ArticlePlant molecular biology2008
Deciphering transcriptional networks that govern Coffea arabica seed development using combined cDNA array and real-time RT-PCR approaches.
Article in Plant molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 70 citations in OpenAlex.
- Evolution of the biochemistry underpinning purine alkaloid metabolism in plants.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2024Review
- Salt Stress-Induced Anthocyanin Biosynthesis Genes andACS omega · 2021Article
- Differential expression of anthocyanin biosynthesis genes in3 Biotech · 2018Article
- Use of a draft genome of coffee (Coffea arabica) to identify SNPs associated with caffeine content.Plant biotechnology journal · 2018Article
- Identification of a seed maturation protein gene from Coffea arabica (CaSMP) and analysis of its promoter activity in tomato.Plant cell reports · 2018Article
- Integrative analysis of the late maturation programme and desiccation tolerance mechanisms in intermediate coffee seeds.Journal of experimental botany · 2018Article
- Dataset on exogenous application of salicylic acid and methyljasmonate and the accumulation of caffeine in young leaf tissues and catabolically inactive endosperms.Data in brief · 2017Article
- Article
- Identification of candidate genes for drought tolerance in coffee by high-throughput sequencing in the shoot apex of different Coffea arabica cultivars.BMC plant biology · 2016Article
- The Greater Phenotypic Homeostasis of the Allopolyploid Coffea arabica Improved the Transcriptional Homeostasis Over that of Both Diploid Parents.Plant & cell physiology · 2015Article
- Differential regulation of caffeine metabolism in Coffea arabica (Arabica) and Coffea canephora (Robusta).Planta · 2015Article
- Lipid transfer proteins in coffee: isolation of Coffea orthologs, Coffea arabica homeologs, expression during coffee fruit development and promoter analysis in transgenic tobacco plants.Plant molecular biology · 2014Article
- Article
- Nitrogen starvation, salt and heat stress in coffee (Coffea arabica L.): identification and validation of new genes for qPCR normalization.Molecular biotechnology · 2013Article
- Differentially expressed genes and proteins upon drought acclimation in tolerant and sensitive genotypes of Coffea canephora.Journal of experimental botany · 2012Article
- Selection of reference genes for quantitative real-time PCR expression studies of microdissected reproductive tissues in apomictic and sexual Boechera.BMC research notes · 2011Article
- An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora.BMC plant biology · 2011Article
- Use of the growing environment as a source of variation to identify the quantitative trait transcripts and modules of co-expressed genes that determine chlorogenic acid accumulation.Plant, cell & environment · 2010Article
- Metabolic pathways in tropical dicotyledonous albuminous seeds: Coffea arabica as a case study.The New phytologist · 2009Article
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Authors and funding
6 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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