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T. T. Pinheiro, Litholdo, Jr., C. G., Sereno, M. L., Leal, Jr., G. A., Albuquerque, P. S. B., and Figueira, A., Establishing references for gene expression analyses by RT-qPCR in Theobroma cacao tissues, vol. 10, pp. 3291-3305, 2011.
Andersen CL, Jensen JL and Orntoft 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. PMid:15289330 Argout X, Fouet O, Wincker P, Gramacho K, et al. (2008). Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions. BMC Genom. 9: 512. PMid:18973681    PMCid:2642826 Argout X, Salse J, Aury JM, Guiltinan MJ, et al. (2011). The genome of Theobroma cacao. Nat. Genet. 43: 101-108. PMid:21186351 Bae H, Kim SH, Kim MS, Sicher RC, et al. (2008). The drought response of Theobroma cacao (cacao) and the regulation of genes involved in polyamine biosynthesis by drought and other stresses. Plant Physiol. Biochem. 46: 174-188. PMid:18042394 Barsalobres-Cavallari CF, Severino FE, Maluf MP and Maia IG (2009). Identification of suitable internal control genes for expression studies in Coffea arabica under different experimental conditions. BMC Mol. Biol. 10: 1. PMid:19126214    PMCid:2629470 Bennett AB (2003). Out of the Amazon: Theobroma cacao enters the genomic era. Trends Plant Sci. 8: 561-563. PMid:14659701 Bomal C, Bedon F, Caron S, Mansfield SD, et al. (2008). Involvement of Pinus taeda MYB1 and MYB8 in phenylpropanoid metabolism and secondary cell wall biogenesis: a comparative in planta analysis. J. Exp. Bot. 59: 3925-3939. PMid:18805909    PMCid:2576632 Brunet J, Varrault G, Zuily-Fodil Y and Repellin A (2009). Accumulation of lead in the roots of grass pea (Lathyrus sativus L.) plants triggers systemic variation in gene expression in the shoots. Chemosphere 77: 1113-1120. PMid:19726070 Bustin SA, Benes V, Garson JA, Hellemans J, et al. (2009). The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin. Chem. 55: 611-622. PMid:19246619 Byers DM and Gong H (2007). Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family. Biochem. Cell Biol. 85: 649-662. PMid:18059524 Calsa T Jr and Figueira A (2007). Serial analysis of gene expression in sugarcane (Saccharum spp.) leaves revealed alternative C4 metabolism and putative antisense transcripts. Plant Mol. Biol. 63: 745-762. PMid:17211512 Carvalho K, de Campos MK, Pereira LF and Vieira LG (2010). Reference gene selection for real-time quantitative polymerase chain reaction normalization in “Swingle” citrumelo under drought stress. Anal. Biochem. 402: 197-199. PMid:20363209 Donson J, Fang Y, Espiritu-Santo G, Xing W, et al. (2002). Comprehensive gene expression analysis by transcript profiling. Plant Mol. Biol. 48: 75-97. PMid:11860215 Gachon C, Mingam A and Charrier B (2004). Real-time PCR: what relevance to plant studies? J. Exp. Bot. 55: 1445-1454. PMid:15208338 Guiltinan MJ, Verica J, Zhang D and Figueira A (2008). Genomics of Theobroma Cacao, “The Food of the Gods”. In: Genomics of Tropical Crop Plants (Moore PH and Ming R, eds.). 1st edn. Springer, New York, 145-170. Gutierrez N, Giménez MJ, Palomino C and Avila CM (2010). Assessment of candidate reference genes for expression studies in Vicia faba L. by real-time quantitative PCR. Mol. Breed. DOI: 10.1007/s11032-010-9456-7. Hong SY, Seo PJ, Yang MS, Xiang F, et al. (2008). Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR. BMC Plant Biol. 8: 112. PMid:18992143    PMCid:2588586 Huggett J, Dheda K, Bustin S and Zumla A (2005). Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 6: 279-284. PMid:15815687 Huis R, Hawkins S and Neutelings G (2010). Selection of reference genes for quantitative gene expression normalization in flax (Linum usitatissimum L.). BMC Plant Biol. 10: 71. PMid:20403198    PMCid:3095345 Iskandar HM, Simpson RS, Casu RE and Bonnett GD (2004). Comparison of reference genes for quantitative real-time polymerase chain reaction analysis of gene expression in sugarcane. Plant Mol. Biol. Rep. 22: 325-337. Jeong YM, Mun JH, Lee I, Woo JC, et al. (2006). Distinct roles of the first introns on the expression of Arabidopsis profilin gene family members. Plant Physiol. 140: 196-209. PMid:16361517    PMCid:1326044 Leal GA Jr, Albuquerque PS and Figueira A (2007). Genes differentially expressed in Theobroma cacao associated with resistance to witches’ broom disease caused by Crinipellis perniciosa. Mol. Plant Pathol. 8: 279-292. PMid:20507499 Lepelley M, Cheminade G, Tremillon N and Simkin A (2007). Chlorogenic acid synthesis in coffee: an analysis of CGA content and real-time RT-PCR expression of HCT, HQT, C3H1, and CCoAOMT1 genes during grain development in C. canephora. Plant Sci. 172: 978-996. Liu JJ, Zamani A and Ekramoddoullah AK (2010). Expression profiling of a complex thaumatin-like protein family in western white pine. Planta 231: 637-651. PMid:19997927 Magneschi L, Kudahettige RL, Alpi A and Perata P (2009). Expansin gene expression and anoxic coleoptile elongation in rice cultivars. J. Plant Physiol. 166: 1576-1580. PMid:19410334 Martin RC, Hollenbeck VG and Dombrowski JE (2008). Evaluation of reference genes for quantitative RT-PCR in Lolium perenne. Crop Sci. 48: 1881-1887. Migocka M and Papierniak A (2010). Identification of suitable reference genes for studying gene expression in cucumber plants subjected to abiotic stress and growth regulators. Mol. Breed. DOI: 10.1007/s11032-010-9487-0. Mondego JM, Carazzolle MF, Costa GG, Formighieri EF, et al. (2008). A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao. BMC Genom. 9: 548. PMid:19019209    PMCid:2644716 Nicot N, Hausman JF, Hoffmann L and 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. PMid:16188960 Park SJ, Cotter PA and Gunsalus RP (1995). Regulation of malate dehydrogenase (MDH) gene expression in Escherichia coli in response to oxygen, carbon, and heme availability. J. Bacteriol. 177: 6652-6656. PMid:7592446    PMCid:177521 Pires JL, Cascardo JCM, Lambert SV and Figueira A (1998). Increasing cocoa butter yield through genetic improvement of Theobroma cacao L.: Seed fat content variability, inheritance, and association with seed yield. Euphytica 103: 115-121. Pre M, Caillet V, Sobilo J and McCarthy J (2008). Characterization and expression analysis of genes directing galactomannan synthesis in coffee. Ann. Bot. 102: 207-220. PMid:18562467    PMCid:2712370 Reid KE, Olsson N, Schlosser J, Peng F, et al. (2006). An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development. BMC Plant Biol. 6: 27. PMid:17105665    PMCid:1654153 Rozen S and Skaletsky H (2000). Primer3 on the WWW for General Users and for Biologists Programmers. In: Bioinformatics Methods and Protocols: Methods in Molecular Biology (Krawetz S and Misener S, eds.). Humana Press, Totowa, 365-386. Salmona J, Dussert S, Descroix F, de Kochko A, et al. (2008). Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches. Plant Mol. Biol. 66: 105-124. PMid:18026845 Schmidt GW and Delaney SK (2010). Stable internal reference genes for normalization of real-time RT-PCR in tobacco (Nicotiana tabacum) during development and abiotic stress. Mol. Genet. Genom. 283: 233-241. PMid:20098998 Silva CRS (2005). Caracterização de Sequências Gênicas Expressas (EST) Durante o Desenvolvimento de Sementes de Theobroma cacao L. com Ênfase na Biossíntese de Ácidos Graxos e Triglicerídeos. Doctoral thesis, Centro de Energia Nuclear na Agricultura, USP, Piracicaba. Silva CRS and Figueira A (2005). Phylogenetic analysis of Theobroma (Sterculiaceae) based on Kunitz-like trypsin inhibitor sequences. Plant Syst. Evol. 250: 93-104. Vandesompele J, De Preter K, Pattyn F, Poppe B, et al. (2002). Accurate normalization of real-time quantitative RT-PCR data by geometric averaging of multiple internal control genes. Genome Biol. 3: RESEARCH0034. Verica JA, Maximova SN, Strem MD, Carlson JE, et al. (2004). Isolation of ESTs from cacao (Theobroma cacao L.) leaves treated with inducers of the defense response. Plant Cell Rep. 23: 404-413. PMid:15340758 World Cocoa Foundation (2010). Available at []. Accessed August 13, 2010.