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Here we describe the development of a quantitative real\u2010time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC\u2010MS and LC\u2010MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild\u2010type <jats:italic>Solanum lycopersicum<\/jats:italic> cv. Ailsa Craig and the <jats:italic>hp1<\/jats:italic> mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene <jats:italic>DDB1<\/jats:italic> from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes.<\/jats:p>","DOI":"10.1111\/j.1365-313x.2011.04750.x","type":"journal-article","created":{"date-parts":[[2011,8,18]],"date-time":"2011-08-18T19:54:03Z","timestamp":1313697243000},"page":"999-1013","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":113,"title":["Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit 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