Genome-Wide Identification, Characterization, and Expression Analysis of the HD-Zip Gene Family in Quinoa (Chenopodium quinoa)

The homeodomain-leucine zipper (HD-Zip) proteins are important transcription factors in the regulation of plant growth and development and abiotic stress responses. However, our understanding of the HD-Zip family is still limited in quinoa. In this study, 41 CqHD-Zip genes were identified in the quinoa genome and then phylogenetically classified into four subfamilies. Their characterizations, chromosomal locations, gene structures, conserved motifs, and phylogenetic relationships were comprehensively analyzed through genome-wide bioinformatics methods. Our RNA-Seq data showed that a subset of the 41 HD-Zip genes exhibited expression changes under salt stress, among which CqHDZ5, CqHDZ12, CqHDZ13, CqHDZ18, CqHDZ19, and CqHDZ21 responded positively to salt stress, and the results were confirmed by qRT-PCR analysis. Tissue expression revealed that CqHDZ5, CqHDZ13, CqHDZ18, and CqHDZ21 were significantly expressed in developing seeds, and CqHDZ12 and CqHDZ19 were highly expressed in roots. Additionally, the transcript levels of these six genes were significantly up-regulated in response to osmotic and low-temperature stress, indicating that they may participate in stress resistance against salt, osmosis, and low temperature. It is shown that HD-Zip is a multifunctional gene family, and the results will provide valuable information for further analysis of the potential role of HD-Zip genes in abiotic stress responses and genetic improvement of quinoa.