Abstract
BackgroundWith rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the post-transcriptional level. In this study, small RNAs and the degradome (parallel analysis of RNA ends) of leaf tissues collected from control and heat-stressed wheat plants immediately at the end of the stress period and 1 and 4 days later were analysed.ResultsSequencing of 24 small RNA libraries produced 55.2 M reads while 404 M reads were obtained from the corresponding 24 PARE libraries. From these, 202 miRNAs were ascertained, of which mature miRNA evidence was obtained for 104 and 36 were found to be differentially expressed after heat stress. The PARE analysis identified 589 transcripts targeted by 84 of the ascertained miRNAs. PARE sequencing validated the targets of the conserved members of miRNA156, miR166 and miR393 families as squamosa promoter-binding-like, homeobox leucine-zipper and transport inhibitor responsive proteins, respectively. Heat stress responsive miRNA targeted superoxide dismutases and an array of homeobox leucine-zipper proteins, F-box proteins and protein kinases. Query of miRNA targets to interactome databases revealed a predominant association of stress responses such as signalling, antioxidant activity and ubiquitination to superoxide dismutases, F-box proteins, pentatricopeptide repeat-containing proteins and mitochondrial transcription termination factor-like proteins.ConclusionThe interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance. Such accurate identification and validation of miRNAs and their target genes are essential to develop novel regulatory gene-based breeding strategies.
Highlights
With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding
We report on the regulatory role of miRNAs in response to heat stress by analyzing an interlaced data set of sRNA and degradome sequences
The interlaced data set generated in this study identified and validated heat stress regulated miRNAs and their target genes associated with thermotolerance
Summary
With rising global temperature, understanding plants’ adaptation to heat stress has implications in plant breeding. MicroRNAs (miRNAs) are small, non-coding, regulatory RNAs guiding gene expression at the posttranscriptional level. Heat stress disrupts membranes and inactivates proteins by unfolding, misfolding and aggregation [2]. Such metabolic imbalances have an adverse impact on all aspects of plant growth and impair several physiological and developmental processes including photosynthesis, respiration, reproduction, grain filling and yield [reviewed by [3] ]. Plants perceive and respond to heat stress using an array of stress signaling pathways to regulate their metabolism and cell function. Small RNAs (sRNAs) are a class of endogenous noncoding RNAs that regulate gene expression at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) are primarily 21 nucleotide (nt)long molecules derived from single stranded precursors with a hairpin structure. miRNA coding genes are transcribed by RNA polymerase II (Pol II) to generate
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