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Comparative Study
. 2025 May 19;26(1):503.
doi: 10.1186/s12864-025-11671-1.

Unveiling the evolutionary and transcriptional landscape of ERF transcription factors in wheat genomes: a genome-wide comparative analysis

Liwen Wang #  1 , Hongjun Zhao #  2 , Runfang Li  3 , Rumei Tian  3 , Kaihua Jia  3 , Yongchao Gong  3 , Song Hou  3 , Nana Li  3 , Yanyan Pu  4
Affiliations
Comparative Study

Unveiling the evolutionary and transcriptional landscape of ERF transcription factors in wheat genomes: a genome-wide comparative analysis

Liwen Wang et al. BMC Genomics. .

Abstract

Ethylene response factors (ERFs), belonging to the AP2/ERF superfamily, play vital roles in plant growth, development, and stress responses. The evolutionary and expression features of the members of the ERF gene family have not yet been extensively analyzed through comprehensive comparative genomics across various diploid, tetraploid, and hexaploid wheat genomes. In this study, we identified a total of 2,967 ERF genes across one diploid, two tetraploid, and five hexaploid wheat genomes using the characteristics of conserved domains of ERF proteins. Phylogenetic analysis revealed that ERF genes clustered into two main groups. Analyses of expansion of the ERF gene family indicated that the members of IIIc and IX (sub)groups were observed to show the expansion in tetraploid and hexaploid wheat compared to diploid wheat. Tandem duplication was identified as a key mechanism for ERF gene family expansion, with varying proportions across different wheat genomes. Ancient evolutionary evidence was traced using Amborella trichopoda as a reference, revealing the retention of gene copies in both tetraploid and hexaploid wheat. Then, we analyzed the expression of ERF genes under salt stress in Triticum aestivum, identifying 86 consistently up-regulated and 14 down-regulated ERF genes, and reported the stress tolerant and disease resistant ERF genes in hexaploid wheat. These findings provide valuable insights into the evolutionary dynamics and functional features of ERF genes in wheat, paving the way for genetic breeding and molecular improvement of wheat species.

Keywords: Triticum lineage; Ethylene response factor; Expression divergence; Genome-wide; Tandem duplication.

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Conflict of interest statement

Declarations. Ethics approval and consent to participate: Not applicable. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.

Figures

Fig. 1
Fig. 1
Distribution and Phylogenetic tree of ERF genes in Arabidopsis and eight wheat genomes. (A) The distribution of AP2, ERF, and RAV genes in various wheat genomes; (B) phylogenetic tree with Maximum Likelihood was constructed by IQTree with 1000 replications
Fig. 2
Fig. 2
Two major allopolyploidization events in genus Triticum and the distribution of ERF genes in the subgenomes in various wheat genomes
Fig. 3
Fig. 3
Statistics of the expressed ERF genes under salt stress. (A) Statistics of the differentially expressed ERF genes in different time points; (B) Venn graphics of up-regulated ERF genes in different time points; (C) Venn graphics of down-regulated ERF genes in different time points; (D) The phylogeny of the members of IIIc and IX (sub)group in wheat Chinese Spring genome
Fig. 4
Fig. 4
Expression profile of the expressed ERF genes under salt stress. (A) Expression heatmap of ERF genes from IIIc subgroup of ERF gene family; (B) Expression heatmap of ERF genes from IX group of ERF gene family
See this image and copyright information in PMC

References

    1. Shiferaw B, Smale M, Braun H-J, Duveiller E, Reynolds M, Muricho G. Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security. Food Secur. 2013;5:291–317.
    1. Lafiandra D, Riccardi G, Shewry PR. Improving cereal grain carbohydrates for diet and health. J Cereal Sci. 2014;59:312–26. - PMC - PubMed
    1. Salamini F, Özkan H, Brandolini A, Schäfer-Pregl R, Martin W. Genetics and geography of wild cereal domestication in the near East. Nat Rev Genet. 2002;3:429–41. - PubMed
    1. IWGSC. A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science. 2014;345:1251788. - PubMed
    1. Jia J, Zhao S, Kong X, Li Y, Zhao G, He W, et al. Aegilops tauschii draft genome sequence reveals a gene repertoire for wheat adaptation. Nature. 2013;496:91–5. - PubMed

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