Selection of housekeeping genes for qRT-PCR analysis in potato tubers under cold stress

Molecular Breeding

Volumn 31, Issue 1, 2013, Pages 39-45

  Lopez Pardo, Raquel ^a   Ruiz de Galarreta, Jose Ignacio ^a   Ritter, Enrique ^a  

^a NEIKER and a Vaccine producing Commercial Company CZVSL   (Spain)

Author keywords

Cold; Housekeeping; Potato tuber; qRT PCR; Solanum tuberosum L.

Indexed keywords

COLD STORAGE; DIGITAL STORAGE; FINANCE; GENE EXPRESSION; HISTOLOGY; POLYMERASE CHAIN REACTION; PROTEINS; RNA; TUBES (COMPONENTS);

COLD; GENE EXPRESSION STUDIES; HOUSEKEEPING; HOUSEKEEPING GENE; INTERNAL CONTROLS; POTATO TUBERS; QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION; REACTION ANALYSIS; REFERENCE GENES; SOLANUM TUBEROSUM L;

TISSUE;

SOLANUM TUBEROSUM;

EID: 84871931865     PISSN: 13803743     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11032-012-9766-z     Document Type: Article

References (27)

1. Andersen CL, Jensen JL, Orntoft TF (2004) Normalization of quantitative real-time 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.
2. Bustin SA (2000) Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol 25: 169-193.
3. Bustin SA, Mueller R (2005) Real-time reverse transcription PCR (qRT-PCR) and its potential use in clinical diagnosis. Clin Sci 109: 365-379.
4. Bustin SA, Gyselman VG, Siddiqi S, Dorudi S (2000) Cytokeratin 20 is not a tissue specific marker for the detection of malignant epithelial cells in the blood of colorectal cancer patients. Int J Surg Invest 2: 49-57.
5. Caldana C, Scheible WR, Mueller-Roeber B, Ruzicic S (2007) A quantitative RT-PCR platform for high-throughput expression profiling of 2500 rice transcription factors. Plant Methods 3: 7. doi: 10. 1186/1746-4811-3-.
6. Dean JD, Goodwin PH, Hsiang T (2002) Comparison of relative RT-PCR and northern blot analyses to measure expression of β-1, 3-glucanasa in Nicatiana benthamiana infected with Colletotrichum destructivum. Plant Mol Biol Rep 20: 347-356.
7. Dheda K, Huggett JF, Chang JS, Kim LU, Bustin SA, Johnson MA, Rook GA, Zumla A (2005) The implications of using an inappropriate reference gene for real-time reverse transcription PCR data normalization. Anal Biochem 344(1): 141-143.
8. Gachon C, Mingam A, Charrier B (2004) Real-Time PCR: what relevance to plant studies. J Exp Bot 55: 1445-1454.
9. Gutierrez L, Mauriat M, Pelloux J, Bellini C, van Wuytswinkel O (2008) Towards a systematic validation of references in real-time RT-PCR. Plant Cell 20: 1734-1735.
10. Haase NU (2007) The canon of potato science: 48. Maillard reaction. Potato Res 50: 407-409.
11. Hellemans J, Mortier G, De Paepe A, Speleman F, Vandersompele J (2007) qBase relative quantification framework and software for management and automated analysis of real. time quantitative PCR data. Genome Biol 8: R19.
12. Hogervorst JG, Schouten LJ, Konings EJ, Goldbohm RA, van den Brandt PA (2007) A prospective study of dietary acrylamide intake and the risk of endometrial, ovarian, and breast cancer. Cancer Epidemiol Biomarkers Prev 16: 2304-2313.
13. Lefever S, Hellemans J, Pattyn F, Przybylski DR, Taylor C, Geurts R, Untergasser A, Vandersompele J (2009) RDML: structured language and reporting guidelines for real-time quantitative PCR data. Nucleic Acids Res 37(7): 2065-2069.
14. Mehta R, Birerdinc A, Hossain N, Afendy A, Chandhoke V (2010) Validation of endogenous reference genes for qRT-PCR analysis of human visceral adipose samples. BMC Mol Biol 11(39): 1471-2199.
15. Nicot N, Hausman JF, Hoffmann L, Evers D (2005) Housekeeping gene selection for real-time RT-PCR normalization in potato during biotic and abiotic stress. J Exp Bot 56: 2907-2914.
16. Nolan T, Hands RE, Bustin SA (2006) Quantification of mRNA using real-time PCR. Nat Protoc 1: 1559-1582.
17. Pfaffl MW (2001) A new mathematical model for relative quantification in real-time RT-PCR. Nucleic Acids Res 29: 2002-2007.
18. Pfaffl MW, Horgan GW, Dempfle L (2002) Relative expression software tool (REST) for group-wise comparison and statistical analysis of relative expression results in real-time PCR. Nucleic Acids Res 30: e36.
19. 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. Biotechnol Lett 26: 509-515.
20. Pinhero RG, Coffin R, Yada RY (2009) Post-harvest storage in potatoes. In: Jaspreet S, Lovedeep K (eds) Potato Chemistry and Technology. Academic, San Diego.
21. Radonic A, Thulke S, Mackay IM, Landt O, Siegert W, Nitsche A (2004) Guideline to reference gene selection for quantitative real-time PCR. Biochem Biophys Res Commun 313: 856-862.
22. Ritter E, Ruiz de Galarreta JI, van Eck HJ, Sánchez I (2008) Construction of a transcriptome map of potato based on the cDNA-AFLP technique. Theor Appl Genet 116: 1003-1013.
23. van Es A, Hartmans KJ (1987) Starch and sugars during tuberization, storage and sprouting. In: Rastovski A, van Es A (eds) Storage of potatoes. PUDOC, Wageningen, pp 141-147.
24. Vandersompele 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 Biol. 3: RESEARCH0034.
25. Vandersompele J, Kubista M, Pfaffl W (2009) Reference gene validation software for improved normalization. In: Logan J, Edwards K, Saunders N (eds) Real Time PCR: Current Technology and Applications. Caister Academic, Norfolk.
26. Walker NJ (2002) A technique whose time has come. Science 296: 557-559.
27. Willems E, Mateizel I, Kemp C, Cauffman G, Sermon K, Leyns L (2006) Selection of reference genes in mouse embryos and in differentiating human and mouse ES cells. Int J Dev Biol 50(7): 627-635.