Figure 1.
(A) Histograms of hypocotyl height for seedings grown under high R∶FR (pink) or low R∶FR (blue) treatments. (B) Hypocotyl height reaction norms of 180 Arabidopsis accessions. Reaction norms for the seven highest-responding accessions (in descending order: 9057, 8242, 6929, 6009, 6914, 6968, 8231) are plotted with red lines, while reaction norms for the seven lowest-responding accession (in ascending order: 6928, 8304, 7515, 6943, 8395, 6916, 8337) are plotted in blue. The three lowest-responding accessions showed a slight negative response to low R∶FR (−0.41, −0.25, and −0.11 millimeters).
Table 1.
Parameters from the phenotype mixed effects model.
Figure 2.
Relationships between phenotypes.
Correlations between height in high R∶FR and height in low R∶FR (A), height in high R∶FR and response to low R∶FR (B), and height in low R∶FR and response to low R∶FR (C). The kernel density plot in panel D shows the distribution of the corrected response phenotype (residuals from a regression of response to low R∶FR against height in high R∶FR).
Figure 3.
Correlations between phenotypes and latitude.
Relationships between phenotypic values and latitude of accession origin for European accessions (A–D) and the correlation ellipses for these comparisons (E).
Figure 4.
Manhattan plots of GWAS results.
Genome-wide distribution of the −log10 P-values of SNP/phenotype associations using the Kruskal-Wallis (left panels) and EMMA (right panels) methods. For clarity, only SNPs with a −log10P-value = 2 are shown. Out of 214548 SNPs assayed, 11102, 6864, 11616, and 5301 SNPs are represented in the Kruskal-Wallis panels (top to bottom) while 2538, 2698, 2399, and 2802 SNPs are represented in the EMMA panels (top to bottom). SNPs are accurately plotted according to their position along the appropriate chromosome. Plotting colors alternate between blue and green in order to facilitate the visualization of individual chromosomes.
Table 2.
Associations with previously-identified SNPs in PHYC and PHYB.
Table 3.
Associations with a priori candidate genes.