Genome-wide characterization and their roles in abiotic stress responses of HD-Zip transcription factors in pepper (Capsicum annuum)

Background Capsicum annuum is a globally cultivated crop of significant agricultural and economic importance. However, its productivity and fruit quality are frequently challenged by a range of abiotic stresses. The HD-Zip (Homeodomain-Leucine Zipper) gene family, unique to plants, is known to play pivotal regulatory roles in abiotic stress adaptation, yet its functional roles in pepper remain largely unexplored. Results This study systematically analyzed the HD-Zip gene family in pepper through bioinformatics, expression profiling, and responses to abiotic stresses and phytohormones to elucidate their roles in stress tolerance. Results revealed 40 HD-Zip transcription factors unevenly distributed across 12 chromosomes, encoding proteins ranging from 211 to 842 amino acids. Subcellular localization predictions indicated nuclear localization for all members, with a subset also showing cytoplasmic localization. Collinearity analysis demonstrated that CaHD-Zip gene expansion was predominantly driven by segmental duplication, with high conservation across dicotyledons. Promoter regions of CaHD-Zip genes were enriched in cis-regulatory elements associated with light and hormonal responses, as well as stress adaptation. Tissue-specific and developmental stage-dependent expression patterns highlighted functional diversification within the family. Notably, some members were specifically induced by abiotic stresses (cold, heat, drought, and salt) and stress-related phytohormones (ABA, MeJA, ET, and SA), suggesting their involvement in stress signaling. Strikingly, CaHD-Zip18 and CaHD-Zip29 were significantly upregulated under all four stresses, implicating them as core regulators of multi-stress responses. Subsequent stress simulation assays and qRT-PCR validation confirmed the reliability of transcriptomic findings. Conclusion This study delivers the first systematic exploration of HD-Zip transcription factors in Capsicum annuum under abiotic stress, providing foundational knowledge and candidate genes for improving stress resilience in pepper breeding programs.