The effect of seed maturation temperature on seed dormancy variation.

<p>Scatter plots and histograms showing the relationship between dormancy traits as well as their phenotypic distribution. Seeds were produced either under warm (21°C; red) or cold (15°C; blue) conditions and after-ripened for either (A) 21, (B) 63 or (C) 105 days. Error bars represent the standard deviation within genotypes (n = 3, in few cases n = 2).</p

The effect of seed maturation temperature on germination trajectories.

<p>Clustering dendrogram reporting the high disparity in germination trajectories across maternal environments (warm or cold) and time (21, 63 or 105 days of after-ripening). The six major clusters are numbered from 1 to 6 and are indicated with colored circles on the nodes of the dendrogram. Lines names are colored according to latitude of origin: south Sweden (red) is defined as the region below 60°N and north Sweden (blue) as the region above 60°N. Heatmap colors represent germination phenotypes, with darker shades indicating higher germination rates.</p

Heritability of seed dormancy traits.

<p>Heritability of seed dormancy traits.</p

The geographic pattern of the dormancy variation.

<p>Correlation between latitude and either (A) GR21 warm or (B) GR21 cold. As in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190242#pone.0190242.g002" target="_blank">Fig 2</a>, we define south Sweden (S) as the region below 60°N and north Sweden (N) as the region above 60°N. See <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0190242#pone.0190242.s001" target="_blank">S1 Fig</a> for the correlations between latitude and the other dormancy phenotypes.</p

GWAS for seed dormancy traits.

<p>Manhattan plots of genome-wide association results for germination rate of seeds set either in (A-C) warm or (D-F) cold environments and after-ripened for (A and D) 21, (B and E) 63 or (C and F) 105 days. The dotted horizontal line indicates a significance level of 0.05 after Bonferroni correction for multiple testing. Triangles show the position of the nine peaks with <i>P</i> values < 10^-6 for at least one phenotype. Triangle color indicates the type of effect: white, ‘common’; black, ‘specific’; grey, ‘unclear’. Are only displayed SNPs with a minor allele frequency ≥ 14%. The GWAS results are fully browsable online: <a href="https://goo.gl/dt53nc" target="_blank">https://goo.gl/dt53nc</a>.</p

reports

Reports (top candidates from GWAS), manhattan/eps files, and phenotypes

Summary of variance explained by SNPs identified using MTMM and VCA.

<p>Numbers in parenthesis are likelihood ratios (LR).</p

Genome-wide G and G x E effects for SNPs and well as local variance components.

<p>Dotted lines correspond to significance cut-offs of <i>p</i>-value = 10⁻⁵ for SNP associations (in blue) and log-likelihood ratios = 5 for variance components (in black).</p

Genetic variation around <i>MSI1 and ROS3</i>.

(A) Zoom-in Manhattan plots (Fig 3) and the genome structure around Chr5:23553506, 23555910 (top), and 23522001 (bottom) illustrated by mapped short-read DNA-seq data (IGV browser). Vertical colored lines in the IGV plots show SNPs. (B) Conditional GWAS for mCHG in RdDM- and CMT2-targeted transposons. mCHH and Chr5:23555910 were both used as co-factors. Gray vertical lines indicate the Chr5:2355910 position, and horizontal lines show the genome-wide significance (p = 0.05 by Bonferroni correction). r2 was calculated from chr5:23553506 and chr5:23555910 for mCHGRdDM and mCHGCMT2, respectively. (PDF)</p

Enrichment for <i>a priori</i> flowering time candidates in using local variance component analysis.

<p>Top row: enrichment and FDR (upper bound among <i>a priori</i> candidates). The horizontal dashed lines at 1 corresponds to no enrichment. Bottom row: Quantile-quantile plots comparing the distribution of likelihood ratios in windows containing <i>a priori</i> candidates with windows that do not. The different curves shows result after removing windows significant using more stringent thresholds (see text). The shaded region corresponds to a 95% confidence interval. See <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1005597#sec011" target="_blank">Methods</a> for details.</p