Genome-Wide Identification of Members of the Juglans mandshurica Maxim. HD-Zip Gene Family and Their Responses to Light Intensity

Homeodomain-Leucine Zipper (HD-Zip) constitutes a distinct class of plant-specific transcription factors (TFs) that serves an essential function in mediating plant responses to environmental cues, with the HD-Zip II subfamily recognized as a major regulator of light-intensity adaptation and other environmental responses. However, the involvement of HD-Zip genes in regulating the light response of Juglans mandshurica Maxim. is largely unexplored. In this study, a genome-wide identification, classification, and expression analysis of the HD-Zip gene family in J. mandshurica was conducted. Furthermore, transcriptomic profiling under varying light-intensity conditions was performed to investigate the transcriptional regulation and potential functional networks of differentially expressed HD-Zip genes. The results showed that a total of 57 HD-Zip family genes were identified in J. mandshurica (named as JmHD-Zip) and classified into four subfamilies (HD-Zip I, HD-Zip II, HD-Zip III and HD-Zip IV). Gene structure and phylogenetic analyses indicated that members within the same subfamily exhibited analogous structural characteristics and shared strong homology with closely related species such as Juglans sigillata Dode and Populus trichocarpa. Torr. & A.Gray ex Hook. Promoter cis-acting element analysis revealed that the promoter regions of JmHD-Zip genes were enriched with multiple regulatory motifs associated with light responsiveness, hormone signaling, and stress regulation. Protein–protein interaction network analysis identified JmHDZ57 and JmHDZ43 as the central genes of the differentially expressed HD-Zip genes. Through validation of gene functions, JmHDZ43 promotes plant growth by coordinating shade-responsive morphogenesis via integration of light and hormone signaling pathways. This study offers a theoretical foundation and candidate gene resources for breeding initiatives and molecular investigations of light adaptation in J. mandshurica and potentially other woody species.