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Boron (B) is an essential micronutrient for plants, but a high concentration of B is toxic. Typical B toxicity symptoms include necrosis of marginal leaves and inhibition of root elongation. Reduction of crop productivity has been reported in high-B contaminated soils, present especially in semi-arid areas in the world. We have previously reported that overexpression of BOR4, an Arabidopsis thaliana (L.) Heynh. efflux-type B transporter, conferred high B tolerance in A. thaliana. In the present study, we characterized physiological roles and expression patterns of endogenous BOR4 in A. thaliana. Decreased shoot growths and increased B concentrations in shoots were found in A. thaliana T-DNA insertion mutants of BOR4 under toxic levels of B supply, compared to the wild type plants. beta-glucuronidase (GUS) staining in the transgenic ProBOR4-GUS plants was predominately detected in root meristems and endodermis of mature portion of the roots. Furthermore, mRNA levels of BOR4 in roots were increased by 2-fold upon 3-day treatment of the high B condition and analysis of the transgenic ProBOR4-GUS plants showed that this high B-dependent induction is controlled by the 5’ flanking sequences of BOR4 ORF. We concluded that endogenous BOR4 is a high-B inducible gene that functions in high-B tolerance.