Survey of High Throughput RNA-Seq Data Reveals Potential Roles for IncRNAs during Development and Stress Response in Bread Wheat

Long non-coding RNAs (IncRNAs) are a family of regulatory RNAs that play essential role in the various developmental processes and stress responses. Recent advances in sequencing technology and computational methods enabled identification and characterization of IncRNAs in certain plant species, but they are less known in Triticum aestivum (bread wheat). Herein, we analyzed 52 RNA seq data (>30 billion reads) and identified 44,698 IncRNAs in T aestivum genome, which were characterized in comparison to the coding sequences (mRNAs). Similar to the mRNAs, IncRNAs were also derived from each sub-genome and chromosome, and showed tissue developmental stage specific and differential expression, as well. The modulated expression of IncRNAs during abiotic stresses like heat, drought, and salt indicated their putative role in stress response. The co-expression of IncRNAs with vital mRNAs including various transcription factors and enzymes involved in Abscisic acid (ABA) biosynthesis, and gene ontology mapping inferred their regulatory roles in numerous biological processes. A few IncRNAs were predicted as precursor (19 IncRNAs), while some as target mimics (1,047 IncRNAs) of known miRNAs involved in various regulatory functions. The results suggested numerous functions of IncRNAs in T aestivurn, and unfolded the opportunities for functional characterization of individual IncRNA in future studies.