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Table S1 Plant material.

Table S2 List of the 328 a priori candidate genes for flowering time.

Table S3 Structure of phenological variation in France in the Fall cohort.

Table S4 Structure of phenological variation in France in the Spring cohort.

Table S5 Genetic coefficient of phenological variation for BT, INT, FT, FP, RP and FRR for each region and cohort.

Table S6 Mean values for genetic diversity parameters of the 49 French stands.

Fig. S1 Violin plots of natural variation for the interval between bolting and flowering (INT), flowering time (FT) and reproductive period (RP).

Fig. S2 Pairwise matrix of similarity between ecological variables.

Fig. S3 Box-and-whiskers plots of ecological variation in French stands.

Fig. S4 Manhattan plots of the genome-wide association mapping (emmax) results and quantile-quantile plot of P-values (negative logarithm, Wilcoxon and emmax) for BT, INT, FT, FP, RP and FRR in each cohort and at different geographic scales.

Fig. S5 Close up of the association peaks at the beginning of chromosome 5 (left) and around FRIGIDA (right) at three different geographical scales for bolting time.

mec12396-sup-0002-TableS7.xlsapplication/msexcel84KTable S7 List of flowering time candidate genes close to the 100 most associated SNPs for each ‘trait × cohort × geographical scale’ combination.

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