Evolution of HD-ZIP transcription factors and their function in cabbage leafy head formation

In this study, <i>HD-ZIP</i> gene sequences from 87 species were analyzed to explore the evolutionary history of this gene family. Despite significant variation in gene family expansion and contraction across species, our findings indicated that HD-ZIP family proteins were conserved in both lower (Charophyta) and higher plants, where they were potentially involved in root, stem, and leaf differentiation. In our analysis of 22 Brassica species, HD-ZIP III protein sequences and domains were conserved. However, within the pan-genome A of 18 <i>Brassica rapa</i> species, differences were observed in auxin-related cis-elements within the HD-ZIP III promoter regions between heading and non-heading cabbage varieties. RNA-seq analysis of wild-type A03 (heading) and mutant <i>fg-1</i> (non-heading) revealed that 131 genes formed a protein interaction network or clustered in the same branch as <i>HD-ZIP</i> family genes. Through GO enrichment and qRT-PCR, several key candidate genes of <i>Brassica rapa</i> ssp. <i>pekinensis</i> A03 associated with leafy head formation in cabbage were identified. These findings established a foundation for understanding the molecular mechanisms by which the <i>HD-ZIP</i> gene family regulated head growth in Chinese cabbage.