Wo principal components are shown (PC1 and PC2) for each analysis. Three replicates per genotype and treatment are shown. The red dotted circles indicate the genotype of the samples. B) Venn diagram of volatiles (left) and genes (right) that change significantly (p<0.05 for the volatile data, and FDR and a q-value of <0.05 for the gene expression data) after shelf-life ripening. Red and blue arrows indicate that the volatile or gene expression increase or decrease, respectively, after treatment. For volatiles, the fold change is indicated in parentheses below each one. For the three compounds that change in both genotypes, the fold change for `Granada' is indicated on the left, while that for `MxR_01' is on the right. For genes, the number of genes increasing or decreasing after treatment is indicated.treatment in both genotypes have been described to impact the aroma of mature fruit (for a description of the aroma of these volatiles, see Additional file 1: Figure S1). Accordingly, the levels of Benzeneacetaldehyde, which is associated with the aroma of immature fruit, decreased after postharvest treatment in `MxR_01'. As a result, with shelf-life simulation (S4+SL), the initially flat-odor `MxR_01' reached higher levels than `Granada' (at S4+SL) for certain pleasant volatiles. This is the case of 2HPyran-2-one 6-pentyl, -Decalactone, 3-Hexen-1-ol acetate (Z)-, -Decalactone, -Octalactone, and -Heptalatone (Additional file 5: Table S2). On the other hand, `Granada' still had higher levels than `MxR_01' for other mature fruitrelated volatiles (Ethyl Acetate, -Jasmolactone, Acetic acid 2-methylpropyl ester, -Hexalactone, 2-Hexen-1-ol acetate (E), and Acetic acid butyl ester). Neither of the twogenotypes showed a predominance of immature-related volatiles in the mature ripening stages, although some differences were detected between cultivars. While `Granada' showed higher levels of 2,4-Heptadienal, (E,E)-, 1-Penten-3one, and 2-Hexenal, `MxR_01' displayed higher levels of Furan, 2-pentyl-, and Hexanal (Additional file 5: Table S2). Moreover, `Granada' at S4+SL showed higher levels for some terpenoid compounds (1,3,8-p-Menthatriene, cis-Linaloloxide, and 4-Acetyl-1-methylcyclohexene) than `MxR_01' (Additional file 5: Table S2). To analyze the effect of shelf-life treatment on the transcriptome, we conducted a PCA analysis with the 4348-gene data set and studied the differentially expressed genes between S4 and S4+SL in both genotypes. The first component (PC1, explaining 42 of HKOH-1r variance) separated samples according to genotypeS chez et al. BMC Genomics 2013, 14:343 http://www.biomedcentral.com/1471-2164/14/Page 8 of(Figure 2A, right). The second component (PC2) explained 15 of variance and separated between the S4 and S4+SL replicates of the `MxR_01' genotypes. While the `Granada' samples remained close together in the first 2 components space, the `MxR_01' samples separated according to treatment (Figure 2A, right), indicating that shelf-life has a greater impact on gene expression in the `MxR_01' genotype than in the `Granada' one. Accordingly, the direct analysis PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/25596739 of the differentially expressed genes between S4 and S4+SL in `Granada' and `MxR_01' revealed a stronger gene expression response to the shelf-life in the `MxR_01' genotype (Figure 2B, right). By taking a False Discovery Rate (FDR) and a q-value of < 0.05 as criteria, we found that for `Granada' 13 genes were differentially expressed after treat, ment (nine up-regulated and four.