Background: Homeodomain-leucine zipper (HD-ZIP) transcription factors play important roles in the growth, development and stress responses of plants, including (presumably) physic nut (Jatropha curcas), which has high drought and salinity tolerance. However, although physic nut's genome has been released, there is little knowledge of the functions, expression profiles and evolutionary histories of the species' HD-ZIP genes. Results: In this study, 32 HD-ZIP genes were identified in the physic nut genome (JcHDZs) and divided into four groups (I-IV) based on phylogenetic analysis with homologs from rice, maize and Arabidopsis. The analysis also showed that most of the JcHDZ genes were closer to members from Arabidopsis than to members from rice and maize. Of the 32 JcHDZ genes, most showed differential expression patterns among four tissues (root, stem cortex, leaf, and seed). Expression profile analysis based on RNA-seq data indicated that 15 of the JcHDZ genes respond to at least one abiotic stressor (drought and/or salinity) in leaves at least at one time point. Transient expression of a JcHDZ16-YFP fusion protein in Arabidopsis protoplasts cells showed that JcHDZ16 is localized in the nucleus. In addition, rice seedlings transgenically expressing JcHDZ16 had lower proline contents and activities of antioxidant enzymes (catalase and superoxide dismutase) together with higher relative electrolyte leakage and malondialdehyde contents under salt stress conditions (indicating higher sensitivity) than wild-type plants. The transgenic seedlings also showed increased sensitivity to exogenous ABA, and increases in the transcriptional abundance of several salt stress-responsive genes were impaired in their responses to salt stress. Further data on JcHDZ16-overexpressing plants subjected to salt stress treatment verified the putative role of JcHDZ genes in salt stress responses. Conclusion:Our results may provide foundations for further investigation of functions of JcHDZ genes in responses to abiotic stress, and promote application of JcHDZ genes in physic nut breeding.

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