Genome-wide analysis of Dof transcription factors in Mediterranean olive reveals structural features, domestication-driven evolution and contribution to fruit trait variation
Laboratory of Genetics, Biodiversity and Bioresources Exploitation (LR11ES41), Higher Institute of Biotechnology of Monastir, University of Monastir, 5000 Monastir (Tunisia). *Authors Inchirah Bettaieb and Jihen Hamdi contributed equally to this work and share first authorship. Corresponding e-mail: dhia_bouktila2000@yahoo.fr
DOI: https://doi.org/10.37855/jah.2026.v28i01.3
Full text PDF The DNA-binding one zinc finger (Dof) transcription factors play essential roles in plant growth and adaptation. This study presents a comprehensive characterization of the Dof gene family in the cultivated Mediterranean olive (Olea europaea subsp. europaea var. europaea), focusing on structural features, evolutionary history, and functional insights based on linking transcriptomic data with morpho-biochemical profiles across three olive cultivars. We identified 76 O. europaea var. europaea Dof (OeDof) genes encoding 81 putative proteins, a larger set than previously reported in wild olive (O. europaea var. sylvestris), suggesting gene family expansion during domestication. OeDof proteins showed considerable variation in their physicochemical properties but maintained a conserved Dof-binding domain, characterized by nine variable regions that may modulate target site specificity. Fifteen conserved motifs were identified, including subgroup-specific motifs likely contributing to functional specialization. Several motifs were annotated, suggesting OeDof involvement in olive fruit metabolic processes. Phylogenetic analysis classified OeDof genes into four groups and nine subgroups, revealing orthologous relationships with Arabidopsis Dof genes. Duplication analysis identified 27 paralogous gene pairs, mostly under purifying selection (Ka/Ks < 1), with several gene pairs showing relaxed selection pressure (0.5 < Ka/Ks < 1), suggesting that, while selective pressure maintains protein function, a relatively high tolerance for nonsynonymous substitutions (i.e. functional divergence) exists. A unique gene pair (OeDof19/OeDof49) underwent positive selection, highlighting its potential role in key biological processes. RNA-Seq analysis classified OeDof genes into six distinct expression patterns across the fruit of three olive cultivars with contrasting morpho-biochemical traits, identifying candidate genes for further functional validation. This genome-wide analysis offers valuable insights into the domestication-linked evolutionary and functional dynamics of Dof genes in Mediterranean olive, laying the foundation for their application in genomics-assisted breeding for improved fruit traits and oil quality.
