Genome wide characterization and identification of candidate HD-Zip genes involved in prickle density in Rosa roxburghii

Rosa roxburghii Tratt., a member of the Rosaceae family and the Rosa genus, bears prickles on its fruits. The HD-Zip gene family is known to play a role in trichome formation and prickles development. However, a complete identification of the HD-Zip gene family in R. roxburghii has not been achieved. Therefore, this study systematically identified and classified 38 HD-Zip genes in R. roxburghii into four subfamilies (HD-Zip I to HD-Zip IV) based on gene structure, conserved sequences in evolution, phylogenetics, and predicted biological functions. Among these genes, RrGL2 and RrHDG2 were found to belong to the HD-Zip IV family. Transcriptome data and qRT-PCR analysis revealed significantly higher expression levels of these genes in flowers and mesophyll tissues without prickles compared to stems, fruits, and leaf veins with prickles. Additionally, the expression of the RrGL2 gene was significantly higher in naturally mutated peduncles, which have fewer prickles, compared to normal prickly peduncles. Furthermore, a non-HD-Zip family gene, RrGL1, positively regulated prickles formation, and its expression significantly decreased in the mutated peduncles. Moreover, both RrGL2 and RrHDG2 were introduced into Arabidopsis thaliana. The transgenic A. thaliana leaves exhibited lower trichome density. Following RrGL2 transfection, the relative expression levels of endogenous genes (AtHDG2 and AtGL2) in A. thaliana significantly decreased. Conversely, after transfection with RrHDG2, the endogenous expression of AtHDG2 in A. thaliana significantly decreased, whereas the relative expression of AtGL2 significantly increased. Furthermore, AtGL1 also decreased in A. thaliana transfected with RrGL2 and RrHDG2. These findings provide valuable insights into the regulatory mechanism of trichome density in R. roxburghii, shed light on the evolution and expression patterns of RrHD-Zip genes, and lay the groundwork for future functional characterization of RrHD-Zip genes.