Genome-wide identification and expression analyses of homeodomain-leucine zipper family genes reveal their involvement in stress response in apple (Malus × domestica)

The homeodomain-leucine zipper (HD-Zip) family has been shown to perform a multitude of functions during plant development and stress responses; however, the family members and functions have not been identified in apple (Malus × domestica). In this study, 83 HD-Zips (MdHDZs) were identified in the apple genome. They were assembled into four subgroups according to the classification in Arabidopsis, where MdHDZs in the same subgroup had similar gene structures and conserved protein motifs. Putative cis-element analysis of MdHDZs promoter regions uncovered numerous elements related to the response of stress and plant hormones. In addition, twelve transcripts of the MdHDZs showed different expression patterns under salt, drought, low temperature and ABA stresses by quantitative reverse transcription-PCR (qRT-PCR) assay. To further explore the function of MdHDZs in apple, MdHDZ3 was selected to verify its function under salt, low temperature and ABA stresses; and genetic transformation was used to obtain MdHDZ3 transgenic apple calli. The results demonstrated that MdHDZ3 increased sensitivity to salt, low temperature and abscisic acid in apple calli, suggesting that MdHDZ3 plays an important role in response to stresses. Subcellular localization and three-dimensional structural analysis revealed that MdHDZ3 was a nuclear-localized protein. Taken together, these findings provide potential information for further identification of HD-Zip proteins in apple.