Polymorphisms in cis-elements confer SAUR26 gene expression difference for thermo-response natural variation in Arabidopsis.

The SAUR26 subfamily genes play an important role in conferring variations of thermo-responsiveness of growth architecture among natural accessions of Arabidopsis thaliana. The expression variations are critical for their activity variations, but how expression variations are generated is unknown. We identified genetic loci for gene expression variations through expression genome-wide association study (eGWAS) and investigated their mechanisms through molecular analyses. We found that cis elements are the major determinants for expression variations of SAUR26, SAUR27, and SAUR28. Polymorphisms in the promoter region likely impact PIF4 regulation while those at the 3'UTR affect mRNA stability to generate variations in SAUR26 expression levels. These polymorphisms also differentially affect the mRNA stability of SAUR26 at two temperatures. This study reveals two mechanisms involving cis elements in generating gene expression diversity, which is likely important for local adaptations in Arabidopsis natural accessions.