Genome-Wide Identification of the WUSCHEL-Related Homeobox (WOX) Gene Family in Sesame (Sesamum indicum L.) and Expression Pattern Analysis Under Light Stress

Background: The WOX (WUSCHEL‑related homeobox) family comprises a plant‑specific transcription factor family that plays pivotal roles in meristem homeostasis maintenance and organogenesis. Sesame ( Sesamum indicum L.) is an important oilseed crop, yet its WOX family regulating plant architecture and environmental adaptability remain largely uncharacterized. To explore the evolutionary patterns and light regulatory functions of the sesame WOX family, we performed genome-wide identification of SiWOX genes and systematically dissected their expression profiles using transcriptome data from roots, stems, and leaves under normal light (NL), high light (HL) and low light (LL) stress. Results: A total of 15 SiWOX genes were identified and unevenly distributed across nine chromosomes. Phylogenetic analysis classified them into three clades: Ancient (1 member), Intermediate (4 members), and WUS Clades (10 members). Members within the same clade shared similar exon-intron structures and conserved motif compositions, and all harbored the highly conserved homeodomain. Cis-acting element analysis revealed abundant light-responsive, hormone-responsive, and stress-related elements in the promoter regions of SiWOX genes. Synteny analysis identified five pairs of intraspecific segmentally duplicated paralogs, as well as eight, ten, and six interspecific collinear gene pairs between sesame and Arabidopsis thaliana , sunflower ( Helianthus annuus ), and rice ( Oryza sativa ), respectively. Transcriptome profiling and qRT-PCR validation demonstrated that SiWOX genes exhibited distinct tissue-specific expression patterns, with SiWOX11a , SiWOX4a / b , and SiWOX8 being significantly up- or down-regulated in roots, stems, and leaves under light stress. Notably, the expression of positive light signaling regulators ( HY5 , FAR1 ) and negative photomorphogenesis regulators ( PIF / bHLH ) showed synergistic or antagonistic correlations with SiWOX genes. Conclusions: This study presents the first genome-wide identification of the WOX transcription factor family in sesame, identifying 15 SiWOX genes with conserved evolutionary features. Expression profiling reveals their tissue-specific responsiveness to light stress and coordinated expression with key photomorphogenesis regulators, suggesting distinct roles in light-modulated root and shoot development. These findings fill the knowledge gap regarding sesame WOX genes and provide candidate targets for breeding improved light-use efficiency and plant architecture.