Combined genomics revealed candidate genes associated with tolerance to soil carbonate in Arabidopsis thaliana

Carbonate-rich soils limit plant performance and crop production. Previously, local adaptation to carbonated soils was detected in wild Arabidopsis thaliana accessions, allowing the selection of two demes with contrasting phenotypes: A1 (carbonate tolerant, c+) and T6 (carbonate sensitive, c-). Here, A1 and T6 parental lines and F3 population derived from their crossing were cultivated on carbonated soil to evaluate growth, fitness, and the segregation pattern of the progeny. To understand the genetic architecture beyond the contrasted phenotypes a bulk segregant analysis sequencing (BSA-Seq) was performed. In parallel, A1 and T6 seedlings were grown hydroponically under control (pH 5.9) and bicarbonate conditions (10 mM NaHCO , pH 8.3) for conducting transcriptomic analysis. Based on BSA-Seq analysis, we identified 69 candidate genes associated with carbonate tolerance; most of them involved in catalytic activities. Root transcriptome analysis revealed a total of 784 differentially expressed genes (DGEs) in the tolerant line A1 . Association analysis of BSA-Seq and transcriptomics of roots and leaves discovered 18 candidate genes involved in bicarbonate stress responses. The screening of the knock-out mutants of these 18 genes suggested that DAO1 (At1G14130), TBL19 (At5G15900), AHH (AT4G20070), JAZ10 (AT5G13220), and INV-E (At5G22510) may have relevant roles in soil carbonate tolerance.