BMC Genomics Research article Colour variation in red grapevines (Vitis vinifera L.): genomic organisation, expression of flavonoid 3'-hydroxylase, flavonoid 3',5'-hydroxylase genes and related metabolite profiling of red cyanidin-/blue delphinidin-based anthocyanins in berry skin Simone D Castellarin1, Gabriele Di Gaspero*1, Raffaella Marconi1, Alberto Nonis1, Enrico Peterlunger1, Sophie Paillard2,3, Anne- Francoise Adam-Blondon2 and Raffaele Testolin1 BioMed Central Open Access Address: 1Dipartimento di Scienze Agrarie e Ambientali, University of Udine, via delle Scienze 208, 33100 Udine, Italy, 2UMR de Génomique Végétale, INRA-CNRS-UEVE, 2, Rue Gaston Crémieux, CP5708, 91057 Evry Cedex, France and 3UMR118 INRA-AgroCampus Rennes, Amélioration des Plantes et Biotechnologies Végétales, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France Email: Simone D Castellarin - castellarin.simone@spes.uniud.it; Gabriele Di Gaspero* - gabriele.digaspero@uniud.it; Raffaella Marconi - marconi@uniud.it; Alberto Nonis - alberto.nonis@uniud.it; Enrico Peterlunger - enrico.peterlunger@uniud.it; Sophie Paillard - paillard@rennes.inra.fr; Anne-Francoise Adam-Blondon - adam@evry.inra.fr; Raffaele Testolin - testolin@uniud.it * Corresponding author Published: 24 January 2006 BMC Genomics 2006, 7:12 doi:10.1186/1471-2164-7-12 This article is available from: http://www.biomedcentral.com/1471-2164/7/12 Received: 01 November 2005 Accepted: 24 January 2006 © 2006 Castellarin et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Structural genes of the phenyl-propanoid pathway which encode flavonoid 3'- and 3',5'-hydroxylases (F3'H and F3'5'H) have long been invoked to explain the biosynthesis of cyanidin- and delphinidin-based anthocyanin pigments in the so- called red cultivars of grapevine. The relative proportion of the two types of anthocyanins is largely under genetic control and determines the colour variation among red/purple/blue berry grape varieties and their corresponding wines. Results: Gene fragments of VvF3'H and VvF3'5'H, that were isolated from Vitis vinifera 'Cabernet Sauvignon' using degenerate primers designed on plant homologous genes, translated into 313 and 239 amino acid protein fragments, respectively, with up to 76% and 82% identity to plant CYP75 cytochrome P450 monooxygenases. Putative function was assigned on the basis of sequence homology, expression profiling and its correlation with metabolite accumulation at ten different ripening stages. At the onset of colour transition, transcriptional induction of VvF3'H and VvF3'5'H was temporally coordinated with the beginning of anthocyanin biosynthesis, the expression being 2-fold and 50-fold higher, respectively, in red berries versus green berries. The peak of VvF3'5'H expression was observed two weeks later concomitantly with the increase of the ratio of delphinidin-/ cyanidin-derivatives. The analysis of structural genomics revealed that two copies of VvF3'H are physically linked on linkage group no. 17 and several copies of VvF3'5'H are tightly clustered and embedded into a segmental duplication on linkage group no. 6, unveiling a high complexity when compared to other plant flavonoid hydroxylase genes known so far, mostly in ornamentals. Conclusion: We have shown that genes encoding flavonoid 3'- and 3',5'-hydroxylases are expressed in any tissues of the grape plant that accumulate flavonoids and, particularly, in skin of ripening red berries that synthesise mostly anthocyanins. The correlation between transcript profiles and the kinetics of accumulation of red/cyanidin- and blue/delphinidin-based anthocyanins indicated that VvF3'H and VvF3'5'H expression is consistent with the chromatic evolution of ripening bunches. Local physical maps constructed around the VvF3'H and VvF3'5'H loci should help facilitate the identification of the regulatory elements of each isoform and the future manipulation of grapevine and wine colour through agronomical, environmental and biotechnological tools. Page 1 of 17 (page number not for citation purposes)