Open Access Research article

Grape berry ripening delay induced by a pre-véraison NAA treatment is paralleled by a shift in the expression pattern of auxin- and ethylene-related genes

Fiorenza Ziliotto1, Massimiliano Corso1, Fabio Massimo Rizzini1, Angela Rasori1, Alessandro Botton1 and Claudio Bonghi12*

Author Affiliations

1 Department of Agronomy, Food, Natural resources, Animals and Environment, DAFNAE, University of Padova, Agripolis – Viale dell’Università 16, 35020, Legnaro, Padova, Italy

2 Centro Interdipartimentale per la Ricerca in Viticoltura ed Enologia, CIRVE, University of Padova, Agripolis – Viale dell’Università 16, 35020, Legnaro, Padova, Italy

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BMC Plant Biology 2012, 12:185  doi:10.1186/1471-2229-12-185

Published: 9 October 2012

Additional files

Additional file 1:

(Figure S1A_B.pdf). A. Parameters considered for sample selection. Analytical and transcriptional parameters, assessed as indicated in Materials and methods, considered for the selection of samples analysed in the microarray experiment. B. Ripening progression of control and NAA-treated fruit. Changes in fruit development and pigmentation at first comparison (60 DAFB), second comparison (110 DAFB) and third comparison (148 DAFB).

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Additional file 2:

(Table S1.xlsx). List of genes differentially expressed in N1/C1, N2/C2 and N3/C2 comparisons.

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Additional file 3:

(Figure S2.jgp). Validation of microarray data by quantitative real-time PCR (qPCR). In order to validate microarray gene expression data, quantitative real-time PCR (qPCR) was performed on fifteen genes whose IDs on the microarray are: Vv_10000861, Vv_10003711, Vv_10010895, Vv_10004167, Vv_10010748, Vv_10010857, Vv_10001614, Vv_10002511, Vv_10011058, Vv_10007514, Vv_10010764, Vv_10005187, Vv_10001287, Vv_10005087, Vv_10004370. Correlation plot and Pearson correlation index were calculated between microarray (X axis) and qPCR (Y axis) log ratios, only for genes with differential expression on the microarray experiment supported by statistically significant P values (P ≤ 0.05). Genes with non-significant statistics (i.e. P > 0.05) were discarded from this analysis.

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Additional file 4:

(Table S2.pdf). Enriched GO terms of genes differentially expressed in N1/C1 comparison. For each term, the GO identifier (GO-ID), the complete Gene Ontology term (Term), the GO category to which it belongs (C = cellular component; F = molecular function; P = biological process), the FDR-corrected P-value and the P-value of the Fisher’s exact test, the number of sequences in the test set and in the background set annotated (#Test and #Ref) and not annotated (#notAnnotTest and #notAnnotRef) with the related GO term, the results of the test (Over- or Under-represented) and the percentages in the two sets are also given. Green and red background colours indicate under- or over-representation, respectively.

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Additional file 5:

(Table S3.pdf). Enriched GO terms of genes differentially expressed in N2/C2 comparison. For each term, the GO identifier (GO-ID), the complete Gene Ontology term (Term), the GO category to which it belongs (C = cellular component; F = molecular function; P = biological process), the FDR-corrected P-value and the P-value of the Fisher’s exact test, the number of sequences in the test set and in the background set annotated (#Test and #Ref) and not annotated (#notAnnotTest and #notAnnotRef) with the related GO term, the results of the test (Over- or Under-represented) and the percentages in the two sets are also given. Green and red background colours indicate under- or over-representation, respectively.

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Additional file 6:

(Table S4.pdf). Enriched GO terms of genes differentially expressed in N3/C2 comparison. For each term, the GO identifier (GO-ID), the complete Gene Ontology term (Term), the GO category to which it belongs (C = cellular component; F = molecular function; P = biological process), the FDR-corrected P-value and the P-value of the Fisher’s exact test, the number of sequences in the test set and in the background set annotated (#Test and #Ref) and not annotated (#notAnnotTest and #notAnnotRef) with the related GO term, the results of the test (Over- or Under-represented) and the percentages in the two sets are also given. Green and red background colours indicate under- or over-representation, respectively.

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Additional file 7:

(Figure S3.jgp). Expression pattern, evaluated by qPCR, of genes involved in water uptake, polyphenols and cell wall metabolism. Expression pattern, evaluated by qPCR, of genes involved in water uptake (TIP1;2-like, Vv_10003817 and AQUA1, Vv_10003711), polyphenols (CHS1, Vv_10010748; CHS3, Vv_10004167; F3H, Vv_10003855; UFGT, Vv_10004481, MYB31, Vv17s0000g06190 and MYB4, Vv4s0023g03710) and cell wall metabolism (PG1, Vv_10003791 and EX1, Vv_10000426). Transcript levels in NAA-treated (square) and control (circle) berries are shown as means of normalized expression ±SE.

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Additional file 8:

(Table S5.pdf). Categorization of genes showing significant change in their expression by using the MapMan platform. Categorization of genes showing significant change in their expression by using the MapMan platform. BinCode, BinName and Description are reported for each gene.

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Additional file 9:

(table S6.pdf). Number of hormone-related genes in Arabidopsis and grape. Number of hormone-related genes in Arabidopsis and grape. For the latter species, information is reported concerning both the whole genome (see the genome release in the Materials and Methods section) and the AROS v1.0 microarray.

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Additional file 10:

(Figure S4.jgp). Schematic representation of the experimental trial. Schematic representation of experimental trial with respect to the berry growth kinetics. The most relevant developmental phases are also indicated. The auxin treatment (NAA) was performed at 53 DAFB, whereas the sampling dates of both treated and untreated berries were at 57 (T1), 60 (T2), 70 (T3), 95 (T4), 110 (T5), and 148 (T6) DAFB. Samples used for the microarray analysis are indicated with black background labels.

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Additional file 11:

(Table S7.pdf). Complete list of the primers sequences used in quantitative real-time PCR experiments.

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