Genome-wide identification and transcription profiling of safflower (Carthamus tinctorius L.) HD-ZIP gene family under water deficit

Safflower (Carthamus tinctorius L.) is a multipurpose oilseed crop with high nutritional value and natural tolerance to stressful conditions including drought. The homeodomain leucine zippers (HD-ZIPs) are a class of highly conserved DNA-binding domains in plant transcription factors (TFs) which involve in different biological processes including growth, development, signal transduction and response to abiotic stresses. To date, the HD-ZIP transcription factors in safflower weren’t characterized in a genome-wide scale and their role in response to drought stress is unknown. In this study, 46 HD-ZIP coding genes were identified across the safflower genome, and gene structures, protein characteristics, conserved motifs, duplication and syntenic patterns, and protein-protein interactions were explored. The TFs were classified into four main subfamilies (I to IV) based on phylogenetic analyses. Segmental duplication has played a prominent role in the expansion of the HD-ZIP TFs. Promoter analysis of the genes highlighted the prevalence of ABRE, MYB, MYC, ARE and STRE cis-elements. Most of safflower HD-ZIPs interact with each other or with other TFs and functional proteins involved in organogenesis and crucial biological processes. The expression profile of safflower HD-ZIPs was explored in seedlings under drought stress using RNA-seq assay. Four genes from HD-ZIP I subfamily including CtHDZIP23 (HB-7), CtHDZIP7 (HB-7), CtHDZIP26 (HAT5) and CtHDZIP3 (HB-40) were significantly upregulated in response to drought stress, and two genes in the subfamily (CtHDZIP9, CtHDZIP41; HB13) were significantly downregulated. However, in HD-ZIP II subfamily only CtHDZIP37 (HAT22) was significantly upregulated. These results were confirmed using real-time qRT-PCR. Our findings highlight the members of the HD-ZIP gene family in response-regulation of drought stress, and will significantly help in understanding the function of the HD-ZIP TFs in response to abiotic stresses in safflower.