Selection of reference genes for normalization of qRT-PCR analysis of differentially expressed genes in soybean exposed to cadmium

Molecular Biology Reports

Volumn 39, Issue 2, 2012, Pages 1585-1594

  Wang, Yi ^a,b   Yu, Kangfu ^a   Poysa, Vaino ^a   Shi, Chun ^a   Zhou, Yonghong ^b  

^a HARROW RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b SICHUAN AGRICULTURAL UNIVERSITY   (China)

Author keywords

Cadmium; GeNorm; Normfinder; QRT PCR; Reference genes; Soybean

Indexed keywords

ACTIN; CADMIUM; F BOX PROTEIN; GLUCOSE 6 PHOSPHATE DEHYDROGENASE; TUBULIN;

ACT2 GENE; ACT3 GENE; ARTICLE; CULTIVAR; CYP2 GENE; ELF1A GENE; ELF1B GENE; EXPOSURE; F BOX GENE; G6PD GENE; GENE EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT LEAF; PLANT ROOT; PLANT STEM; PP2A GENE; QUANTITATIVE ANALYSIS; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SOYBEAN; TUB GENE; UBC2 GENE; DRUG EFFECT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; METHODOLOGY; REAL TIME POLYMERASE CHAIN REACTION; SOIL POLLUTANT; STANDARD;

GLYCINE MAX;

CADMIUM; GENE EXPRESSION; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; PLANT LEAVES; PLANT ROOTS; PLANT STEMS; REAL-TIME POLYMERASE CHAIN REACTION; SOIL POLLUTANTS; SOYBEANS;

EID: 84860325158     PISSN: 03014851     EISSN: 15734978     Source Type: Journal    
DOI: 10.1007/s11033-011-0897-9     Document Type: Article

References (36)

1. McGrath SP, Zhao FJ, Lombi E (2001) Plant and rhizosphere processes involved in phytoremediation of metal-contaminated soils. Plant Soil 232:207-214 (Pubitemid 32643837)
2. Clemens S (2001) Molecular mechanisms of plant metal tolerance and homeostasis. Planta 212:475-486 (Pubitemid 32235425)
3. Kazantzis G (2004) Cadmium, osteoporosis and calcium metabolism. Biometals 17:493-498 (Pubitemid 41214255)
4. 2? on growth and metabolism of cabbage. Plant Sci 163:753-758 (Pubitemid 35280844)
5. Mittler R, Vanderauwera S, Gollery M, Van Breusegem F (2004) Reactive oxygen gene network of plant. Trends Plant Sci 9:490-498 (Pubitemid 39301187)
6. Prasad SM, Zeeshan M (2005) UV-B radiation and cadmium-induced changes in growth, photosynthesis, and antioxidant enzymes of cyanobacterium Plectonema boryanum. Biol Planta-rum 49:229-236 (Pubitemid 40607499)
7. Jonak C, Nakagami H, Hirt H (2004) Heavy metal stress. Activation of distinct mitogen-activated protein kinase pathways by copper and cadmium. Plant Physiol 136:3276-3283
8. Maksymiec W, Krupa Z (2006) The effects of short-term exposition to Cd, excess Cu ions and jasmonate on oxidative stress appearing in Arabidopsis thaliana. Environ Exp Bot 57:187-194 (Pubitemid 44269301)
9. Yeh CM, Chien PS, Huang HJ (2007) Distinct signalling pathways for induction of MAP kinase activities by cadmium and copper in rice roots. J Exp Bot 58:659-671
10. Jegadeesan S, Yu K, Poysa V, Gawalko E, Morrison MJ, Shi C, Cober E (2010) Mapping and validation of simple sequence repeat markers linked to a major gene controlling seed cadmium accumulation in soybean [Glycine max(L.) Merr]. Theor Appl Genet 121:283-294
11. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible W (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Genome Anal 139:5-17 (Pubitemid 43951587)
12. Bustin SA, Benes V, Nolan T, Pfaffi MW (2005) Quantitative real-time RT-PCR-a perspective. J Mol Endocrinol 34:597-601
13. Hong SM, Bahn SC, Lyu A, Jung HS, Ahn JH (2010) Identification and testing of superior reference genes for a starting pool of transcript normalization in Arabidopsis. Plant Cell Physiol 51:1694-1706
14. Jian B, Liu B, Bi YR, Hou WS, Wu CX, Han TF (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9:59
15. Remans T, Smeets K, Opdenakker K, Mathijsen D, Vangronsveld J, Cuypers A (2008) Normalisation of real-time RT-PCR gene expression measurements in Arabidopsis thaliana exposed to increased metal concentrations. Planta 227:1343-1349
16. Maroufi A, Bockstaele EV, Loose MD (2010) Validation of reference genes for gene expression analysis in chicory (Cicho-rium intybus) using quantitative real-time PCR. BMC Mol Biol 11:15
17. Gutierrez L, Mauriat M, Guenin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, Wuytswinkel OV (2008) The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse tran-scription-polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J 6:609-618 (Pubitemid 351989484)
18. Sigh R, Green MR (1993) Sequence-specific binding of transfer RNA by glyceraldehyde-3-phosphate dehydrogenase. Science 259:365-368 (Pubitemid 23055678)
19. Ishitani R, Sunaga K, Hirano A, Saunders P, Katsube N, Chuang DM (1996) Evidence that glyceraldehyde-3-phosphate dehydro-genase is involved in age-induced apoptosis in mature cerebellar neurons in culture. J Neurochem 66:928-935
20. 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 Biol 3:RESEARCH0034
21. Hu RB, Fan CM, Li HY, Zhang QZ, Fu YF (2009) Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol Biol 10:93
22. Libault M, Thibivilliers S, Bilgin DD, Radwan O, Benitez M, Clough SJ, Stacey G (2008) Identification of four soybean reference genes for gene expression normalization. Plant Genome 1:44-54
23. Kulcheski FR, Marcelino-Guimaraes FC, Nepomuceno AL, Ab-delnoor RV, Margis R (2010) The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Anal Biochem 406:185-192
24. Basa B, Solti A, Sárcári E, Tamás L (2009) Housekeeping gene selection in poplar plants under Cd-stress: comparative study for real-time PCR normalisation. Funct Plant Biol 26:1079-1087
25. Andersen CL, Jensen JJ, Ørntoft TF (2004) Normalization of real-time quantitative reverse transcription-PCR data: a modelbased variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res 64:5245-5250 (Pubitemid 39006544)
26. Ablett GR, Stirling BT, Fischer JD (1999) Westag 97 soybean. Can J Plant Sci 79:371-372 (Pubitemid 29530751)
27. Poysa V, Buzzell RI (2001) AC Hime Soybean. Can J Plant Sci 8:443-444 (Pubitemid 33105331)
28. Arao T, Ae N, Sugiyama M, Takahashi M (2003) Genotypic differences in cadmium uptake and distribution in soybeans. Plant Soil 251:247-253 (Pubitemid 36580028)
29. Redjala T, Sterckeman T, Morel JL (2009) Cadmium uptake by root: contribution of apoplast and high- and low-affinity membrane transport systems. Environ Exp Bot 67:235-242
30. Uraguchi S, Mori S, Kuramata M, Kawasaki A, Arao T, Ishikawa S (2009) Root-to-root Cd translocation via the xylem is the major process determining shoot and grain cadmium accumulation in rice. J Exp Bot 60:2677-2688
31. Cordoba EM, Die JV, González-Verdejo CI, Nadal S, Román B (2011) Selection of reference genes in Hedysarum coronarium under carious stresses and stages of development. Anal Biochem 409:236-243
32. 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 (Pubitemid 41507227)
33. Xu M, Zhang B, Su X, Zhang S, Huang M (2011) Reference gene selection for quantitative real-time polymerase chain reaction in Populus. Anal Biochem 408:337-339
34. Huis R, Hawkins S, Neuteling G (2010) Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.). BMC Plant Biol 10:87
35. Smith RD, Walker JC (1996) Plant protein phosphatases. Ann Rev Plant Phys Plant Mol Biol 47:101-125
36. Filby AL, Tyler CR (2007) Appropriate housekeeping genes for use in expression profiling the effects of environmental estrogens in fish. BMC Mol Biol 8:10