Systematic analysis of the DOF transcription factor family in Scutellaria baicalensis Georgi identifies genes preferentially expressed in roots and induced by methyl jasmonate

Scutellaria baicalensis Georgi is an important medicinal plant whose roots accumulate abundant 4′-deoxyflavones. However, the transcriptional regulation associated with this specialized metabolism remains incompletely understood. DNA-binding with One Finger (DOF) proteins are plant-specific transcription factors involved in development, hormone signaling, stress responses, and specialized metabolism. Here, 32 SbDOF genes were identified from the S. baicalensis genome and analyzed for their phylogenetic relationships, conserved motifs, gene structures, duplication patterns, promoter elements, and expression profiles. The 32 SbDOF proteins were assigned to nine phylogenetic groups and shared a conserved DOF domain, while variation in motif composition and gene structure was observed among individual members. Eleven collinear gene pairs, one tandemly duplicated pair, and one proximal pair were identified within the genome. Ka/Ks values for duplicated pairs with reliable estimates were below 1, suggesting purifying selection. Interspecific collinearity was detected between S. baicalensis and eight examined species, with up to 29 of the 32 SbDOF loci involved in collinear relationships in individual species comparisons. Promoter regions were predicted to contain numerous cis-acting elements associated with light, hormone signaling, stress responses, development and metabolism. SbDOF genes exhibited distinct expression profiles among roots, stems, leaves, and petals, and qRT-PCR validation identified SbDOF15 , SbDOF19 , SbDOF24 , SbDOF30 , and SbDOF31 as preferentially expressed in roots. These five root-preferential genes were also significantly induced by methyl jasmonate (MeJA) treatment. These findings provide a systematic characterization of the SbDOF family in S. baicalensis and identify several candidate genes for further investigation of their functions in MeJA responses and their potential roles in regulatory and metabolic processes.