1. Quantifying dynamics of light tolerance of Arabidopsis plants during ontogenesis Fabricio E. L. Carvalho 1, Maxwell A. Ware 1 and Alexander V. Ruban 1* School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, UK Supporting information

2. Table S1. Physiological markers of the four ontogenetic phases studied (juvenile, adult, reproductive and senescent). Arabidopsis thaliana plants were grown at 24°C (day)/18°C (night), 45% humidity, 175± 20 μmol m -2 s -1 actinic light and photoperiod of 10 hours. *Average and standard deviation (n=6). Different letters mean significant differences tested by Tukey’s test, with p≤0.05.

3. Fig. S1. Photosynthetic dynamics of Arabidopsis thaliana plants aged 3 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

4. Fig. S2. Photosynthetic dynamics of Arabidopsis thaliana plants aged 5 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

5. Fig. S3. Photosynthetic dynamics of Arabidopsis thaliana plants aged 9 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

6. Fig. S4. Photosynthetic dynamics of Arabidopsis thaliana plants aged 10 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

7. Fig. S5. Photosynthetic dynamics of Arabidopsis thaliana plants aged 12 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

8. Fig. S6. Anthocyanin visible absorption spectra profile measured in leaves of 7 week old Arabidopsis thaliana plants. The absorbance was measured with a spectrophotometer (U-330, Hitachi, Tokyo, Japan) using wavelengths ranging from 400 to 750 nm, with 1 nm of resolution. The spectra represent the average of extracts from 3 independent leaves.

9. Fig. S7. Electron transport rate vs light intensity curves measured in Arabidopsis thaliana plants from 1 to 13 weeks old. Lines represent regression fit curves (Exponential Rise to Maximum; Single, 2 Parameter f = a*(1-exp(-b*x))) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

10. Intermediate leaves Fig. S8. Photosynthetic dynamics of intermediate leaves in Arabidopsis thaliana aged 8 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).

11. Inner leaves Fig. S9. Photosynthetic dynamics of inner leaves in Arabidopsis thaliana aged 8 weeks. (A) Relationship between PSII yield (closed circles), qPd (open circles) and NPQ parameters. The continuous line represents the theoretical yield, calculated by equation 1 of materials and methods. Error bars show the SEM (n=30). (B) Relationship between NPQ, light intensity and qPd parameters. qPd is represented by diamond symbols, with the grey-scale shading reflecting the extent of photodamage. (C) Percentage of photoinhibited leaves. Lines represent regression fit curves (sigmoidal, Hill, three parameter; f=axb/cb+xb) with 95% confidence values plotted using SigmaPlot12 (Systat Software, Inc., Chicago, IL, USA).