Selection of suitable housekeeping genes for gene expression study in caraway (Bunium persicum)
Paper Details
Selection of suitable housekeeping genes for gene expression study in caraway (Bunium persicum)
Abstract
One of the most important issues in genetic engineering and molecular genetics is to study target gene expression that is aimed to quantify data resulted from measuring mRNA levels. Studying amount of gene expression by Real time PCR technique should normalize and compare the amount of mRNA in target gene to amount of mRNA in a housekeeping gene. The level of housekeeping gene expression is stable in different tissues and in all growth stages of an organism and it is not affected by experimental treatments. In each test of gene expression, several housekeeping genes should be studied in order to choose the best housekeeping gene for normalization of data resulted from the target gene expression. In the present study, stability of three housekeeping gene expressions, including actin-beta (ACT), ubiquitin (UBC) and elongation factor 1-alpha (EF1A) has been evaluated in germination, multi-leaf and flowering stages using real time PCR technique. Results obtained from data analysis via geNorm and Bestkeeper-1 software tools showed that EF1A gene is expressed more stable than two other genes and standard error (SE) is higher in the ACT and UBC genes and they are less expressed than EF1A. Concerning studies done on stability, uniformity and stability of EF1A gene expression in different ecotypes ofB. persicum is recommended to normalize data of the target gene expression.
Andersen CL, Jensen JL, Orntoft TF. 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 Research 64, 5245–5250.
Artico S, Nardeli SM, Brilhante O, Grossi-de-Sa MF, Alves-Ferreira M. 2010. Identification and evaluation of new reference genes in Gossypium hirsutum for accurate normalization of real-time quantitative RT-PCR data. BMC Plant Biology 10, 49.
Bustin SA. 2000. Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. Journal of Molecular Endocrinology 25, 169-193.
Manager CFX. 1999. University of Chicago. All rights reserved.
Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GAW, Zumla A. 2005. The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Analytical Biochemistry 344, 141–143.
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.
Infante C, Matsuoka MP, Asensio E, Canavate JP, Reith M, Manchado M. 2008. Selection of housekeeping genes for gene expression studies in larvae from flatfish using real-time PCR. BMC Molecular Biology 9, 28.
Integrated DNA Technologies, Inc. 2014. Privacy 1710 Commercial Park Coralville, IA 52241 USA.
Jalilzadeh-Amin G, Maham M, Dalir-Naghadeh B, Kheiri F. 2011. Effects of Bunium persicum (Boiss.) Essential oil on the contractile responses of smooth muscle (An in vitro Study). Veterinary Research Forum 2, 87-96.
Libault M, Thibivilliers S, Bilgin DD, Radwan O, Benitez M. 2008. Identification of four soybean reference genes for gene expression normalization. Plant Genome 1, 44–54.
Lovdal T, Lillo C. 2009. Reference gene selection for quantitative real-time PCR normalization in tomato subjected to nitrogen, cold, and light stress. Anal Biochemistry 387, 238–242.
Mafra V, Kubo KS, Alves-Ferreira M, Ribeiro-Alves M, Stuart RM. 2012. Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions. PLoS One 7, 31263.
McCurley AT, Callard GV. 2008. Characterization of housekeeping genes in zebrafish: male-female differences and effects of tissue type, developmental stage and chemical treatment. BMC Molecular Biology 9, 102.
Migocka M, Papierniak A. 2011. Identification of suitable reference genes for studying gene expression in cucumber plants subjected to abiotic stress and growth regulators. Molecular Breeding 28, 343–357.
Mitter K, Kotoulas G, Magoulas A, Mulero V, Sepulcre P, Figueras A, Novoa B, Sarropoulou E. 2009. Evaluation of candidate reference genes for QPCR during ontogenesis and of immune-relevant tissues of European seabass (Dicentrarchus labrax). Comparative Biochemistry and Physiology – Part B: Biochemistry and Molecular Biology 153, 340-347.
Multid Analyses. 2015. .se. Accessed on 18 Feb 2015. http://www.multid
Oroojalian F, Kasra-Kermanshahi R, Azizi M, Bassami MR. 2010. Synergistic antibacterial activity of the essential oils from three medicinal plants against some important food-borne pathogens by microdilution method. Iranian Journal of Medicinal and Aromatic Plants 26(2), 133-146.
Pfaffl MW. 2001. A new mathematical model for relative quantification in realtime RT-PCR. Nucleic Acids Research 29(9), e45.
Pfaffl MW, Tichopad A, Prgomet C, Neuvians TP. 2004. Determination of stable housekeeping genes, differentially regulated target genes and sample integrity: BestKeeper – Excel-based tool using pair-wise correlations. Biotechnology Letters 26, 509-515.
Sæle O, Nordgreen A, Hamre K, Olsvik PA. 2009. Evaluation of candidate reference genes in Q-PCR studies of Atlantic cod (Gadus morhua) ontogeny, with emphasis on the gastrointestinal tract. Comparative Biochemistry and Physiology – Part B: Biochemistry and Molecular Biology 152, 94–101.
Shamsi-Fard MH, Mirzaghaderi G, Majdi M. 2014. Transcript expression analysis of geranyl diphosphate synthase gene in different tissues of black cumin (Nigella sativa L.). Iranian Journal of Rangelands and Forests Plant Breeding and Genetic Research 22(2), 143-155.
Small BC, Murdock CA, Bilodeau-Bourgeois AL, Peterson BC, Waldbieser GC. 2008. Stability of reference genes for real-time PCR analyses in channel catfish (Ictalurus punctatus) tissues under varying physiological conditions. Comparative Biochemistry and Physiology – Part B: Biochemistry and Molecular Biology 151, 296-304.
Sofi PA, Zeerak NA, Singh P. 2009. Kala zeera (Bunium persicum Bioss.): a Kashmirian high value crop. Turkish Journal of Biology 33, 249-258.
Strube C, Buschbaum S, Wolken S, Schnieder T. 2008. Evaluation of reference genes for quantitative real-time PCR to investigate protein disulfide isomerase transcription pattern in the bovine lungworm Dictyocaulus viviparus. Gene 425, 36-43.
Tang RY, Dodd A, Lai D, McNabb WC, Love DR. 2007. Validation of zebrafish (Danio rerio) reference genes for quantitative real-time RT-PCR normalization. Acta Biochimica et Biophysica Sinica 39, 384-390.
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, 1-12.
Wan H, Zhao Z, Qian C, Sui Y, Malik AA. 2010. Selection of appropriate reference genes for gene expression studies by quantitative real-time polymerase chain reaction in cucumber. Anal Biochemistry 399, 257–261.
Warzybok A, Migocka M. 2013. Reliable reference renes for normalization of gene expression in cucumber grown under different nitrogen nutrition. Plos One 8(9), 1-11.
Yousefzadi M, Sharifi M, Behmanesh M, Ghasempour A, Moyano E, Palazon J. 2012. The effect of light on gene expression and podophyllotoxin biosynthesis in Linum album cell culture. Plant Physiology Biochemistry 56, 41-46.
Zhang L, He LL, Fu QT, Xu ZF. 2013. Selection of Reliable Reference Genes for Gene Expression Studies in the Biofuel Plant Jatropha curcas Using Real-Time Quantitative PCR. International Journal of Molecular Sciences 14, 24338-24354.
Zhong Q, Zhang Q, Wang Z, Qi J, Chen Y, Li S, Sun Y, Li C, Lan X. 2008. Expression profiling and validation of potential reference genes during Paralichthys olivaceus embryogenesis. Marine Biotechnology 10, 310–318.
Davod Darvishi Zeidabadi, Mokhtar Jalali Javaran, Hamid Dehghani, Sajad Rashidi Monfared, Amin Baghizadeh (2015), Selection of suitable housekeeping genes for gene expression study in caraway (Bunium persicum); JBES, V7, N3, September, P50-58
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