Figure 3. Genetic architecture underlying plasticity of ERD in response to N availability.
A. Manhattan plot representing the significant association for FC between optimal and limiting N of ERD on chromosome 1. The analysis was run with easyGWAS (https://easygwas.ethz.ch/), using the sequenced genomes dataset (n=58) with FaST-LMM and minimum allele frequency > 10 %. The green line represents the Bonferroni significance level (α < 0.1), and the associations are shown as dots (-log10 p-value). The chromosomal position (bp) is represented under the graphs. B. FC of ERD for Col-0 WT and for the T-DNA lines of the candidate genes between the plants grown at limiting and at optimal N conditions (n=10). C. ERD of Col-0 WT and of the T-DNA lines grown under limiting (Lim) and optimal (Opt) N (n=10). Significant differences to the WT according to Mann–Whitney U test are represented by one (p-value < 0.05), or two (p-values < 0.01) asterisks above each column. D. Boxplot representing the two haplogroups for the FC between optimal and limited N of ERD, including the accessions which were sequenced in this work (n = 148). The significance of the difference between the haplogroups based on their ERD FC was tested using Mann–Whitney U test.
Figure 4. The role of PROTON1 in plasticity of ERD in response to N availability. A. Relative expression of PROTON1(At1g19880 ) in proton1 T-DNA line, represented as the Log2 fold change (FC) in comparison to the WT in each N conditions.B. Relative expression of PROTON1 (At1g19880 ) in response to limiting N (Lim), using the expression levels at optimal N (Opt) as reference. C. WT and proton1 grown under limiting N. Photo was taken 18 days after pricking (DAT). D.Number of days to the first open flower in WT and proton1 under both limiting and optimal N. E. Relative expression of N-related genes in Col WT and proton1 under limiting N, represented as the fold change (FC) to the WT (n=5). F.Relative expression of N-related genes in Col WT and proton1under optimal N, represented as the FC to the WT (n=5). Significant differences to the WT according to Mann-Whitney U test are represented by one (p-value < 0.05), or two (p-value > 0.01) asterisks above each column.
Figure 5. Plasticity of primary metabolites in response to N availability of Arabidopsis accessions. A. Boxplots for CV of each metabolite across accessions grown under limiting, intermediate and optimal N. The metabolites are colored according to their classification. B. Metabolites whose CV levels showed significant correlation with plasticity of the four complex traits. Significant Spearman correlation after Benjamini-Hochberg correction (FDR < 0.05) are represented as red for positive, or blue for negative. Abbreviations: adenosine-5-monophosphate (AMP), dehydroascorbate (DHA), fructose-6-phosphate (F6P), gamma aminobutyric acid (GABA), glucose-6-phosphate (G6P), glycerol-3-phosphate (G3P), n= 43.
Figure 6. Plasticity of ERD and FT in response to different environments in Arabidopsis accessions. A. Fold changes (FC) of ERD between indicated conditions. B. Fold change of flowering time (FT) between indicated conditions. The FCs were calculated for plants grown under low light (LL , n = 10), high light (HL, n=15), short days (SD, n=10), or in the polytunnel (PT, n=15) in comparison to those grown under long days and normal lights (Ctrl, n=10). The FC values are represented on a scale from ranging from 2 (red) to 0 (blue) in comparison to the control. They were calculated based on the means from plants grown under limiting (Lim) or intermediate (Int) N and those grown under optimal (Opt) N (n = 4 for each condition). Black denotes missing data. C. Pearson correlation analysis between the FCs of ERD. D. Pearson correlation analysis between the FCs of FT. Adjusted p-values were calculated using Benjamini-Hochberg correction. Significant Spearman rs correlations (FDR < 0.05) are represented as red for positive, or blue for negative, n = 19.