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Boron (B) is one of the essential nutrients for plant growth and reproduction. Transcriptome analyses have identified genes regulated by B deficiency, but their function mostly remains elusive. To identify the functions of B deficiency-inducible genes, T-DNA insertion mutants of 10 B deficiency-induced genes were obtained, and their growth properties in response to B conditions were examined. Among the lines examined, mutants of the transcription factor WRKY6 showed growth defect compared with the wild-type under B deficiency, but not under normal conditions. This growth defect was commonly observed among three independently isolated wrky6 mutants. There was no significant difference in B concentration between wrky6-3 and the wild-type. Promoter activity of WRKY6 was induced around the root tip under B deficiency. These results established that WRKY6 is a low-B-induced transcription factor gene that is essential for normal root growth under low-B conditions. Transcriptome analysis around the root tip identified WRKY6-regulated genes under B deficiency. Our findings represent the first identification of a transcription factor involved in the response to B deficiency.