Supplementary figure 1 Genetic relationships between accessions used in this project

The accessions high-lighted in red represent a sub-group of highly polymorphic Arabidopsis accessions previously described (Clark et al, 2007) and are used as reference. Data for 149 SNPs ( used to assess the relationship between the accessions. The analysis was performed using MEGA software (Tamura et al. (2007); Kumar et al (2008)) and further information can be obtained from

Supplementary figure 2 Characterization of flowering responses of mutants, transgenic lines and accessions under a range of day lengths

  1. Two sets of mutant or transgenic lines impaired in the function of the photoperiod pathway. The later flowering group of three mutants are fca1co-2 (closed diamonds, dashed line) and fca1co-3 (open diamonds, dashed line) and fca1lhy1 (closed triangles, dashed line). The earlier flowering group of five mutants are 35S::COcry1cry2 (closed circles, solid line), 35S::GI in Col-0 background (closed triangles, solid line), 35S::GI in Ler background (open triangles, solid line), cop1-4 (closed squares, solid line) and edi1-1 (open squares, solid line).
  2. Comparison of flowering times of single co-2, co-3, lhy-1 and fca-1 mutants with double fca-1co-2, fca-1co-3, fca-1lhy-1 mutants. Closed circles : co-2, open circles : co-3, closed triangles fca-1, open triangles fca-1co-2, closed squares fca-1co-3, open squares : fca-1lhy-1, closed diamonds : lhy-1.
  3. Comparison of flowering times of circadian clock impaired lhy-11 cca1-11 double mutant with wild-type and the late flowering CCA1-OX lhy1-1 line. Ler (orange circles), CCA1-OX lhy1-1 (red triangles) and lhy-11cca1-11 (green squares).
  4. Comparison of the flowering times of photoreceptor mutants and wild-type plants. phyA (orange circles), phyB (green triangles) and Ler (yellow squares).
  5. Comparison of flowering times of Bs-1 and Cen-0 with the Be-1 and Co accessions. Be-1 and Co flower with the same number of leaves under LD 14 h as Bs-1 and Cen-0 respectively, but they do not show the rapid accelaration of flowering time observed under LD 16 h for Bs-1 and Cen-0. Be-0 : closed circles, Co : closed squares, Cen-0 : open circles, Bs-1 : closed triangles, Ler : open squares.

Supplementary figure 3. Comparison of day-length responses of accessions, mutants and transgenic lines by principal component analysis.

  1. Comparison of responses of accessions, mutants and transgenic plants using the two components that capture the highest proportion of variation. The yellow rectangle represents the space defined by the photoperiodic responses of mutants. The mutants that show extreme PC2 values are illustrated with the black squares while all the accessions are illustrated with the blue circles.
  2. Principal component analysis comparing discrimination efficiency between SD of 8 and 10 h (Y axis; PC4) and overall discrimination between SD and LD (X axis; PC1). The yellow rectangle represents the space defined by the photoperiodic responses of mutants. The mutants that show extreme PC4 values are illustrated with the black squares while all the accessions are illustrated with the blue circles.
  3. Principal component analysis comparing discrimination efficiency between LD of 14 and 16 h (Y axis; PC5) and overall discrimination between SD and LD (X axis; PC1). The yellow rectangle represents the space defined by the photoperiodic responses of mutants. The mutants that show extreme PC5 values are illustrated with the black squares while all the accessions are illustrated with the blue circles.
  4. Principal component analysis comparing flowering phenotypes of accessions selected for genetic characterization. Each of the five variable components PC2, 3, 4, 5 and 6 are plotted on the Y axis and overall discrimination between SD and LD (PC1) is plotted on the X axis. The colour code represents the colours used for each component plotted on the Y axis. Each of the five selected accessions (Bs-1, Cen-0, Dijon-G, Ler and Shakdhara) is indicated.

Supplementary Figure 4. Day-length loadings of the principal components analysis.

A. Combination of all daylength loadings for all components Y-axis corresponds to Principal Components 2 to 6 respectively. Each principal component is indicated on the index.

B. Daylength loadings of component 2 (Y-axis) vs PC1 (X-axis). This component separates LD 12

h from the rest. Value in parenthesis indicates the percentage of variability that PC3 explains in the dataset.

C. Daylength loadings of component 3 (Y-axis) vs PC1 (Xaxis). This component separates SD 6 h from the rest. Value in parenthesis indicates the percentage of variability that PC3 explains in the dataset.

D. Daylength loadings of component 4 (Y-axis) vs PC1 (X-axis). This component separates SD of 10 from 8 h. Value in parenthesis indicates the percentage of variability that PC4 explains in the dataset. E. Daylength loadings of component 5 (Y-axis) vs PC1 (X-axis). This component separates LD 14 from LD 16 h. Value in parenthesis indicates the percentage of variability that PC5 explains in the dataset.

F. Daylength loadings of component 6 (Y-axis) vs PC1 (X-axis). This component separates LD 14 from both LD 12 and 16 h. Value in parenthesis indicates the percentage of variability that PC6 explains in the dataset.

Supplementary figure 5. Segregation of delayed flowering in F2 populations grown under intermediate long days and its response to vernalization.

A-D. Flowering times of F2 plants derived from crossing Ler to Bs-1 grown under four different conditions.

E-H. Flowering times of F2 plants derived from crossing Ler to Cen-0 grown under four different conditions.

In all cases the horizontal axis represents flowering time plotted as leaf number in intervals of 5 leaves and the vertical axis represents number of plants in each interval. Range of flowering times shown by the parents are indicated by the labelled horizontal lines, and in some cases similar data are represented for the F1 heterozygotes. The green rectangles indicate late flowering plants under 14 h days that are not observed at all or in such high frequencies under 16 h. The day length under which each population was grown is indicated (14 or 16) and whether the population was vernalized (+V) or not vernalized (-V).

Supplementary Figure 6. Properties of linkage maps made in this work.

A. Linkage map of Bs-1 x Ler cross.

B. Linkage map of the Cen-0 x Ler cross.

C. Linkage map ofthe Dijon-G x Sha cross.

Latin numbers indicate the corresponding linkage groups.

  1. Descriptive summary of the properties of each linkage map.

Supplementary Figure 7. Alignment of the three linkage maps to the Arabidopsis

physical map.

Panels A-E correspond to the alignment of chromosome 1 to 5respectively. No major disruptions of recombination were identified. Y-axis : Genetic distance (cM), X-axis physical distance (Mbp). Blue circles : Cen-0 x Ler cross, Green circles : Bs-1 x Ler cross, Red circles : Dijon-G x Sha cross.

Supplementary References

Clark RM, Schweikert G, Toomajian C, Ossowski S, Zeller G, Shinn P,

Warthmann N, Hu TT, Fu G, Hinds DA, Chen H, Frazer KA, Huson DH,

Schölkopf B, Nordborg M, Rätsch G, Ecker JR, Weigel D. (2007) Common sequence

polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science.

317(5836):338-42 .

Kumar S, Dudley J, Nei M & Tamura K (2008) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics 9: 299-306.

Tamura K, Dudley J, Nei M & Kumar S (2007) MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Molecular Biology and Evolution 24: 1596-1599.