Genome-wide identification and characterization of a plant-specific Dof transcription factor gene family in olive (Olea europaea) and its comparison with Arabidopsis

Mariyam,; Shafiq, Muhammad; Haseeb, Muhammad Tahir; Atif, Rana Muhammad; Naqvi, Syed Agha Armaghan Asad Abbas; Ali, Numan; Javed, Muhammad Arshad; Gillani, Fizza S.; Haider, Muhammad Saleem

doi:10.1007/s13580-021-00366-7

Cited by 2 publications

(3 citation statements)

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“…In A. thaliana , DOF2.1 pro , DOF5.3 pro , DOF4.6 pro gene expression in leaves an early stage plays an important role in vascular development ( Gardiner et al., 2010 ). The expression of OeuDOF4 gene was significantly upregulated in olive, which indicated that OEUDOF 4 gene was involved in the development of olive leaves ( Mariyam et al., 2021 ). Moreover, prior studies have shown the pivotal involvement of DOF genes across multiple stages of grape fruit development and ripening ( Da Silva et al., 2016 ).…”

Section: Discussionmentioning

confidence: 99%

“…Genome-wide analysis of wheat DNA-binding with one finger (Dof) transcription factor genes: evolutionary characteristics and diverse abiotic stress responses. BMC Genomics 21, 1-18. doi: 10.1186/s12864-020-6691-0 Lohani, N., Babaei, S., Singh, M. B., and Bhalla, P. L. (2021). Genome-wide in silico identification and comparative analysis of Dof gene family in Brassica napus.…”

Section: Discussionmentioning

confidence: 99%

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Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Cai,

Xie,

Han

et al. 2024

Front. Plant Sci.

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BackgroundPopulus simonii, a notable native tree species in northern China, demonstrates impressive resistance to stress, broad adaptability, and exceptional hybridization potential. DOF family is a class of specific transcription factors that only exist in plants, widely participating in plant growth and development, and also playing an important role in abiotic stress response. To date, there have been no reported studies on the DOF gene family in P. simonii, and the expression levels of this gene family in different tissues of poplar, as well as its expression patterns under cold, heat, and other stress conditions, remain unclear.MethodsIn this study, DOF gene family were identified from the P. simonii genome, and various bioinformatics data on the DOF gene family, gene structure, gene distribution, promoters and regulatory networks were analyzed. Quantitative real time PCR technology was used to verify the expression patterns of the DOF gene family in different poplar tissues.ResultsThis research initially pinpointed 41 PSDOF genes in P. simonii genome. The chromosomal localization results revealed that the PSDOF genes is unevenly distributed among 19 chromosomes, with the highest number of genes located on chromosomes 4, 5, and 11. A phylogenetic tree was constructed based on the homology between Arabidopsis thaliana and P. simonii, dividing the 41 PSDOF genes into seven subgroups. The expression patterns of PSDOF genes indicated that specific genes are consistently upregulated in various tissues and under different stress conditions, suggesting their pivotal involvement in both plant development and response to stress. Notably, PSDOF35 and PSDOF28 serve as pivotal hubs in the interaction network, playing a unique role in coordinating with other genes within the family.ConclusionThe analysis enhances our comprehension of the functions of the DOF gene family in tissue development and stress responses within P. simonii. These findings provide a foundation for future exploration into the biological roles of DOF gene family.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Cai,

Xie,

Han

et al. 2024

Front. Plant Sci.

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“…Genome-wide analysis of Dof family TFs has been reported in several plant species such as Arabidopsis and rice (Lijavetzky et al, 2003), sorghum (Kushwaha et al, 2011), cotton (Chattha et al, 2020) and olive (Mariyam et al, 2021). However, a comparative genome-wide analysis of Dof family TFs among cultivated and wild rice relatives is missing so far.…”

Section: Introductionmentioning

confidence: 99%

Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate

Tabassum

Raza²,

Riaz³

et al. 2022

Front. Plant Sci.

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DNA-binding with one finger (Dof) transcription factors have been demonstrated to regulate various stresses and developmental processes in plants. Their identification and comparative evolutionary analyses in cultivated and wild species of genus oryza were yet to be explored. In this context, we report a comprehensive genomics atlas of DNA-binding with one finger (Dof) family genes in 13 diverse rice genomes (five cultivated and eight rice wild-relatives) through a genome-wide scanning approach. A galore of 238 Dof genes, identified across the genus Oryza, are categorized into seven distinct subgroups by comparative phylogenetic analysis with the model plant Arabidopsis. Conserved motifs and gene structure analyses unveiled the prevalence of species- and subgroups-specific structural and functional diversity that is expediating with the evolutionary period. Our results indicate that Dof genes might have undergone strong purifying selections and segmental duplications to expand their gene family members in corresponding Oryza genomes. We speculate that miR2927 potentially targets the Dof domain to regulate gene expression under different climatic conditions, which are supported by in-silico and wet-lab experiments-based expression profiles. In a nutshell, we report several superior haplotypes significantly associated with early flowering in a treasure trove of 3,010 sequenced rice accessions and have validated these haplotypes with two years of field evaluation-based flowering data of a representative subpanel. Finally, we have provided some insights on the resolution of Oryza species phylogeny discordance and divergence highlighting the mosaic evolutionary history of the genus Oryza. Overall, this study reports a complete genomic landscape of the Dof family in cultivated and wild Oryza species that could greatly facilitate in fast-track development of early maturing and climate-resilient rice cultivars through modern haplotype-led breeding.

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Genome-wide identification and characterization of a plant-specific Dof transcription factor gene family in olive (Olea europaea) and its comparison with Arabidopsis

Cited by 2 publications

References 91 publications

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Identification and functional analysis of the DOF gene family in Populus simonii: implications for development and stress response

Exploration of the genomic atlas of Dof transcription factor family across genus Oryza provides novel insights on rice breeding in changing climate

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