Abstract
MicroRNAs (miRNAs) guide regulation at the post-transcriptional level by inducing messenger RNA (mRNA) degradation or translational inhibition of their target protein-coding genes. Durum wheat miRNAs may contribute to the genotypic water-deficit stress response in different durum varieties. Further investigation of the interactive miRNA-target regulatory modules and experimental validation of their response to water stress will contribute to our understanding of the small RNA-mediated molecular networks underlying stress adaptation in durum wheat. In this study, a comprehensive genome-wide in silico analysis using the updated Triticum transcriptome assembly identified 2055 putative targets for 113 conserved durum miRNAs and 131 targets for four novel durum miRNAs that putatively contribute to genotypic stress tolerance. Predicted mRNA targets encode various transcription factors, binding proteins and functional enzymes, which play vital roles in multiple biological pathways such as hormone signalling and metabolic processes. Quantitative PCR profiling further characterised 43 targets and 5 miRNAs with stress-responsive and/or genotype-dependent differential expression in two stress-tolerant and two stress-sensitive durum genotypes subjected to pre-anthesis water-deficit stress. Furthermore, a 5′ RLM-RACE approach validated nine mRNA targets cleaved by water-deficit stress-responsive miRNAs, which, to our knowledge, has not been previously reported in durum wheat. The present study provided experimental evidence of durum miRNAs and target genes in response to water-deficit stress in contrasting durum varieties, providing new insights into the regulatory roles of the miRNA-guided RNAi mechanism underlying stress adaptation in durum wheat.
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Acknowledgments
This research was funded in part by the Grains Research and Development Corporation (GRDC). We thank Durum Breeding Australia’s southern breeding program, who supplied germplasm for this study. Haipei Liu is supported by a China Scholarship Council (CSC) scholarship and the University of Adelaide.
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This article forms part of a special issue of Functional and Integrative Genomics entitled ‘miRNA in model and complex organisms’ (Issue Editors: Hikmet Budak and Baohong Zhang)
Electronic supplementary material
Electronic supplementary materials Table S1
qPCR primers of 43 target genes used in this study. (XLSX 15 kb)
Electronic supplementary materials Table S2
Forward qPCR primers of five stress-responsive durum miRNAs used in this study. (XLSX 9 kb)
Electronic supplementary materials Table S3
5′ RLM-RACE adaptor and primers used in this study. (XLSX 10 kb)
Electronic supplementary materials Table S4
Predicted target genes of 69 conserved water-deficit stress-responsive miRNAs and their GO annotations. (XLSX 182 kb)
Electronic supplementary materials Table S5
Predicted targets of 44 conserved durum miRNAs (identified using MiRBase) and their GO analysis results. (XLSX 165 kb)
Electronic supplementary materials Table S6
Predicted targets of four novel stress-responsive durum miRNAs identified using the new Triticum assembly and their GO analysis results. (XLSX 31 kb)
Electronic supplementary materials Table S7
Combined Gene Ontology classification at different GO levels of the predicted targets of 69 conserved stress-responsive miRNAs for biological processes (a), molecular functions (b) and cell components (c). (XLSX 277 kb)
Electronic supplementary materials Table S8
Combined Gene Ontology classification at different GO levels of predicted targets of four novel stress-responsive miRNAs for biological processes (a), molecular functions (b) and cell components (c). (XLSX 87 kb)
Electronic supplementary materials Table S9
Combined Gene Ontology classification at different GO levels of predicted targets of 44 conserved durum miRNAs for biological processes (a), molecular functions (b) and cell components (c). (XLSX 168 kb)
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Liu, H., Able, A.J. & Able, J.A. Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes. Funct Integr Genomics 17, 237–251 (2017). https://doi.org/10.1007/s10142-016-0515-y
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DOI: https://doi.org/10.1007/s10142-016-0515-y