Comparative genomics and transcriptomics provide insights into the sunflower Trihelix transcription factor family involved in abiotic stresses

Trihelix transcription factors, characterized by three tandem α-helical structures in their conserved DNA-binding domain, regulate plant growth, development, and abiotic stress responses. Despite sunflower's ( Helianthus annuus L.) remarkable abiotic stress tolerance, the systematic Trihelix expression response under such stresses remains lacking. In this study, we identified 52 sunflower Trihelix family genes (HaTrihelix), unevenly distributed on 15 chromosomes. Whole-genome duplication (WGD) and transposed duplication (TRD) mainly contribute to this family expansion under strong purifying selection. Phylogenetic analysis grouped sunflower, Arabidopsis, and rice Trihelix genes into five subfamilies: SIP1, GT1, GT2, GT-γ and SH4. Expression profiling revealed tissue-specific patterns and diverse responses to eight phytohormones. Under abiotic stresses, HaTrihelix genes responded strongly to temperature extremes, salt, and cadmium—particularly in roots under cadmium stress—but showed limited response to drought. Salicylic acid-mediated salt stress alleviation involved multiple key HaTrihelix genes, which was validated by RT-qPCR. Co-expression analysis indicated subfamily-specific functional divergence: all subfamilies contribute to growth and stress resistance, yet specialize in distinct metabolic pathways, defense responses, and molecular functions. This study provides a foundational resource for functional characterization of sunflower Trihelix genes and for breeding stress-tolerant varieties.