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Figure S1. Chalcone synthase (CHS) activity assay showing naringenin formed by transiently expressed CHS protein extracts.

Figure S2. Methodology for transient expression of three chalcone synthase (CHS) proteins and CHS activity assay.

Figure S3. Quantitative RT-PCR analysis of three CHS genes in ‘Royal Gala’ roots, bark, leaves and three developmental stages of fruit skin and cortex.

Figure S4. (a) Primers used for GenomeWalker® analysis of T-DNA integration sites. (b) The sequence data obtained using Genome Walker® amplifications revealed that lines A2, A6 and A7 have different genomic DNA regions alongside the T-DNA right border.

Figure S5. Specificity of CHS-1, CHS-2 and CHS-3 qPCR primers.

Figure S6. Chalcone synthase activity in ‘Royal Gala’ and CHS-silenced lines A3 and A5.

Figure S7. Total phenolic compounds in the axillary buds of four chalcone synthase silenced lines and wild type ‘Royal gala’.

Figure S8. Quantitative RT-PCR analysis of MdPKS-2 expression in four CHS-silenced lines.

Figure S9. An LC-MS analysis of fruit from ‘Royal Gala’ and one CHS-silenced line (Line A5).

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