Genome-wide association study and transcriptomics reveal the genetic architecture of alkalinity tolerance in Arabidopsis thaliana

Alkalinity stress significantly restricts global plant productivity, yet the genetic basis for plant tolerance remains largely uncharacterized. In this study, a genome-wide association study was performed using 218 diverse natural Arabidopsis thaliana ecotypes to identify the top 73 SNPs associated with alkalinity tolerance, measured by relative root length in hydroponic growth media containing NaHCO3 at pH 8.0. Prominent association peaks were localized near genes involved in lipid metabolism (GGL20), protein degradation (AT3G17570), and vesicle-mediated protein sorting (VPS13B and AT5G57210). Expression level and protein polymorphisms in these genes were associated with alkalinity tolerance. T-DNA mutants of GGL20, AT3G17570, and the chromatin-modifying gene AFR1 showed alkaline hypersensitivity, reduced root length, iron content, and rosette size, and elevated hydrogen peroxide. Conversely, mutants of the DNA repair gene ETG1 exhibited greater tolerance than wild type in hydroponics, solid media, and soil assays, confirming their role in alkalinity tolerance. Transcriptome and network analyses revealed that alkalinity responses significantly overlap with iron deficiency pathways, identifying hub genes involved in ribosome assembly and translation control. These findings provide a comprehensive map of the genetic and transcriptional landscape of alkalinity adaptation and offer promising candidate genes for engineering crops resilient to alkaline soil conditions.