The DOI matches its Crossref record; 40 of the 40 references it cites were found in a registry or an index.
Reference Genes for Accurate Transcript Normalization in Citrus Genotypes under Different Experimental Conditions
Open accessAbstract
Real-time reverse transcription PCR (RT-qPCR) has emerged as an accurate and widely used technique for expression profiling of selected genes. However, obtaining reliable measurements depends on the selection of appropriate reference genes for gene expression normalization. The aim of this work was to assess the expression stability of 15 candidate genes to determine which set of reference genes is best suited for transcript normalization in citrus in different tissues and organs and leaves challenged with five pathogens (Alternaria alternata, Phytophthora parasitica, Xylella fastidiosa and Candidatus Liberibacter asiaticus). We tested traditional genes used for transcript normalization in citrus and orthologs of Arabidopsis thaliana genes described as superior reference genes based on transcriptome data. geNorm and NormFinder algorithms were used to find the best reference genes to normalize all samples and conditions tested. Additionally, each biotic stress was individually analyzed by geNorm. In general, FBOX (encoding a member of the F-box family) and GAPC2 (GAPDH) was the most stable candidate gene set assessed under the different conditions and subsets tested, while CYP (cyclophilin), TUB (tubulin) and CtP (cathepsin) were the least stably expressed genes found. Validation of the best suitable reference genes for normalizing the expression level of the WRKY70 transcription factor in leaves infected with Candidatus Liberibacter asiaticus showed that arbitrary use of reference genes without previous testing could lead to misinterpretation of data. Our results revealed FBOX, SAND (a SAND family protein), GAPC2 and UPL7 (ubiquitin protein ligase 7) to be superior reference genes, and we recommend their use in studies of gene expression in citrus species and relatives. This work constitutes the first systematic analysis for the selection of superior reference genes for transcript normalization in different citrus organs and under biotic stress.
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Vandesompele, J., De Preter, K., Pattyn, F., Poppe, B., Van Roy, N., De Paepe, A., & Speleman, F. (2002) · Genome Biology · doi:10.1186/gb-2002-3-7-research0034 · Cited by 20,038
Andersen, C. L., Jensen, J. L., & Ørntoft, T. F. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-0496 · Cited by 7,127
Hellemans, J., Mortier, G., De Paepe, A., Speleman, F., & Vandesompele, J. (2007) · Genome Biology · doi:10.1186/gb-2007-8-2-r19 · Cited by 4,023
Czechowski, T., Stitt, M., Altmann, T., Udvardi, M. K., & Scheible, W.-R. (2005) · Plant Physiology · doi:10.1104/pp.105.063743 · Cited by 3,203
Quantification of mRNA using real-time RT-PCR
Nolan, T., Hands, R. E., & Bustin, S. A. (2006) · Nature Protocols · doi:10.1038/nprot.2006.236 · Cited by 2,247
Real-Time PCR for mRNA Quantitation
Wong, M. L., & Medrano, J. F. (2005) · BioTechniques · doi:10.2144/05391rv01 · Cited by 1,786
Nicot, N., Hausman, J.-F., Hoffmann, L., & Evers, D. (2005) · Journal of Experimental Botany · doi:10.1093/jxb/eri285 · Cited by 1,329
Jain, M., Nijhawan, A., Tyagi, A. K., & Khurana, J. P. (2006) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2006.04.140 · Cited by 1,183
Reid, K. E., Olsson, N., Schlosser, J., Peng, F., & Lund, S. T. (2006) · BMC Plant Biology · doi:10.1186/1471-2229-6-27 · Cited by 883
Expósito-Rodríguez, M., Borges, A. A., Borges-Pérez, A., & Pérez, J. A. (2008) · BMC Plant Biology · doi:10.1186/1471-2229-8-131 · Cited by 787
Cited by
Selection of Reference Genes for Quantitative Real-Time PCR in Bamboo (Phyllostachys edulis)
Fan, C., Ma, J., Guo, Q., Li, X., Wang, H., & Lu, M. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056573 · Cited by 301
Park, S.-C., Kim, Y.-H., Ji, C. Y., Park, S., Jeong, J. C., Lee, H.-S., & Kwak, S.-S. (2012) · PLoS ONE · doi:10.1371/journal.pone.0051502 · Cited by 160
Metadata
- Authors
- Mafra, V., Kubo, K. S., Alves-Ferreira, M., Ribeiro-Alves, M., Stuart, R. M., Boava, L. P., Rodrigues, C. M., & Machado, M. A.
- Venue
- PLoS ONE
- Publisher
- Public Library of Science (PLoS)
- Published
- 2012-02-09
- Volume
- 7
- Issue
- 2
- Pages
- e31263
- ISSN
- 1932-6203 (ISSN-L)
- OpenAlex
- W2032551656
- Cited by
- 366
- References
- 40
- FWCI
- 9.99
- Type
- journal article
- Language
- en
- Open access
- gold
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- Mafra, V., Kubo, K. S., Alves-Ferreira, M., Ribeiro-Alves, M., Stuart, R. M., Boava, L. P., Rodrigues, C. M., & Machado, M. A. (2012). Reference Genes for Accurate Transcript Normalization in Citrus Genotypes under Different Experimental Conditions. PLoS ONE. https://doi.org/10.1371/journal.pone.0031263
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