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Series GSE69339 Query DataSets for GSE69339
Status Public on Oct 01, 2015
Title Genome-wide identification of differentially expressed microRNAs in leaves and the developing head of four durum genotypes during water deficit stress
Organism Triticum turgidum subsp. durum
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Background: MicroRNAs are endogenous small noncoding RNAs that play critical roles in plant abiotic stress responses. The interaction between miRNA-mRNA targets and their regulatory pathways in response to water deficit stress has been investigated in many plant species. However, the miRNA transcriptome of durum wheat (Triticum turgidum L. ssp. durum) is poorly characterised, with little known about miRNA functions related to water deficit stress. Yield loss in durum wheat can be exacerbated due to minimal rainfall in the early reproductive stages of development during Spring in Australia. This study describes genotypic differences in the miRNAome between water deficit tolerant/sensitive durum, using flag leaf and developing head tissue, and more specifically identifies miRNAs associated with water deficit stress.
Results: Small RNA libraries (96 in total) were constructed from flag leaf and developing head tissues of four durum genotypes (Tamaroi, Yawa, EGA Bellaroi, Tjilkuri), with or without water deficit stress. Illumina sequencing and subsequent analysis detected 110 conserved miRNAs and 159 novel candidate miRNA hairpins. Statistical analysis of the abundance of sequencing reads revealed 66 conserved miRNAs and five novel miRNA hairpins showing differential expression under water deficit stress. During stress, several conserved and novel miRNAs showed unambiguous inverted regulatory profiles between the durum genotypes studied. Several miRNAs were also identified to have different abundance in the flag leaf compared to the developing head regardless of treatment. Predicted mRNA targets from four novel durum miRNAs were characterised using Gene Ontology (GO) which revealed functions common to stress responses and plant development.
Conclusion: For the first time, we present a comprehensive study of the miRNA transcriptome of flag leaf and developing head tissues in different durum genotypes under water deficit stress. The identification of differentially expressed miRNAs provides molecular evidence that miRNAs are potential determinants of water stress tolerance in durum wheat. GO analysis of predicted targets contributes to the understanding of genotype-specific physiological responses leading to stress tolerance capacity. Further functional analysis of specific stress responsive miRNAs identified, and their interaction with mRNA targets is ongoing and will assist in developing future durum wheat varieties with enhanced water deficit stress tolerance.
 
Overall design A total of 96 small RNA libraries were analysed [4 durum genotypes * 2 tissue types * 2 treatment groups (control and water stress) * 6 biological replicates] in this study. Please see Methods, Liu et al.(2015)
 
Contributor(s) Liu H, Searle IR, Watson-Haigh NS, Baumann U, Mather DE, Able AJ, Able JA
Citation(s) 26562166
Submission date May 28, 2015
Last update date May 15, 2019
Contact name Jason A Able
E-mail(s) [email protected]
Organization name University of Adelaide
Department School of Agriculture, Food and Wine
Lab Able Lab
Street address GN10b, Waite Main Buiding, Waite Road
City Urrbrae
State/province SA
ZIP/Postal code 5064
Country Australia
 
Platforms (1)
GPL20257 Illumina HiSeq 2500 (Triticum turgidum subsp. durum)
Samples (96)
GSM1698121 Tamaroi-FL-CG-1-a
GSM1698122 Tamaroi-FL-CG-1-b
GSM1698123 Tamaroi-FL-CG-1-c
Relations
BioProject PRJNA285254
SRA SRP058826

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE69339_Conserved_miRNA_RPM.tab.gz 69.2 Kb (ftp)(http) TAB
GSE69339_Novel_pre-miRNA_CPM.tab.gz 28.7 Kb (ftp)(http) TAB
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Raw data are available in SRA
Processed data are available on Series record

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