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Accumulation of the stress hormone abscisic acid (ABA) in response to drought and low water-potential controls many downstream acclimation mechanisms. However, mechanisms controlling ABA accumulation itself are less known. There was a 10-fold range of variation in ABA levels among nearly 300 Arabidopsis thaliana accessions exposed to the same low water-potential severity. Genome-wide association analysis (GWAS) identified genomic regions containing clusters of ABA-associated SNPs. Candidate genes within these regions included few genes with known stress or ABA-related function. The GWAS data were used to guide reverse genetic analysis, which found effectors of ABA accumulation. These included plasma-membrane-localized signaling proteins such as receptor-like kinases, aspartic protease, a putative lipid-binding START domain protein, and other membrane proteins of unknown function as well as a RING U-box protein and possible effect of tonoplast transport on ABA accumulation. Putative loss-of-function polymorphisms within the START domain protein were associated with climate factors at accession sites of origin, indicating its potential involvement in drought adaptation. Overall, using ABA accumulation as a basis for a combined GWAS-reverse genetic strategy revealed the broad natural variation in low-water-potential-induced ABA accumulation and was successful in identifying genes that affect ABA levels and may act in upstream drought-related sensing and signaling mechanisms. ABA effector loci were identified even when each one was of incremental effect, consistent with control of ABA accumulation being distributed among the many branches of ABA metabolism or mediated by genes with partially redundant function.

Natural variation identifies genes affecting drought-induced abscisic acid accumulation in Arabidopsis thaliana