Genome-Wide Identification and Expression Analysis of the Homeodomain-Leucine Zipper Gene Family in Brachypodium distachyon and Expression Patterns of HD-ZIP Genes under Drought Stress Condition

The Homeodomain-Leucine Zipper (HD-ZIP) gene family is important for regulating development and stress responses. Although extensively studied in various species, HD-ZIP genes in Brachypodium distachyon, a model for temperate cereals, remain underexplored, particularly in abiotic stress context. This study identified 40 non-redundant HD-ZIP genes in B. distachyon using a genome-wide search, residing across five chromosomes. Phylogenetic analysis among B. distachyon, Arabidopsis thaliana and Oryza sativa classified these genes into four groups on conserved domains basis, reflecting functional divergence. Gene structure and conserved motifs showed functional characterization of BrdHDZ genes in B. distachyon genome. Cis-regulatory elements involved in abiotic stress and hormones regulation were identified in promoter regions. Expression profiles under drought stress, analyzed using RNA-Seq data, revealed BrdHDZ genes regulation as stress-responsive candidates such as BrdHDZ10, 13, and 16 were downregulated under drought stress conditions. Synteny analysis with A. thaliana confirmed evolutionary conservation. This systematic characterization of the HD-ZIP gene family in B. distachyon provides key role for further functional analysis, enhancing understanding of molecular mechanisms governing development and stress tolerance, with potential applications for improving cereal crop resilience.