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Background  Wild soybean ( Glycine soja ) is a highly adaptive plant species which can grow well in saline-alkaline soils. In soybean genome, there exist about 140 HD-Zip (Homeodomain-leucine Zipper) genes. HD-Zip transcription factor family is one of the largest plant specific superfamilies and plays important roles in response to abiotic stresses. Although HD-Zip transcription factors have been broadly reported to be involved in plant resistance to abiotic stresses like salt and drought, their roles in response to bicarbonate stress is largely unknown.    Results  From our previous transcriptome profile analysis of wild soybean treated by 50 mM NaHCO 3 , we identified an HD-Zip gene ( Gshdz4 ) which showed high response to the alkaline stress. Our result of qRT-PCR showed that the expression of  Gshdz4  was induced by alkaline stress (NaHCO 3 ) in both leaves and roots of wild soybean. Overexpression of  Gshdz4  in  Arabidopsis  resulted in enhanced tolerance to NaHCO 3  and KHCO 3  during the process of plant growth and development. However, the growths of transgenic and WT plants were not significantly different on the medium with high pH adjusted by KOH, implicating  Gshdz4  is only responsible for resisting HCO 3  −  but not high pH. The transgenic plants had less MDA contents but higher POD activities and chlorophyll contents than the WT plants. Moreover, the transcript levels of stress-related genes, such as  NADP-ME ,  H   +   -Ppase ,  RD29B  and  KIN1  were increased with greater extent in the transgenic plants than the wild plants. On the contrary,  Gshdz4  overexpression lines were much sensitive to osmotic stress at seed germination and stocking stages compared to the wild plants.    Conclusions  We revealed that the important and special roles of  Gshdz4  in enhancing bicarbonate tolerance and responding to osmotic stress. It is the first time to elucidate these novel functions of HD-ZIP transcription factors. All the evidences broaden our understanding of functions of HD-Zip family and provide clues for uncovering the mechanisms of high tolerance of wild soybean to saline-alkaline stresses.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-016-0872-7) contains supplementary material, which is available to authorized users.

bmc plant biology

A novel Glycine soja homeodomain-leucine zipper (HD-Zip) I gene, Gshdz4, positively regulates bicarbonate tolerance and responds to osmotic stress in Arabidopsis