity and the effect on the real-time qRT-PCR performance. Mol. Aspects Med. 27: 126-139.   DOI   ScienceOn
6 Fu, Y., Z. Shi, M. Wu, J. Zhang, L. Jia, and X. Chen. 2011. Identification and differential expression of microRNAs during metamorphosis of the Japanese flounder(Paralichthys olivaceus). Plos One 6:e22957.   DOI
7 Garcia-Crespo, D., R. A. Juste, and A. Hurtado. 2005. Selection of ovine housekeeping genes for normalisation by real-time RT-PCR; analysis of PrP gene expression and genetic susceptibility to scrapie. BMC Vet. Res. 1:3.   DOI
8 Andersen, C. L., J. L. Jensen, and T. F. Orntoft. 2004. Normalization of real-time quantitative reverse transcription-PCR data: A model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 64:5245-5250.   DOI   ScienceOn
9 Bustin, S. A., V. Benes, J. A. Garson, J. Hellemans, J. Huggett, M. Kubista, R. Mueller, T. Nolan, M. W. Pfaffl, G. L. Shipley, J. Vandesompele, and C. T. Wittwer. 2009. The MIQE guidelines: Minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55: 611-622.   DOI   ScienceOn
10 Kidd, M., B. Nadler, S. Mane, G. Eick, M. Malfertheiner, M. Champaneria, R. Pfragner, and I. Modlin. 2007. GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Physiol. Genomics 30:363-370.   DOI   ScienceOn
11 Kortner, T. M., E. C. Valen, H. Kortner, I. S. Marjara, A. Krogdahl, and A. M. Bakke. 2011. Candidate reference genes for quantitative real-time PCR (qPCR) assays during development of a diet-related enteropathy in Atlantic salmon (Salmo salar L.) and the potential pitfalls of uncritical use of normalization software tools. Aquaculture 318: 355-363.   DOI   ScienceOn
12 Lanoix, D., A. A. Lacasse, J. St-Pierre, S.C. Taylor, M. Ethier-Chiasson, J. Lafond, and. C. Vaillancourt. 2012. Quantitative PCR pitfalls: The case of the human placenta. Mol. Biotechnol 52 234-243.   DOI   ScienceOn
13 Lardizabal, M. N., A. L. Nocito, S. M. Daniele, L. A. Ornella, J. F. Palatnik, and L. M. Veggi. 2012. Reference genes for real-time PCR quantification of microRNAs and messenger RNAs in rat models of hepatotoxicity. PloS one 7:e36323.   DOI
14 Lisowski, P., M. Pierzchala, J. Goscik, C. S. Pareek, and L. Zwierzchowski. 2008. Evaluation of reference genes for studies of gene expression in the bovine liver, kidney, pituitary, and thyroid. J. Appl. Genet. 49:367-372.   DOI
15 Mehta, R., A. Birerdinc, N. Hossain, A. Afendy, V. Chandhoke, Z. Younossi, and A. Baranova. 2010. Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples. BMC Mol. Biol. 11:39.   DOI   ScienceOn
16 Moioli, B., M. D'Andrea, and F. Pilla. 2007. Candidate genes affecting sheep and goat milk quality. Small Rumin. Res 68: 179-192.   DOI   ScienceOn
17 Wang, G. P. and C. S. Xu. 2010. Reference gene selection for real-time RT-PCR in eight kinds of rat regenerating hepatic cells. Mol. Biotechnol. 46:49-57.   DOI   ScienceOn
18 Spalenza, V., F. Girolami, C. Bevilacqua, F. Riondato, R. Rasero, C. Nebbia, P. Sacchi, and P. Martin. 2011. Identification of internal control genes for quantitative expression analysis by real-time PCR in bovine peripheral lymphocytes. Vet. J. 189: 278-283.   DOI   ScienceOn
19 Vandesompele, J., K. De Preter, F. Pattyn, B. Poppe, N. Van Roy, A. De Paepe, and F. Speleman. 2002. Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3: research0034.1-0034.11
20 Veys, K., A. J. Labro, E. De Schutter, and D. J. Snyders. 2012. Quantitative single-cell ion-channel gene expression profiling through an improved qRT-PCR technique combined with whole cell patch clamp. J. Neurosci. Methods 209:227-234.   DOI   ScienceOn
21 Yoon, J. R., P. D. Laible, M. Gu, H. N. Scott, and F. R. Collart. 2002. Express primer tool for high-throughput gene cloning and expression. Biotechniques 33:1328-1333.
22 Zhang, J., Z. L. Tang, N. Wang, L. Q. Long, and K. Li. 2012. Evaluating a set of reference genes for expression normalization in multiple tissues and skeletal muscle at different development stages in pigs using quantitative real-time polymerase chain reaction. DNA Cell Biol. 31:106-113.   DOI   ScienceOn
23 Zi, X. D., H. W. Xu, and Y. Wang. 2012. Variation in sequences and mRNA expression levels of inhibin subunits alpha (INHA) and beta A (INHBA) genes between prolific and nonprolific goat breeds. Mol. Reprod. Dev. 79:238-238.   DOI   ScienceOn
24 Perez, R., I. Tupac-Yupanqui, and S. Dunner. 2008. Evaluation of suitable reference genes for gene expression studies in bovine muscular tissue. BMC Mol. Biol. 9:79.   DOI   ScienceOn
25 Nesvadbova, M. and A. Knoll. 2011. Evaluation of reference genes for gene expression studies in pig muscle tissue by real-time PCR. Czech J. Anim. Sci. 56:213-216.
26 Novinscak, A., V. J. Gadkar, and M. Filion. 2011. Optimization of RNA isolation and qRT-PCR strategies to monitor microbial gene expression in soil. Phytopathology 101: S130-S130.
27 Nygard, A. B., C. B. Jorgensen, S. Cirera, and M. Fredholm. 2007. Selection of reference genes for gene expression studies in pig tissues using SYBR green qPCR. BMC Mol. Biol. 8:67.   DOI
28 Pfaffl, M. W., A. Tichopad, C. Prgomet, and T. P. Neuvians. 2004. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper - Excel-based tool using pair-wise correlations. Biotechnol. Lett. 26:509-515.   DOI   ScienceOn
29 Pierzchala, M., C. S. Pareek, P. Urbanski, D. Goluch, M. Kamyczek, M. Rozycki, and J. Kuryl. 2011. Selection of reference genes for gene expression studies in porcine hepatic tissue using quantitative real-time polymerase chain reaction. Anim. Sci. Pap. Rep. 29:53-63.
30 Radonic, A., S. Thulke, I. M. Mackay, O. Landt, W. Siegert, and A. Nitsche. 2004. Guideline to reference gene selection for quantitative real-time PCR. Biochem. Biophys. Res. Commun. 313: 856-862.   DOI   ScienceOn
31 Rivera-Vega, L., P. Mamidala, J. L. Koch, M. E. Mason, and O. Mittapalli. 2012. Evaluation of Reference Genes for Expression Studies in Ash (Fraxinus spp.). Plant Mol. Biol. Rep. 30:242-245.   DOI
32 Schmid, H., C. D. Cohen, A. Henger, S. Irrgang, D. Schlondorff, and M. Kretzler. 2003. Validation of endogenous controls for gene expression analysis in microdissected human renal biopsies. Kidney Int. 64:356-360.   DOI   ScienceOn
33 Chechi, K., Y. Gelinas, P. Mathieu, Y. Deshaies, and D. Richard. 2012. Validation of reference genes for the relative quantification of gene expression in human epicardial adipose tissue. PloS one 7:e32265.   DOI