Growth conditions 
Selected seeds were surface sterilized by soaking in 70% (v/v) ethanol for 1 min, suspended in 30% (v/v) commercial Clorox bleach and 1 drop of Tween-20 for 5 min and rinsed 5 times in sterile 18 MΩmilli-Q water. Seeds were kept in water, at 4 ºC, in dark conditions for 48h to synchronize germination.
Hydroponic culture : A. thaliana seeds from 6 A1(c+) and 6 T6(c-) lines were sown in 0.2 ml tubes containing 0.6 % phyto agar (Duchefa, Harlem, The Netherlands) prepared in nutrient solution 1/2 Hoagland solution (HS), pH 5.9 in a growth chamber (12 light/12 dark hours, 150 µmol cm−2·s−1, 40% humidity and 25° C).  The bottom of the tubes containing seedlings was cut off and the tubes were placed in 150 ml hydroponic container with aerated nutrient solution 1/2 Hoagland, pH 5.9. After 15 days post-germination, treatment was applied, and seedlings were separated in different sets. The treatments consisted of control (½ HS at pH 5.9), high pH (½ HS at pH 8.3), and bicarbonate (½HS at pH 8.3 and 10 mM NaHCO3). Solutions were buffered with different proportions of MES and BTP (BIS-TRIS propane) depending on the final pH.  Plants of A1(c+), T6(c-) used for transcriptomic analysis were collected after 48 hours under treatment. Plants of A1(c+), T6(c-), Col-0 and the 18 T-DNA knockout mutants were collected after 10 days under treatment. Image analysis for root length measurements were performed with Image J, software16 [22].
Greenhouse experiments : four cultivations were conducted consecutively under the same conditions: (1) 6 A1(c+), 6 T6(c-) , 6 A1xT6 and 6 T6xA1 F1 lines; (2) 5 A1(c+), 2 T6(c-) , 10 A1xT6 and 4 T6xA1 F2 families; (3) 5 A1(c+), 2 T6(c-), 66 A1xT6 and 28 T6xA1 F3 families; (4) Col-0 and the 18 T-DNA mutants of candidate genes. Plants were cultivated in carbonated soil (LP) mixed with perlite (3:1) (Table 1) in 6x6cm square pots under semi-controlled conditions (12-h light/12-h dark photoperiod, temperature between 15-25 ºC). Five seeds of each line were sown in pots and distributed randomly in the greenhouse. Two weeks after germination, seedlings were thinned out so that only one plant per pot was left. Irrigation with distilled water was applied twice a week at the bottom of the trays. For the third cultivation, 2 leaves per plant were collected 20 days after germination and stored at -80 oC for subsequent DNA extraction and sequencing of the selected plants. Rosette diameter and bolting time were monitored, and silique number was counted at maturity in all the experiments.