Genome-Wide Association Study Pinpoints Novel Genes Regulating Seedling Root Growth Variation of Arabidopsis thaliana Under Drought.

Developing drought-resilient crops requires a precise understanding of molecular signalling in the root, the primary organ encountering drought. This study unravelled novel genetic loci regulating drought tolerance by exploiting the natural variation in seedling root growth of Arabidopsis thaliana under PEG-induced drought stress. Through a genome-wide association study of 207 worldwide A. thaliana ecotypes from regions with varied rainfall, 68 protein-coding genes were identified with the top 50 SNPs. Functional enrichment and network analyses demarcated key processes involved in stress tolerance, including DNA repair, tRNA editing, protein folding, cell cycle regulation, stress granule assembly and the pyridoxal 5'-phosphate (PLP) salvage pathway. Expression level polymorphisms, promoter cis-element variations and amino acid substitutions associated with phenotype and climate were identified. Reverse genetic evaluation using T-DNA insertion knockout/knockdown mutants confirmed the involvement of candidate genes: AT1G06690 (PLP pathway), AT4G26990, RBP45C (stress granules), ACD55.5 (protein folding), PCMP-A4 (AT1G14470; RNA editing), SKS6, ANAC094 (cell wall remodelling) and INCENP (cell cycle), with seedling drought tolerance. Specifically, knockdown of AT1G06690 resulted in higher root hydrogen peroxide accumulation, highlighting the importance of the PLP pathway in mitigating oxidative stress. These molecular insights offer new biotechnological and breeding tools to enhance crop drought tolerance by modulating root traits.