Genome-wide identification, evolutionary analysis, and stress-responsive expression profiling of the TmAP2 transcription factor subfamily in domesticated einkorn wheat
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Published on: July 16, 2019
Yongping Miao1, Xingge Ding1, Lei Wu1
1State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Wenjiang, Chengdu, 611130, China.
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.
