*4.7. Statistical Analysis*

Means of each accession grown under the two treatments were compared using the nonparametric Wilcoxon's rank-sum test, and *p*-values were adjusted for multiple comparisons using the Benjamini-Hochberg procedure [39]. Correlation analysis was performed on average responses per accession using Spearman's rank correlation coefficient analysis. When correlation analysis was performed on response ratios, log−2 transformed values were used. Data were analyzed in R, using the packages 'ggplot2' by Hadley Wickham, 'Hmisc' by Frank Harrell and 'ggpubr' by Alboudakel Kassambra. The number of biological replicates per genotype and experiment was 5–7.

**Supplementary Materials:** The following is available online at http://www.mdpi.com/2223-7747/9/3/316/s1, Table S1: Correlation matrix for response ratio in traits under fluctuating light divided by those under uniform light (Δ = FL/U), in FL experiment 1, Table S2: Correlation matrix for response ratio in traits under fluctuating light divided by those under uniform light (Δ = FL/U), in FL experiment 2, Figure S1: Relationship between correlation coefficients shown in Table S1 (FL 1) vs. correlation coefficients in Table S2, Figure S2: Relationships between the response ratio of dark-adapted Fv/Fm under fluctuating light divided by PLA under uniform light (Δ = FL/U) and A) the response ratio of projected leaf area as well as B) the response ratio of the number of visible leaves, Figure S3: Temperature (◦C, left, red) and light intensity (μmol m-2 s-1, right, blue) measured in climate chamber for U (**A**) and FL (B,C) over the course of a day (A,B) and for 1 h (C) logged at 30 s interval, Figure S4: Data acquisition from chlorophyll a fluorescence pictures.

**Author Contributions:** Conceptualization, U.A. and E.K.; Methodology, U.A. and E.K.; Formal Analysis, all authors; Investigation, E.K.; Writing—Original Draft Preparation, E.K. and U.A.; Writing—Review and Editing, all authors; Visualization, all authors; Supervision, U.A.; Project Administration, U.A.; Funding Acquisition, U.A. All authors have read and agreed to the published version of the manuscript.

**Funding:** This research was funded by an ERA-CAPS grant from the Deutsche Forschungsgemeinschaft (DFG) to U.A (AR 808/4-1).

**Acknowledgments:** The authors thank Urszula Luzarowska and Roel van Bezouw for providing SNP information.

**Conflicts of Interest:** The authors declare no conflict of interest.
