Combinatorial stress accumulation of wheat small RNAs: Functions and applications

The known complexity of crop phenotypic responses to environmental conditions should be reflected in our exploration of the transcriptional controls that regulate them. While studies of gene coding regions and expression are crucial in determining the causal elements associated with crop stress phenotypes, the diverse roles and impacts of non-coding small RNAs should be considered when selecting targets for downstream applications - particularly when gene-editing in economically important species. This study expands beyond the limitations of our previous transcriptomic work and examined the patterns of small RNA accumulation across seven single and combinatorial heat, drought and salt stress treatments. Observed regulation from DICER-associated small RNAs (siRNAs and miRNAs) on putative target mRNAs was minimal. Weighted gene co-expression network analysis revealed 4 out of 13 modules with demonstrable differences in expression patterns across treatments. Notably, Module 10 had reduced expression in all double and triple stress combinations and Module 6 had increased counts in the triple stress treatment. Lastly, DESeq2 identified small RNA with significant differential expression under stress. Differential expression patterns and sequence characteristics of Cluster 2028, Cluster 28310, SNG 29225, SNG 25144, SNG 21020 and SNG 12050 suggest a possible use of these small RNA as biomarkers to determine levels of stress being perceived by wheat plants. Additional research on the biogenesis and mobility of non-DICER associated and unannotated small RNAs is needed to understand their roles in stress perception and stress signal transduction, compared to effects of the more direct transcriptional regulation done by siRNA and miRNA clusters.