Selection and validation of suitable reference genes for mRNA qRT-PCR analysis using somatic embryogenic cultures, floral and vegetative tissues in citrus

Plant Cell, Tissue and Organ Culture

Volumn 113, Issue 3, 2013, Pages 469-481

  Liu, Zheng ^a   Ge, Xiao Xia ^a   Wu, Xiao Meng ^a   Kou, Shu Jun ^a   Chai, Li Jun ^a   Guo, Wen Wu ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Citrus; qRT PCR; Reference gene; Validation

Indexed keywords

CITRUS; EXPERIMENTAL CONDITIONS; GENE EXPRESSION PROFILES; GENE EXPRESSION STUDIES; Q-RT-PCR; REFERENCE GENES; TEMPERATURE TREATMENTS; VALIDATION;

BIOLOGICAL ORGANS; GENES; GROWTH KINETICS; ISOMERS; ORCHARDS; PLANTS (BOTANY); TISSUE;

TRANSCRIPTION;

CITRUS;

EID: 84878213256     PISSN: 01676857     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11240-013-0288-0     Document Type: Article

References (54)

1. Albrecht U, Bowman KD (2008) Gene expression in Citrus sinensis (L.) Osbeck following infection with the bacterial pathogen Candidatus Liberibacter asiaticus causing Huanglongbing in Florida. Plant Sci 175: 291-306.
2. Andersen CL, Jensen JL, Ørntoft 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 Res 64: 5245-5250.
3. 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 Biol 10: 49.
4. Beekman L, Tohver T, Dardari R, Léguillette R (2011) Evaluation of suitable reference genes for gene expression studies in bronchoalveolar lavage cells from horses with inflammatory airway disease. BMC Mol Biol 12: 5.
5. Biswas MK, Chai LJ, Qiang X, Deng XX (2012) Generation, functional analysis and utility of Citrus grandis EST from a flower-derived cDNA library. Mol Biol Rep 39: 7221-7235.
6. Boava LP, Cristofani-Yaly M, Mafra VS, Karen K, Kishi LT, Takita MA, Ribeiro-Alves M, Machado MA (2011) Global gene expression of Poncirus trifoliata, Citrussunki and their hybrids under infection of Phytophthora parasitica. BMC Genomics 12: 39.
7. Cai XD, Fu J, Deng XX, Guo WW (2007) Production and molecular characterization of potential seedless cybrid plants between pollen sterile Satsuma and two seedy Citrus cultivars. Plant Cell Tissue Organ Cult 90: 275-283.
8. Carvalho K, de Campos MKF, Pereira LFP, Vieira LGE (2010) Reference gene selection for real-time quantitative polymerase chain reaction normalization in "Swingle" citrumelo under drought stress. Anal Biochem 402: 197-199.
9. Chai L, Ge X, Xu Q, Deng X (2011) CgSL2, an S-like RNase gene in 'Zigui shatian' pummelo (Citrus grandis Osbeck), is involved in ovary senescence. Mol Biol Rep 38: 1-8.
10. Chandna R, Augustine R, Bisht NC (2012) Evaluation of candidate reference genes for gene expression normalization in Brassica juncea using real time quantitative RT-PCR. PLoS ONE 7: e36918.
11. Chang E, Shi S, Liu J, Cheng T, Xue L, Yang X, Yang W, Lan Q, Jiang Z (2012) Selection of reference genes for quantitative gene expression studies in Platycladus orientalis (Cupressaceae) using real-time PCR. PLoS ONE 7: e33278.
12. Chen L, Zhong HY, Kuang JF, Li JG, Lu WJ, Chen JY (2011) Validation of reference genes for RT-qPCR studies of gene expression in banana fruit under different experimental conditions. Planta 234: 377-390.
13. Cruz F, Kalaoun S, Nobile P, Colombo C, Almeida J, Barros L, Romano E, Grossi-de-Sá MF, Vaslin M, Alves-Ferreira M (2009) Evaluation of coffee reference genes for relative expression studies by quantitative real-time RT-PCR. Mol Breed 23: 607-616.
14. Czechowski T, Stitt M, Altmann T, Udvardi MK, Scheible WR (2005) Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis. Plant Physiol 139: 5-17.
15. Deng XX (1987) Studies on the isolation, regeneration and fusion of protoplasts in citrus. PhD thesis Huazhong Agricultural University.
16. Expósito-Rodríguez M, Borges AA, Borges-Pérez A, Pérez JA (2008) Selection of internal control genes for quantitative real-time RT-PCR studies during tomato development process. BMC Plant Biol 8: 131.
17. Fan J, Chen C, Brlansky RH, Gmitter FG Jr, Li Z-G (2010) Changes in carbohydrate metabolism in Citrus sinensis infected with 'Candidatus Liberibacter asiaticus'. Plant Pathol 59: 1037-1043.
18. Gachon C, Mingam A, Charrier B (2004) Real-time PCR: what relevance to plant studies? J Exp Bot 55: 1445-1454.
19. Ge XX, Fan GE, Chai LJ, Guo WW (2010) Cloning, molecular characterization and expression analysis of a SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE gene (CitSERK1-like) in Valencia sweet orange. Acta Physiol Plant 32: 1197-1207.
20. Ge XX, Chai LJ, Liu Z, Wu XM, Deng XX, Guo WW (2012) Transcriptional profiling of genes involved in embryogenic, non-embryogenic calluses and somatic embryogenesis of Valencia sweet orange by SSH-based microarray. Planta 236: 1107-1124.
21. Gmitter FG Jr, Chen C, Machado MA, de Souza AA, Ollitrault P, Froelicher Y, Shimizu T (2012) Citrus genomics. Tree Genet Genomes 8: 611-626.
22. Grosser JW, Gmitter FG Jr (2011) Protoplast fusion for production of tetraploids and triploids: applications for scion and rootstock breeding in citrus. Plant Cell Tissue Organ Cult 104: 343-357.
23. Gutierrez L, Mauriat M, Guénin S, Pelloux J, Lefebvre JF, Louvet R, Rusterucci C, Moritz T, Guerineau F, Bellini C, van Wuytswinkel O (2008) The lack of a systematic validation of reference genes: a serious pitfall undervalued in reverse transcription polymerase chain reaction (RT-PCR) analysis in plants. Plant Biotechnol J 6: 609-618.
24. Harris MJ, Dugger WM (1986) Levels of free and conjugated abscisic acid in developing floral organs of the navel orange (Citrus sinensis [L.] Osbeck cv Washington). Plant Physiol 82: 1164-1166.
25. Hu R, Fan C, Li H, Zhang Q, Fu Y-F (2009) Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR. BMC Mol Biol 10: 93.
26. Jain M, Nijhawan A, Tyagi AK, Khurana JP (2006) Validation of housekeeping genes as internal control for studying gene expression in rice by quantitative real-time PCR. Biochem Biophys Res Commun 345: 646-651.
27. Jian B, Liu B, Bi Y, Hou W, Wu C, Han T (2008) Validation of internal control for gene expression study in soybean by quantitative real-time PCR. BMC Mol Biol 9: 59.
28. Kim B-R, Nam H-Y, Kim S-U, Kim S-I, Chang Y-J (2003) Normalization of reverse transcription quantitative-PCR with housekeeping genes in rice. Biotechnol Lett 25: 1869-1872.
29. Kulcheski FR, Marcelino-Guimaraes FC, Nepomuceno AL, Abdelnoor RV, Margis R (2010) The use of microRNAs as reference genes for quantitative polymerase chain reaction in soybean. Anal Biolchem 406: 185-192.
30. Li QF, Sun SSM, Yuan DY, Yu HX, Gu MH, Liu QQ (2010) Validation of candidate reference genes for the accurate normalization of real-time quantitative RT-PCR data in rice during seed development. Plant Mol Biol Rep 28: 49-57.
31. 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.
32. Lin YL, Lai ZX (2010) Reference gene selection for qPCR analysis during somatic embryogenesis in longan tree. Plant Sci 178: 359-365.
33. Liu YZ, Liu Q, Tao NG, Deng XX (2006) Efficient isolation of RNA from fruit peel and pulp of ripening navel orange (Citrus sinesis Osbeck). J Huazhong Agric Univ 25: 300-304.
34. Liu Q, Zhu A, Chai L, Zhou W, Yu K, Ding J, Xu J, Deng X (2009) Transcriptome analysis of a spontaneous mutant in sweet orange [Citrus sinensis (L.) Osbeck] during fruit development. J Exp Bot 60: 801-813.
35. Mafra V, Kubo KS, Alves-Ferreia M, Ribeiro-Alves M, Stuart RM, Boava LP, Rodrigues CM, Machado MA (2012) Reference genes for accurate transcript normalization in citrus genotypes under different experimental conditions. PLoS ONE 7(2): e31263.
36. Mallona L, Lischewski S, Weiss J, Hause B, Egea-Cortines M (2010) Validation of reference genes for quantitative real-time PCR during leaf and flower development in Petunia hybrida. BMC Plant Biol 10: 4.
37. Maroufi A, van Bockstaele E, Loose MD (2010) Validation of reference genes for gene expression analysis in chicory (Cichorium intybus) using quantitative real-time PCR. BMC Mol Biol 11: 15.
38. Nicot N, Hausman J-F, 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.
39. Nishikawa F, Endo T, Shimada T, Fujii H, Shimizu T, Omura M (2009) Differences in seasonal expression of flowering genes between deciduous trifoliate orange and evergreen Satsuma mandarin. Tree Physiol 29: 921-926.
40. 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.
41. Pihur V, Datta S, Datta S (2009) RankAggreg, an R package for weighted rank aggregation. BMC Bioinformatics 10: 62.
42. 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.
43. Schlögl PS, dos Santos AKW, Vieira LN, Floh EIS, Guerra MP (2012) Gene expression during early somatic embryogenesis in Brazilian pine (Araucaria angustifolia (Bert) O Ktze). Plant Cell Tissue Organ Cult 108: 173-180.
44. Shimada T, Hirabayashi T, Endo T, Fujii H, Kita M, Omura M (2005) Isolation and characterization of the somatic embryogenesis receptor-like kinase gene homologue (CitSERK1) from Citrus unshiu Marc. Sci Hortic 103: 233-238.
45. Tan FC, Swain SM (2007) Functional characterization of AP3, SOC1 and WUS homologues from citrus (Citrus sinensis). Physiol Plant 131: 481-495.
46. 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: 7.
47. Wen L, Tan B, Guo WW (2012) Estimating transgene copy number in precocious trifoliate orange by TaqMan real-time PCR. Plant Cell Tissue Organ Cult 109: 363-371.
48. Wu XM, Liu MY, Ge XX, Qiang X, Guo WW (2011) Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange. Planta 233: 495-505.
49. 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.
50. Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo OJ, Tang Z, Guo WW, Kuang H, Zhang HY, Roose ML, Nagarajan N, Deng XX, Ruan Y (2013) The draft genome of sweet orange (Citrus sinensis). Nat Genet 45: 59-66.
51. Yan J, Yuan F, Long G, Qin L, Deng Z (2012) Selection of reference genes for quantitative real-time RT-PCR analysis in citrus. Mol Biol Rep 38: 1831-1838.
52. Yang X, Zhang X (2010) Regulation of somatic embryogenesis in higher plants. Crit Rev Plant Sci 29: 36-57.
53. Zheng TG, Qiu WM, Fan GE, Zheng BB, Guo WW (2011) Construction and characterization of a cDNA library from floral organs and fruitlets of Citrus reticulata. Biol Plant 55: 431-436.
54. Zhong HY, Chen JW, Li CQ, Chen L, Wu JY, Chen JY, Lu WJ, Li JG (2010) Selection of reliable reference genes for expression studies by reverse transcription quantitative real-time PCR in litchi under different experimental conditions. Plant Cell Rep 30: 641-653.