Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor Family in Prunella vulgaris

The Dof (DNA binding with one finger) transcription factor family is a plant-specific group of transcription factors that play critical roles in plant growth and development, stress response, and the regulation of secondary metabolism. <i>Prunella vulgaris</i> (<i>P. vulgaris</i>) has attracted considerable attention due to its medicinal value, with rosmarinic acid being one of its key bioactive components. However, the systematic identification of the Dof transcription factor family in <i>P. vulgaris</i> and its regulatory role in rosmarinic acid biosynthesis remains poorly understood. In this study, based on the whole-genome data of <i>P. vulgaris</i>, we identified 48 Dof transcription factor genes distributed across 14 chromosomes using bioinformatics approaches. Physicochemical analysis revealed that the encoded proteins have molecular weights ranging from 15,482.44 to 55,875.53 Da, amino acid lengths between 142 and 509, and theoretical isoelectric points from 4.84 to 10.2. All proteins were predicted to be hydrophilic and localized in the nucleus. Phylogenetic analysis classified them into four subfamilies, and multiple sequence alignment confirmed that all members contain a conserved C2-C2-type zinc finger domain. Analysis of cis-regulatory elements in the promoter regions identified numerous elements related to light responsiveness, hormone response, and development. Transcriptomic expression profiling demonstrated distinct tissue-specific expression patterns of Dof genes, with some showing high expression in spikes and seeds. Correlation analysis between gene expression and rosmarinic acid content identified three candidate genes potentially involved in the regulation of rosmarinic acid biosynthesis, which were further validated by RT-qPCR. Moreover, protein-protein interaction network predictions indicated 242 interactions among 23 Dof proteins. This study provides the first systematic identification of the Dof transcription factor family in <i>P. vulgaris</i>, offering important insights into the transcriptional regulation of rosmarinic acid biosynthesis and presenting potential genetic targets for enhancing rosmarinic acid production through genetic engineering.