Tables and Figure legends
Table 1. Physical and chemical properties of the natural carbonated soil excavated from Les Planes d’Hostoles (LP, 42° 03ʹ 45.1ʺ N; 2° 32ʹ 46.6ʺ E). O.M.= organic matter; mineral nutrient concentrations are means ± SD (SD= standard deviation).
Figure 1. Root growth and ionome. (A) Root length (cm),(B) root ionome profile (mean-standardized values of 12 elements), and (C) root Fe concentration (μg/g) and Fe translocation ratio (leaf [Fe] / root [Fe]) of A1(c+), T6(c-) and Col-0 A. thaliana plants cultivated in hydroponics under control (pH 5.7), high pH (pH 8.3) and bic (10 mM NaHCO3, pH 8.3) conditions for 10 days. Numbers indicate significant differences between treatments per accession and letters indicate significant differences between accessions under the same treatment (t-test, p < 0.05).
Figure 2 . Transcriptomics. (A) Total number and heatmap profile of differentially expressed genes (DEGs) from pairwise comparisons bic vs control (dark blue) and high pH vscontrol (light blue) in A1(c+) and T6(c-) demes. (B) Total number of pairwise comparisons bic vs control in roots and leaves of A1(c+) and T6(c-) demes. Bubble plots indicating (C) significant Gene Ontology (GO) analysis and(D) heatmap of KEGG pathway analysis of A1(c+)and T6(c-) root DEGs in bic vs control comparison. Arrows indicate up or downregulated genes. (E) Venn diagrams of pairwise comparisons A1(c+) bic vsT6(c-) bic and A1(c+) control vsT6(c-) control in roots and leaves. Selected DEGs are highlighted in brown for root and green for leaves. DEGs, GO and KEGG terms were filtered at log fold change (LFC > 1, LFC < -1), and adjusted p-value < 0.05.
Figure 3. Protein–protein interaction network of bicarbonate stress . Gene protein interaction network of the 208 root DEGs up or down regulated in the tolerant A1(c+) under the bic treatment. Each sphere corresponds to one gene, nodes represent protein interactions (source: STRING.org) and colors represent GO terms (source: bib.fleming.gr).
Figure 4. Arabidopsis thaliana soil carbonate tolerance inheritance and BSA-Seq . (A) Rosette diameter (mm);(B) percentage of flowered plants and plants with more or less than 10 siliques; and (C) fitness (silique number) of A1(c+), T6(c-) parents, F1 and F2 progeny from reciprocal crosses cultivated in natural carbonated soil.(D) Percentage of plants that did not prosper (NP, purple bars), plants that did not flower (NF, grey bars), and plants that produce more than 10 siliques (orange bars) from A1xT6 F3 and T6xA1 F3 progeny cultivated in natural carbonated soil. Selected families for BSA analysis are indicated in bold. (E) Allele frequency distribution of SNPs detected between the sensitive parent (T6(c-)) and the F3 tolerant pool. (F)Chromosome distribution of genes associated with the SNPs from BSA left and right tails. (G) Summary table of the SNPs and genes detected and shared between parent’s comparison (A1(c+)vs T6(c-)) and between T6(c-) and the F3 tolerant pool comparison. Letters indicate significant differences (Tukey’s HSD, p < 0.05).
Figure 5. Combined analysis for bicarbonate tolerance candidate genes detection. (A) Number and (B) description of putative candidate genes obtained from the genomic and transcriptomic association analysis of A1(c+) and T6(c-) demes. Relative fold change (bic vs control) of the 18 candidate genes in the (C) leaves and (D) roots of A1(c+) (orange bars) and T6(c-) (purple bars) plants submitted to bic stress (10 mM NaHCO3, pH 8.3) for 48 hours.