Fig 1.
Regional growth rate estimates in HL and LL.
Predicted growth curves averaged over region (from drm function). The growth curves were estimated from diameter measurements at different time points. Diameter measurements for HL are from day 11 to 46 and for LL from day 24 to 89. An illustration of the parameters that are estimated from these growth curves are included in the plot (Final Size is a diameter, t50 a time point and Slope the fold increase in the linear phase). HL (dashed line), LL (solid line), China (orange), Northern Europe (green), Spain (purple) and Western Europe (red).
Fig 2.
Significant regional differentiation of Final Size and t50 in HL and LL.
A.thaliana genotypes are grouped based on geographical origin. Box plots show regional variation in Final Size (upper row) and t50 (lower row) for HL (left) and LL (right). Groups that do not share a letter are significantly different according to Tukey’s HSD (p-value < 0.05). Region information: China (CH, n = 20), Northern Europe (NE, n = 58), Spain (SP, n = 119) & Western Europe (WE, n = 29).
Table 1.
Multi- and uni-variate analyses of growth variation in response to light regime, genotype and their interaction.
The multivariate analysis was conducted on the estimates of FS, t50 and slope for all 270 genotypes in three replicates and accounting for block effects nested within light treatment.
Fig 3.
GWAS-results for 4 phenotypes.
Manhattan plots of GWAS of t50 in LL with all European genotypes (a), with a peak on Chromosome 1, GxE of Final Size with all European genotypes (b) with a peak on Chromosome 2, Slope in HL within Spain (c) with a peak on Chromsome 3 and t50 in HL in Northern Europe (d) with a peak on Chromosome 1. The dotted line shows the corresponding Bonferroni threshold adjusted for a p-value of 0.05.
Fig 4.
Loss-of-function association and phenotype of t50 in LL/GxE.
Manhattan plot of a GWAS with loss-of-funcion alleles and t50LL (a) and t50GxE (c) as input phenotypes with the same association (AT2G17750) above the Bonferroni threshold (dashed line). Boxplot of the phenotype of t50LL (b) and t50GxE (d) versus the allele state at AT2G17750 (0 means functional, 1 is a loss-of-function). The colors separate the populations into Spain (purple) and Northern Europe (green).
Fig 5.
Expected distribution for quantitative trait differentiation between the Spanish and Northern European population.
Qst. The expectation is based on a multivariate normal distribution assuming a neutral trait with polygenic basis. Vertical lines indicate observed Qst for the individual growth parameters, FS (Solid line), t50 (Dashed line), Slope (Dot line), in HL (orange) and LL (cyan). The red arrows show the 90th, 95th and 99th percentiles of the distribution.
Table 2.
FS and t50 quantitative differentiation (Qst) exceed differentiation given by single SNPs.