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Background  Histone deacetylases (HDACs) function as key epigenetic factors in repressing the expression of genes in multiple aspects of plant growth, development and plant response to abiotic or biotic stresses. To date, the molecular function of HDACs is well described in  Arabidopsis thaliana , but no systematic analysis of this gene family in soybean ( Glycine max ) has been reported.    Results  In this study, 28  HDAC  genes from soybean genome were identified, which were asymmetrically distributed on 12 chromosomes. Phylogenetic analysis demonstrated that GmHDACs fall into three major groups previously named RPD3/HDA1, SIR2, and HD2. Subcellular localization analysis revealed that YFP-tagged GmSRT4, GmHDT2 and GmHDT4 were predominantly localized in the nucleus, whereas GmHDA6, GmHDA13, GmHDA14 and GmHDA16 were found in both the cytoplasm and nucleus. Real-time quantitative PCR showed that  GmHDA6 ,  GmHDA13 ,  GmHDA14 ,  GmHDA16  and  GmHDT4  were broadly expressed across plant tissues, while  GmHDA8, GmSRT2 ,  GmSRT4  and  GmHDT2  showed differential expression across various tissues. Interestingly, we measured differential changes in  GmHDACs  transcripts accumulation in response to several abiotic cues, indicating that these epigenetic modifiers could potentially be part of a dynamic transcriptional response to stress in soybean. Finally, we show that the levels of histone marks previously reported to be associated with plant HDACs are modulated by cold and heat in this legume.    Conclusion  We have identified and classified 28  HDAC  genes in soybean. Our data provides insights into the evolution of the  HDAC  gene family and further support the hypothesis that these genes are important for the plant responses to environmental stress.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1454-7) contains supplementary material, which is available to authorized users.

Characterization and subcellular localization of histone deacetylases and their roles in response to abiotic stresses in soybean