Genome-Wide Identification and Expression Analysis of the Homeodomain–Leucine Zipper Family in Rice (Oryza sativa L.) Under Abiotic Stress and in seed development

Abstract The homeodomain–leucine zipper(HD-ZIP) gene family is involved in a variety of physiological processes in plants and plays a number of roles in rice. However, the analysis of this gene family in rice (Oryza sativa L.) is not comprehensive. The genome-wide characterization of HD-ZIP family was explored by using high-quality rice genome sequence combined with transcriptome. The HD-ZIP superfamily has four subfamilies in rice, including 31 HOX gene members in subfamilies I, II, and III, and nine rice outermost cell-specific gene (ROC) members in subfamily IV. Four subfamily members can interact with many reproductive and developmental related proteins, and subfamily II is regulated by miR396 family. We explored the expression patterns of HD-ZIPs in different rice tissues and analysis of high temperature and low temperature stress by RT-PCR showed that HD-ZIPs played an important role in the early stage of stress. The transcriptome results of diploid and tetraploid grains at different development stages showed that most HD-ZIP members were highly expressed in the early stage of grain development, and the expression of some members in tetraploid glumes was significantly higher than that in diploid glumes. These findings indicate the evolutionary process, characteristics and expression profile of HD-ZIP gene family in rice, and reveal their role in rice development and response to abiotic stress.