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.