Genome-Wide Analysis of the HD-Zip Gene Family in Chinese Cabbage (<i>Brassica rapa</i> subsp. <i>pekinensis</i>) and the Expression Pattern at High Temperatures and in Carotenoids Regulation

HD-Zip, a special class of transcription factors in high plants, has a role in plant development and responding to external environmental stress. Heat stress has always been an important factor affecting plant growth, quality, and yield. Carotenoid content is also an important factor affecting the color of the inner leaf blades of Chinese cabbage. In this study, the genomes of three Brassicaceae plants were selected: Chinese cabbage (<i>Brassica rapa</i> subsp<i>. pekinensis</i>), <i>Brassica oleracea</i>, and <i>Brassica napus</i>. We identified 93, 96, and 184 <i>HD-Zip</i> genes in the <i>B. rapa</i>, <i>B. oleracea</i>, and <i>B. napus</i>, respectively. The HD-Zip gene family was classified into four subfamilies based on phylogeny: I, II, III, and IV;. The results of cis-acting element analysis suggested that HD-Zip family genes may participate in various biological processes, such as pigment synthesis, cell cycle regulation, defense stress response, etc. Conserved motifs prediction revealed that three motifs exist among the four HD-Zip gene families and that different motifs exhibit significant effects on the structural differences in HD-Zips. Synteny, Ks, and 4DTv results displayed that genome-wide triplication events act in HD-Zip gene family expansion. Transcriptome data showed that 18 genes responded (>1.5-fold change) to heat stress in Chinese cabbage, and 14 of 18 genes were from the HD-Zip I subfamily. Three genes had up-regulation, and eight genes had down-regulation in high-carotenoid-content Chinese cabbage. The <i>BraA09g011460.3C</i> expression level was up-regulated after heat stress treatment and significantly reduced in varieties with high carotenoid content, indicating its potential for heat stress tolerance and carotenoid content regulation. This study provided important gene resources for the subsequent breeding of Chinese cabbage.