Open Access Highly Accessed Research article

The genes and enzymes of the carotenoid metabolic pathway in Vitis vinifera L.

Philip R Young1, Justin G Lashbrooke1, Erik Alexandersson12, Dan Jacobson1, Claudio Moser3, Riccardo Velasco3 and Melané A Vivier1*

Author Affiliations

1 Institute for Wine Biotechnology, Department of Viticulture and Oenology, Stellenbosch University, Matieland, 7602, South Africa

2 Department of Plant Protection Biology, Swedish University of Agricultural Sciences, SE-230 53, Alnarp, Sweden

3 Genomics and Biology of Fruit Crops Department, IASMA Research and Innovation Centre, Fondazione Edmund Mach Via E. Mach 1, San Michele all'Adige, 38010, , TN, Italy

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BMC Genomics 2012, 13:243  doi:10.1186/1471-2164-13-243

Published: 15 June 2012

Additional files

Additional file 1:

Gene names, relevant accession numbers and putative gene assignments for the predicted genes encodingcarotenoid biosynthetic and catabolic enzymes. Gene sequences isolated in this study are underlined.

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Additional file 2:

Chromosomal localisation of the carotenoid metabolic genes. The 37 of the 42 carotenoid metabolic pathway members are depicted on the heterozygous ENTAV115 V. vinifera L. cv Pinot noir genome sequence assembly together with the closest genetic markers and with other well distributed markers along the chromosomes as taken from Troggio et al. [[18].]. The genes from Additional file 2: Table SM1 are in italic (red); isolated genes are in bold italic (red). Relative positions on each chromosome in bp are indicated on the left of each linkage group (LG).

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Additional file 3:

Expression of the carotenoid biosynthetic/catabolic genes at the three berry developmental stages. Average expression values of the carotenoid metabolic genes at the three stages of berry development (E-L stage 31, -34 and −38). Average expression values from the Nimblegen whole-genome grape arrays are shown with their standard deviations (n = 3). Genes in bold indicate significant differential expression (q-value ≤ 0.05; n = 3) in the green stage (E-L stage 31) versus véraison stage (E-L stage 34)a; véraison stage (E-L stage 34) versus ripe/harvest stage (E-L stage 38)b; green stage (E-L stage 31) versus ripe/harvest stage (E-L stage 38)c.

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Additional file 4:

Photosynthetic pigments concentrations and ratios in three berry developmental stages. Photosynthetic pigments extracted from green, véraison and ripe/harvest stage berries were separated by HPLC and quantified relative to authentic standards. Average carotenoid and chlorophyll concentrations in berries are shown in ng/mg FW, with the respective standard deviations (n = 3). Pigments in bold indicate significant differences (q-value ≤ 0.05; n = 3) in pigment concentrations in the green stage (E-L stage 31) versus véraison stage (E-L stage 34)a; véraison stage (E-L stage 34) versus ripe/harvest stage (E-L stage 38)b; green stage (E-L stage 31) versus ripe/harvest stage (E-L stage 38)c.

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Additional file 5:

Abscisic acid concentration in the three berry developmental stages. Abscisic acid was extracted from the three stages of berry development (E-L stage 31, -34 and −38) and analysed using UPLC MS/MS and quantified relative to an authentic standard. Abscisic acid concentrations in berries are shown in ng/g FW, with the respective standard deviations (n = 3). Significant differences in ABA concentrations (q-value ≤ 0.05; n = 3) in the green stage (E-L stage 31) versus véraison stage (E-L stage 34)a; véraison stage (E-L stage 34) versus ripe/harvest stage (E-L stage 38)b; green stage (E-L stage 31) versus ripe/harvest stage (E-L stage 38)c.

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Additional file 6:

PCR primers used in this study. The table lists the primers used, the respective sequences, melting temperatures (Tm’s) and a brief description of the amplified product. Where applicable, restriction sites incorporated to facilitate cloning are indicated in lowercase letters in the respective primer sequence.

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Additional file 7:

Plasmids and constructs used in this study. Plasmids constructed in this study were named according to the carotenoid biosynthetic/catabolic gene they contained. The primers used and the size of the PCR product cloned are listed in the respective columns.

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