Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches
Due to its economic importance, Coffea arabica is becoming the subject of increasing genomic research and, in particular, the genes involved in the final chemical composition of the bean and the sensorial quality of the coffee beverage. The aim of the present study was to decipher the transcriptional networks that govern the development of the C. arabica seed, a model for non-orthodox albuminous seeds of tropical origin. For this purpose, we developed a transcriptomic approach combining two techniques: targeted cDNA arrays, containing 266 selected candidate gene sequences, and real-time RT-PCR on a large subset of 111 genes. The combination of the two techniques allowed us to limit detection of false positives and to reveal the advantages of using large real-time RT-PCR screening. Multivariate analysis was conducted on both datasets and results were broadly convergent. First, principle component analysis (PCA) revealed a dramatic re-programming of the transcriptional machinery between early cell division and elongation, storage and maturation phases. Second, hierarchical clustering analysis (HCA) led to the identification of 11 distinct patterns of gene expression during seed development as well as to the detection of genes expressed at specific developmental stages that can be used as functional markers of phenological changes. In addition, this study led to the description of gene expression profiles for quality-related genes, most of them formerly uncharacterised in Coffea. Their involvement in storage compound synthesis and accumulation during endosperm development and final metabolic re-adjustments during maturation is discussed.
KeywordsCoffea Seed development Ripening Transcript profiling Gene clustering
This work was supported by the European Union, Région Réunion and IRD (DOCUP Réunion 2000–2006). We thank Xavier Sabau for skilled technical support in cDNA array spotting using facilities and robotics of the genotyping platform at the Montpellier Languedoc-Roussillon Genopole (http://www.genopole-montpellier-lr.org). The authors also wish to acknowledge Dr. Aurélie Lécolier (IRD) for stimulating discussions and Dr. David Pot (CIRAD) and James Tregear (IRD) for critical reading of the manuscript. Finally, we acknowledge anonymous referees for their critical comments which greatly improved the manuscript.
- Beisson F, Koo AJ, Ruuska S, Schwender J, Pollard M, Thelen JJ, Paddock T, Salas JJ, Savage L, Milcamps A, Mhaske VB, Cho Y, Ohlrogge JB (2003) Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database. Plant Physiol 132:681–697PubMedCrossRefGoogle Scholar
- Canales RD, Luo Y, Willey JC, Austermiller B, Barbacioru CC, Boysen C, Hunkapiller K, Jensen RV, Knight CR, Lee KY, Ma Y, Maqsodi B, Papallo A, Peters EH, Poulter K, Ruppel PL, Samaha RR, Shi L, Yang W, Zhang L, Goodsaid FM (2006) Evaluation of DNA microarray results with quantitative gene expression platforms. Nat Biotechnol 24:1115–1122PubMedCrossRefGoogle Scholar
- Dentan E (1985) Etude microscopique du développement et de la maturation du grain de café. Proc Int Congr ASIC 11:381–398Google Scholar
- Leloup V, Louvrier A, Liardon R (1995) Degradation mechanisms of chlorogenic acids during roasting. Proc Int Congr ASIC 16:192–198Google Scholar
- Leroy T, Marraccini P, Dufour M, Montagnon C, Lashermes P, Sabau X, Ferreira LP, Jourdan I, Pot D, Andrade AC, Glaszmann JC, Vieira LG, Piffanelli P (2005) Construction and characterization of a Coffea canephora BAC library to study the organization of sucrose biosynthesis genes. Theor Appl Genet 111:1032–1041PubMedCrossRefGoogle Scholar
- Mahesh V, Million-Rousseau R, Ullmann P, Chabrillange N, Bustamante J, Mondolot L, Morant M, Noirot M, Hamon S, de Kochko A, Werck-Reichhart D, Campa C (2007) Functional characterization of two p-coumaroyl ester 3′-hydroxylase genes from coffee tree: evidence of a candidate for chlorogenic acid biosynthesis. Plant Mol Biol 64:145–159PubMedCrossRefGoogle Scholar
- Pammenter NW, Berkak P (1999) A review of recalcitrant seed physiology in relation to desiccation-tolerance mechanisms. Seed Sci Res 9:13–37Google Scholar
- Soeda Y, Konings MC, Vorst O, van Houwelingen AM, Stoopen GM, Maliepaard CA, Kodde J, Bino RJ, Groot SP, van der Geest AH (2005) Gene expression programs during Brassica oleracea seed maturation, osmopriming,and germination are indicators of progression of the germination process and the stress tolerance level. Plant Physiol 137:354–368PubMedCrossRefGoogle Scholar
- Vieira LGE, Andrade AC, Colombo CA, Moraes AHA, Metha A, Oliveira AC, Labate CA, Marino CL, Monteiro-Vitorello CB, Monte DC, Giglioti E, Kimura ET, Romano E, Kuramae EE, Lemos EGM, Almeida ERP, Jorge EC, Albuquerque EVS, da Silva FR, Vinecky F, Sawazaki HE, Dorry HFA, Carrer H, Abreu IN, Batista JAN, Teixeira JB, Kitajima JP, Xavier KG, Lima LM, Camargo LEA, Pereira LFP, Coutinho LL, Lemos MVF, Romano MR, Machado MA, Costa MMC, Grossi de Sá MF, Goldman MHS, Ferro MIT, Tinoco MLP, Oliveira MC, Van Sluys MA, Shimizu MM, Maluf MP, Eira MTS, Guerreiro Filho O, Arruda P, Mazzafera P, Mariani PDSC, Oliveira RLBC, Harakava R, Balbao SF, Tsai SM, Mauro SMZ, Santos SN, Siqueira WJ, Costa GGL, Formighieri EF, Carazzolle MF, Pereira GAG (2006) Brazilian coffee genome project: an EST-based genomic resource. Braz J Plant Physiol 18:95–108Google Scholar
- Wormer TM (1964) The growth of the coffee berry. Ann Bot 28:47–55Google Scholar