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Peer-reviewedCC BY-NC-NDBMC plant biology

Genome-wide identification, evolutionary analysis, and stress-responsive expression profiling of the TmAP2 transcription factor subfamily in domesticated einkorn wheat.

  • Yongping Miao1
  • Xingge Ding1
  • Lei Wu1
  • Haofan Yang1
  • Xuyang Chen1
  • Wenhui Zou1
  • Ming Hao2
  • Lin Huang2
  • Shunzong Ning2
  • Zhongwei Yuan2
  • Bo Jiang2
  • Xuejiao Chen2
3 more authors
  • Xue Chen2
  • Dengcai Liu3,4
  • Lianquan Zhang5,6
6 affiliations
  1. 1State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
  2. 2Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
  3. 3State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. [email protected].
  4. 4Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. [email protected].
  5. 5State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. [email protected].
  6. 6Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China. [email protected].
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Abstract

Background

The plant-specific AP2/ERF transcription factor superfamily plays important roles in plant growth, development, and responses to environmental stress. Einkorn wheat (Triticum monococcum), the earliest domesticated diploid wheat species, contains genetic variation relevant to biotic and abiotic stress resistance. However, the AP2 subfamily in domesticated einkorn has not been systematically characterized.Results

In this study, 23 TmAP2 genes were identified in the domesticated einkorn genome and classified into three phylogenetic groups. Analyses of gene structure, conserved motifs, and predicted cis-regulatory elements revealed both conserved features and lineage-associated variation among family members. Public RNA-seq data provided a descriptive overview of TmAP2 transcript abundance across six tissues, whereas replicated RNA-seq and qRT-PCR analyses identified contrasting transcriptional responses to Puccinia striiformis f. sp. tritici (Pst) infection and osmotic stress treatments. TmAP2-13-5A showed strong and sustained induction under NaCl treatment but weak expression during Pst infection, indicating a strong transcriptional response to osmotic stress. Population analysis of 61 domesticated einkorn accessions revealed greater haplotype richness in promoter regions than in full genomic regions for several TmAP2 genes. The promoter haplotypes of TmAP2-13-5A showed differences in geographic distribution, and several polymorphic sites occurred within or adjacent to predicted stress-responsive cis-elements. These observations identify upstream-region polymorphisms for further analysis of their possible effects on stress-responsive transcription.Conclusion

This study characterizes the genomic organization, expression patterns, and haplotype variation of the AP2 subfamily in domesticated einkorn. The transcriptional response and upstream-region variation of TmAP2-13-5A support further functional and regulatory analysis of this gene.

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Cite

BibTeXRIS
BibTeX
@article{miao2026genomewide,
  title = {{Genome-wide identification, evolutionary analysis, and stress-responsive expression profiling of the TmAP2 transcription factor subfamily in domesticated einkorn wheat.}},
  author = {Yongping Miao and Xingge Ding and Lei Wu and Haofan Yang and Xuyang Chen and Wenhui Zou and Ming Hao and Lin Huang and Shunzong Ning and Zhongwei Yuan and Bo Jiang and Xuejiao Chen and Xue Chen and Dengcai Liu and Lianquan Zhang},
  journal = {BMC plant biology},
  year = {2026},
  month = aug,
  doi = {10.1186/s12870-026-09662-9},
  url = {https://europepmc.org/article/MED/42958018},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Genome-wide identification, evolutionary analysis, and stress-responsive expression profiling of the TmAP2 transcription factor subfamily in domesticated einkorn wheat.
AU  - Yongping Miao
AU  - Xingge Ding
AU  - Lei Wu
AU  - Haofan Yang
AU  - Xuyang Chen
AU  - Wenhui Zou
AU  - Ming Hao
AU  - Lin Huang
AU  - Shunzong Ning
AU  - Zhongwei Yuan
AU  - Bo Jiang
AU  - Xuejiao Chen
AU  - Xue Chen
AU  - Dengcai Liu
AU  - Lianquan Zhang
PY  - 2026
DA  - 2026/08/04
JO  - BMC plant biology
DO  - 10.1186/s12870-026-09662-9
UR  - https://europepmc.org/article/MED/42958018
AB  - Background  The plant-specific AP2/ERF transcription factor superfamily plays important roles in plant growth, development, and responses to environmental stress. Einkorn wheat (Triticum monococcum), the earliest domesticated diploid wheat species, contains genetic variation relevant to biotic and abiotic stress resistance. However, the AP2 subfamily in domesticated einkorn has not been systematically characterized.Results  In this study, 23 TmAP2 genes were identified in the domesticated einkorn genome and classified into three phylogenetic groups. Analyses of gene structure, conserved motifs, and predicted cis-regulatory elements revealed both conserved features and lineage-associated variation among family members. Public RNA-seq data provided a descriptive overview of TmAP2 transcript abundance across six tissues, whereas replicated RNA-seq and qRT-PCR analyses identified contrasting transcriptional responses to Puccinia striiformis f. sp. tritici (Pst) infection and osmotic stress treatments. TmAP2-13-5A showed strong and sustained induction under NaCl treatment but weak expression during Pst infection, indicating a strong transcriptional response to osmotic stress. Population analysis of 61 domesticated einkorn accessions revealed greater haplotype richness in promoter regions than in full genomic regions for several TmAP2 genes. The promoter haplotypes of TmAP2-13-5A showed differences in geographic distribution, and several polymorphic sites occurred within or adjacent to predicted stress-responsive cis-elements. These observations identify upstream-region polymorphisms for further analysis of their possible effects on stress-responsive transcription.Conclusion  This study characterizes the genomic organization, expression patterns, and haplotype variation of the AP2 subfamily in domesticated einkorn. The transcriptional response and upstream-region variation of TmAP2-13-5A support further functional and regulatory analysis of this gene.
SN  - 1471-2229
ER  -