Open Access Research article

An integrative “omics” approach identifies new candidate genes to impact aroma volatiles in peach fruit

Gerardo Sánchez12*, Mónica Venegas-Calerón3, Joaquín J Salas3, Antonio Monforte1, María L Badenes4 and Antonio Granell1*

Author Affiliations

1 Instituto de Biología Molecular y Celular de Plantas (IBMCP), Ingeniero Fausto Elio s/n, Valencia 46022, Spain

2 Instituto Nacional de Tecnología Agropecuaria (INTA), Ruta N°9 Km 170, San Pedro 2930, Argentine

3 Instituto de la Grasa (IG-CSIC), Av. Padre García Tejero, 4, Sevilla 41012, Spain

4 Instituto Valenciano de Investigaciones Agrarias (IVIA), Carretera Moncada-Náquera, Km 4,5, Valencia, Náquera 46113, Spain

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BMC Genomics 2013, 14:343  doi:10.1186/1471-2164-14-343

Published: 23 May 2013

Additional files

Additional file 1: Figure S1:

Volatile compounds analyzed in this study. For each volatile, the cluster that they belongs to according to Figure  1 (upper left corner), the chemical structure, the CAS number, the group and the odor description are shown. n.a., not available. *Bold indicates those volatiles whose retention time was verified by an authentic standard. **References for odor descriptions are: 1, Derail et al., 1999 [34]; 2, Guillot et al., 2006 [61]; and w, http://www.thegoodscentscompany.com. webcite

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Additional file 2: Table S1:

Genes analyzed by qRT-PCR analysis. For each gene, the microarray id (id), the identifier of the ChillPeach database (unigene id), the functional annotation, and the most similar gene from the peach genome sequence (Match) are shown. The forward and reverse primers and amplicon length are indicated for each gene tested. Validation indicates the Pearson correlation coefficient (PCC) between the microarray and qRT-PCR data for each gene. The gene profile was considered validated if PCC was higher than 0.7. Norm: indicates the gene used as normalizator in the qRT-PCR analysis. The gene annotated as “0.00E+00” indicate that either no homologue was found or the homologue found has unknown function. For a detailed description of ChillPeach unigene functional annotation see Ogundiwin et al. [5].

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Additional file 3: Figure S2:

Maturity time-course series of the ‘Granada’ and ‘MxR_01’ genotypes. A) Color index B) Firmness C) Weight D) Soluble Solids Content (SSC) E) CO2 consumption F) Ethylene production. Bars represent the LSD range.

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Additional file 4: Figure S3:

Comparison of volatile contents in ‘Granada ’and ‘MxR_01’ at commercial maturity stage (S4). The values are expressed as fold changes on the Log2 scale. The positive region of the y-axis was used for values higher in ‘Granada’ as compared to ‘MxR_01’, and the indicated fold change is ‘Granada’/‘MxR_01’, while the negative region is used for values that are higher in ‘MxR_01’ as compared to ‘Granada’, and the indicated fold change is ‘MxR_01’/ “Granada”. All the differences are significant (p<0.05).

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Additional files 5: Table S2:

Comparison of volatile content in ‘Granada’ and ‘MxR_01’ after shelf-life simulation (S4+SL). The fold change between genotypes is shown. The ANOVA p value for each volatile compound is indicated.

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Additional file 6: Table S3:

Genes showing the same trends after the shelf-life condition in both genotypes. The fold change (up-regulated: S4+SL/S4; down-regulated: S4/S4+SL) for the ‘Granada’ and ‘MxR_01’ genotypes is indicated. For each gene, the microarray id (id), the unigene id and annotation and the most similar gene predicted in the peach genome (Match) are shown. The most similar Arabidopsis gene with the GO molecular function, the description, and the E-value are also provided.

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Additional file 7: Table S4:

Genes affected by the shelf-life response with a 2-fold cut-off. The fold change for up-regulated (S4+SL/S4) and down-regulated (S4/S4+SL) genes in both genotypes is shown. The number of genes for each list are indicated in parentheses. For each gene, the microarray id (id), the unigene id and annotation and the most similar gene predicted in the peach genome (Match) are shown. The most similar Arabidopsis gene with the GO molecular function, the description and the E-value are also provided. n.f.: not found.

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Additional file 8: Table S5:

Correlation matrix of the complete dataset. The Pearson correlation coefficient is shown.

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Additional file 9: Figure S4:

Hierarchical cluster analysis for identifying the genes correlating with the 52 VOCs. A) The heatmap and cluster analyses of the gene-volatile data set (4348 genes and 52 volatiles). Three replicates per stage are shown. Data are expressed as the log2 of a ratio (sample/common reference). B) Details of the HCA where volatile compounds are present with genes. Volatiles are indicated with a red letter. For each gene, the id and unigene annotation and identifier are provided (in parentheses) when available. Three replicates per stage are shown. Sub-clusters are named according to the volatile members that they have. For example, the volatiles of C1, according to Figure  1, appear in three sub-clusters named C1.1, C1.2, and C1.3.

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Additional file 10: Table S6:

Extended description for the candidate genes identified. Besides the information provided in Table  1, in this table, the ChillPeach database identifier (Unigene ID) and the localization of the gene in the peach genome is shown. The most similar Arabidopsis gene with its description and E-value are also provided. n.f.: not found. The genes annotated as “0.00E+00” indicate that either no homologue was found or the homologue found has unknown function. For a detailed description of ChillPeach unigene functional annotation see Ogundiwin et al. [5].

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Additional file 11: Table S7:

The ten genes that best correlated with γ-decalactone (upper) and γ-jasmodecalactone (bottom). For each gene, the microarray id (id), the unigene id and annotation, the Pearson Correlation coefficient (PC), and the most similar gene predicted in the peach genome are shown (Match). The most similar Arabidopsis gene with the GO molecular function, the description, and the E-value are also provided. n.f.: not found. The gene annotated as “0.00E+00” indicate that either no homologue was found or the homologue found has unknown function. For a detailed description of ChillPeach unigene functional annotation see Ogundiwin et al. [5].

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Additional file 12: Table S8:

Sub-cluster of genes obtained by CNA. For each gene, the microarray id (id), the unigene id and annotation, and a set of topological network parameters of its node are shown. The gene annotated as “0.00E+00” indicate that either no homologue was found or the homologue found has unknown function. For a detailed description of ChillPeach unigene functional annotation see Ogundiwin et al. [5].

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Additional file 13: Figure S5:

Correlation network of VOCs with genes correlating with the compounds of clusters C4 to C13. A) Network of VOCs and genes. The nodes representing volatiles are colored according to the cluster that they belong to (according to Figure  1). Genes are represented as gray nodes. Edges are colored according to their strength. The edge codification is indicated to the right of the network. Node size indicates its connectivity. The bigger the node, the higher the connectivity measured with the node degree (i.e., the number of edges connecting the node). A sub-cluster of genes is indicated with E. B) Magnification of volatile groups (C4, C11, C12, C5, and C13) showing the interactions with genes in detail. The genes annotated as “0.00E+00” indicate that either no homologue was found or the homologue found has unknown function. For a detailed description of ChillPeach unigene functional annotation see Ogundiwin et al. [5].

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Additional file 14: Figure S6:

Profile of the candidate gene (PPN001H09) expression assayed by microarray (left) and qRT-PCR (right) analysis. For both analyses, the Relative Quantitation (RQ) in arbitrary units is shown. The y-axis is on the log10 scale.

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Additional file 15: Figure S7:

Alignment of PpFAD 1B_6 with FAD-type enzymes. Conserved amino acids are shaded in red. Open boxes indicate the predicted transmembrane domains (TM). The three His motifs (one HXXXHH and two HXXHH) are underlined. Sequence alignment was performed with MegAlign (DNAStar). PpFAD 1B-6, Prunus persica Fatty Acid Desaturase allele 1B-6; AtFAD2, Arabidopsis thaliana, Fatty Acid Desaturase type 2; RcFAH, Ricinus communis Fatty Acid Hydroxylase; LfFAHD, Lesquerella fendleri Fatty Acid Hydroxylase/Desaturase; CpFAE, Crepis palaestina Fatty Acid Epoxygenase. For AtFAD2, RcFAH, LfFAHD, and CpFAE, the NCBI accession numbers are provided following each name.

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Additional file 16: Table S9:

Composition of fatty acid in yeast expressing PpFAD_1B-6. The % of total fatty acid content is shown for palmitic acid (16:0), palmitoleic acid (16:1), estearic acid (18:0), and ricinoleic acid (18:1-OH). No significant differences in fatty acid levels between treatments were detected by ANOVA (p<0.05), indicated by the same letter. The inducing and non-inducing conditions are indicated by + and -, respectively. The mean of three determinations (n=3) are shown. n.d.: not detected.

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