Comprehensive whole-genome analysis of the HD-Zip gene family in Rubus chingii and its functional characterization in...

Rubus chingii is a dual-purpose medicinal and edible berry crop whose cultivation and harvesting are significantly impeded by prickly stems. The plant-specific transcription factor HD-Zip promotes epidermal cell development, yet its specific role in R. chingii prickle formation remains largely unexplored. This study identified 31 HD-Zip members, which were classified into four subgroups (I - IV). The distribution of these genes on the seven chromosomes indicated that the gene loci were not evenly distributed, and segmental duplication was the primary mechanism of amplification. Expression profiling showed that HD-Zip I genes (e.g., RcHB12) are highly expressed during fruit maturation. Compared with smooth stem cultivars, HD-Zip IV genes (e.g., RcGL2, RcANL2) and RcHB12 exhibit upregulated expression in prickly stems. Protein interaction experiments confirmed that RcHB12 forms dimers with RcHDG11, RcANL2, and RcPDF2. Heterologous expression in Arabidopsis gl2 mutants demonstrated that RcGL2 and RcHB12 partially complement trichome development. Collectively, these findings establish a crucial role for RcHD-Zip TFs in both fruit maturation and prickle morphogenesis, offering critical insights for the target genetic improvement of Chinese raspberry.