Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua

https://doi.org/10.17221/20/2018-PPSCitation:Liu J., Li P., Lu L., Xie L., Chen X., Zhang B. (2019): Selection and evaluation of potential reference genes for gene expression analysis in Avena fatua. Plant Protect. Sci., 55: 61-71.
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Eight commonly used candidate reference genes, 18S ribosomal RNA (rRNA) (18S), 28S rRNA (28S), actin (ACT), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), elongation factor 1 alpha (EF1α), ribosomal protein L7 (RPL7), Alpha-tubulin (α-TUB), and TATA box binding protein-associated factor (TBP), were evaluated under various experimental conditions to assess their suitability in different developmental stages, tissues and herbicide treatments in Avena fatua. The results indicated the most suitable reference genes for the different experimental conditions. For developmental stages, 28S and EF1α were the optimal reference genes, both EF1α and 28S were suitable for experiments of different tissues, whereas for herbicide treatments, GAPDH and ACT were suitable for normalizations of expression data. In addition, GAPDH and EF1α were the suitable reference genes.

References:
Andersen Claus Lindbjerg, Jensen Jens Ledet, Ørntoft Torben Falck (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 https://doi.org/10.1158/0008-5472.CAN-04-0496
 
Bagnall N.H., Kotze A.C. (2010): Evaluation of reference genes for real-time PCR quantification of gene expression in the Australian sheep blowfly, Lucilia cuprina. Medical & Veterinary Entomology, 24: 176–181.
 
Bettencourt Brian R, Hogan Catherine C, Nimali Mario (2007): Polyglutamine expansion in Drosophila: thermal stress and Hsp70 as selective agents. Journal of Biosciences, 32, 537-547 https://doi.org/10.1007/s12038-007-0053-9
 
Bustin S. A., Benes V., Garson J. A., Hellemans J., Huggett J., Kubista M., Mueller R., Nolan T., Pfaffl M. W., Shipley G. L., Vandesompele J., Wittwer C. T. (2009): The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments. Clinical Chemistry, 55, 611-622 https://doi.org/10.1373/clinchem.2008.112797
 
Cavan Graeme, Cussans John, Moss Stephen (2001): Managing the risks of herbicide resistance in wild oat. Weed Science, 49, 236-240 https://doi.org/10.1614/0043-1745(2001)049[0236:MTROHR]2.0.CO;2
 
Chandna Ruby, Augustine Rehna, Bisht Naveen C., Schönbach Christian (2012): Evaluation of Candidate Reference Genes for Gene Expression Normalization in Brassica juncea Using Real Time Quantitative RT-PCR. PLoS ONE, 7, e36918- https://doi.org/10.1371/journal.pone.0036918
 
Cheng Daifeng, Zhang Zhiling, He Xiaofang, Liang Guangwen, Terenius Olle (2013): Validation of Reference Genes in Solenopsis invicta in Different Developmental Stages, Castes and Tissues. PLoS ONE, 8, e57718- https://doi.org/10.1371/journal.pone.0057718
 
Cruzhipolito H., Osuna M.D., Domínguezvalenzuela J.A., Espinoza N., De Prado R. (2011): Mechanism of resistance to accase-inhibiting herbicides in wild oat (Avena fatua) from Latin America. Journal of Agricultural & Food Chemistry, 59: 7261–7267.
 
Duhoux Arnaud, Délye Christophe, Schönbach Christian (2013): Reference Genes to Study Herbicide Stress Response in Lolium sp.: Up-Regulation of P450 Genes in Plants Resistant to Acetolactate-Synthase Inhibitors. PLoS ONE, 8, e63576- https://doi.org/10.1371/journal.pone.0063576
 
Expósito-Rodríguez Marino, Borges Andrés A, Borges-Pérez Andrés, Pérez José A (2008): Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biology, 8, 131- https://doi.org/10.1186/1471-2229-8-131
 
Gantasala Nagavara, Papolu Pradeep, Thakur Prasoon, Kamaraju Divya, Sreevathsa Rohini, Rao Uma (2013): Selection and validation of reference genes for quantitative gene expression studies by real-time PCR in eggplant (Solanum melongena L). BMC Research Notes, 6, 312- https://doi.org/10.1186/1756-0500-6-312
 
Glare E M (): beta-Actin and GAPDH housekeeping gene expression in asthmatic airways is variable and not suitable for normalising mRNA levels. Thorax, 57, 765-770 https://doi.org/10.1136/thorax.57.9.765
 
Holm L.G., Plucknett D.L., Pancho J.V., Herberger K.P. (1977): The World’s Worst Weeds. Distribution and Biology. Honolulu, East-West Center by the University Press of Havaii.
 
Horňáková Darina, Matoušková Petra, Kindl Jiří, Valterová Irena, Pichová Iva (2010): Selection of reference genes for real-time polymerase chain reaction analysis in tissues from Bombus terrestris and Bombus lucorum of different ages. Analytical Biochemistry, 397, 118-120 https://doi.org/10.1016/j.ab.2009.09.019
 
Huggett J., Dheda K., Bustin S., Zumla A. (2005): Real-time RT-PCR normalisation; strategies and considerations. Genes & Immunity, 6: 279.
 
Keith B K, Lehnhoff E A, Burns E E, Menalled F D, Dyer W E, Marshall Jon (2015): Characterisation of Avena fatua populations with resistance to multiple herbicides. Weed Research, 55, 621-630 https://doi.org/10.1111/wre.12172
 
Kim Bo-Ra, Nam Hee-Young, Kim Soo-Un, Kim Su-Il, Chang Yung-Jin (2003): Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnology Letters, 25, 1869-1872 https://doi.org/10.1023/A:1026298032009
 
Li R., Wang S., Duan L., Li Z.H., Christoffers M.J., Mengistu L.W. (2009): Genetic diversity of wild oat (Avena fatua) populations from china and the united states. Weed Science, 55: 95–101.
 
Li R., Zhang J., Chen G. (2010): Advance of study on identification of weed herbicide resistance. Chinese Agricultural Science Bulletin, 26: 289–292.
 
Liang Pei, Guo Yajie, Zhou Xuguo, Gao Xiwu, Smagghe Guy (2014): Expression Profiling in Bemisia tabaci under Insecticide Treatment: Indicating the Necessity for Custom Reference Gene Selection. PLoS ONE, 9, e87514- https://doi.org/10.1371/journal.pone.0087514
 
Logan J., Edwards K., Saunders N. (eds) (2009): Real-Time PCR: Current Technology and Applications. Norfolk, Caister Academic Press.
 
Lord Jeffrey C., Hartzer Kris, Toutges Michelle, Oppert Brenda (2010): Evaluation of quantitative PCR reference genes for gene expression studies in Tribolium castaneum after fungal challenge. Journal of Microbiological Methods, 80, 219-221 https://doi.org/10.1016/j.mimet.2009.12.007
 
Lu Yanhui, Yuan Miao, Gao Xiwu, Kang Tinghao, Zhan Sha, Wan Hu, Li Jianhong, Schönbach Christian (2013): Identification and Validation of Reference Genes for Gene Expression Analysis Using Quantitative PCR in Spodoptera litura (Lepidoptera: Noctuidae). PLoS ONE, 8, e68059- https://doi.org/10.1371/journal.pone.0068059
 
Ma K.S., Li F., Liang P.Z., Chen X.W., Liu Y., Gao X.W. (2016): Identification and validation of reference genes for the normalization of gene expression data in qRT-PCR qPCR analysis in Aphis gossypii (Hemiptera: Aphididae). Journal of Insect Science, 16: 1–9.
 
Mallona Izaskun, Lischewski Sandra, Weiss Julia, Hause Bettina, Egea-Cortines Marcos (2010): Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biology, 10, 4- https://doi.org/10.1186/1471-2229-10-4
 
Overbergh L., Giulietti A., Valckx D., Decallonne B., Bouillon R., Mathieu C. (2003): The use of real-time reverse transcriptase PCR for the quantification of cytokine gene expression. Journal of Biomolecular Techniques: JBT, 14: 33–43.
 
Petit Cécile, Pernin Fanny, Heydel Jean-Marie, Délye Christophe (2012): Validation of a set of reference genes to study response to herbicide stress in grasses. BMC Research Notes, 5, 18- https://doi.org/10.1186/1756-0500-5-18
 
Pfaffl M. W. (): A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Research, 29, 45e-45 https://doi.org/10.1093/nar/29.9.e45
 
Pfaffl Michael W., Tichopad Ales, Prgomet Christian, Neuvians Tanja P. (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 https://doi.org/10.1023/B:BILE.0000019559.84305.47
 
Ryan G.F. (1970): Resistance of common groundsel to simazine and atrazine. Weed Science, 18: 614–616.
 
Ruan W., Lai M. (2007): Actin, a reliable marker of internal control? Clinica Chimica Acta, 385: 1–5.
 
Spiess A.-N., Deutschmann C., Burdukiewicz M., Himmelreich R., Klat K., Schierack P., Rodiger S. (2015): Impact of Smoothing on Parameter Estimation in Quantitative DNA Amplification Experiments. Clinical Chemistry, 61, 379-388 https://doi.org/10.1373/clinchem.2014.230656
 
Spiess Andrej-Nikolai, Rödiger Stefan, Burdukiewicz Michał, Volksdorf Thomas, Tellinghuisen Joel (2016): System-specific periodicity in quantitative real-time polymerase chain reaction data questions threshold-based quantitation. Scientific Reports, 6, - https://doi.org/10.1038/srep38951
 
Tellinghuisen Joel, Spiess Andrej-Nikolai (2014): Comparing real-time quantitative polymerase chain reaction analysis methods for precision, linearity, and accuracy of estimating amplification efficiency. Analytical Biochemistry, 449, 76-82 https://doi.org/10.1016/j.ab.2013.12.020
 
Thellin O., Zorzi W., Lakaye B., De Borman B., Coumans B., Hennen G., Grisar T., Igout A., Heinen E. (1999): Housekeeping genes as internal standards: use and limits. Journal of Biotechnology, 75, 291-295 https://doi.org/10.1016/S0168-1656(99)00163-7
 
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. doi:10.1186/gb-2002-3-7-research0034https://doi.org/10.1186/gb-2002-3-7-research0034
 
Wang Xia, Ma Xiao, Huang Linkai, Zhang Xinquan (2015): Identification of the Valid Reference Genes for Quantitative RT-PCR in Annual Ryegrass (Lolium multiflorum) under Salt Stress. Molecules, 20, 4833-4847 https://doi.org/10.3390/molecules20034833
 
Wrzesińska B, Kierzek R, Obrępalska-Stęplowska A, Iannetta Pietro (2016): Evaluation of six commonly used reference genes for gene expression studies in herbicide-resistant Avena fatua biotypes. Weed Research, 56, 284-292 https://doi.org/10.1111/wre.12209
 
Zarivi Osvaldo, Cesare Patrizia, Ragnelli Anna Maria, Aimola Pierpaolo, Leonardi Marco, Bonfigli Antonella, Colafarina Sabrina, Poma Anna Maria, Miranda Michele, Pacioni Giovanni (2015): Validation of reference genes for quantitative real-time PCR in Périgord black truffle ( Tuber melanosporum ) developmental stages. Phytochemistry, 116, 78-86 https://doi.org/10.1016/j.phytochem.2015.02.024
 
Zhang Songdou, An Shiheng, Li Zhen, Wu Fengming, Yang Qingpo, Liu Yichen, Cao Jinjun, Zhang Huaijiang, Zhang Qingwen, Liu Xiaoxia (2015): Identification and validation of reference genes for normalization of gene expression analysis using qRT-PCR in Helicoverpa armigera (Lepidoptera: Noctuidae). Gene, 555, 393-402 https://doi.org/10.1016/j.gene.2014.11.038
 
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