Genome-wide identification of pear HD-Zip gene family and expression patterns under stress induced by drought, salinity, and pathogen

Abstract

Homeodomain-leucine zipper (HD-Zip) transcription factor genes are unique in the plant kingdom. Studies have shown that HD-Zip transcription factor has four subfamilies (subfamilies I–IV), and each subfamily exerts similar or diverse functions in the growth and development as well as environmental stress responses of plants. Although a genome-wide analysis of this transcription factor has been performed in some species, systematic identification of sequences and expression patterns under biotic and abiotic stress have not been carried out in pear. In this study, we identified 52 putative HD-Zip genes within the pear genome. Based on the phylogenetic analysis, HD-Zip transcription factors were classified into four subfamilies: 18, 13, 5, and 16 members were identified separately in subfamilies I, II, III, and IV, respectively. Genes in the same subfamily shared the constituent structure and conserved motifs, thereby implying that the HD-Zip genes that shared similar structures may exert similar functions. Moreover, abundant stress-related and pathogen-related cis-elements were observed in the promoter region of the pear HD-Zip I and II genes. Transcript abundance level of 20 selected HD-Zip I and II genes were analyzed by quantitative real-time RT-PCR (qRT-PCR) during the infection of Alternaria alternata, and abiotic stress conditions such as drought and salinity treatment. The results confirmed that some genes display stress-inducible and pathogen-inducible expression patterns.