Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.)
- 1.4k Downloads
MicroRNAs (miRNAs) are small endogenous RNAs of ~22 nucleotides that have been shown to play regulatory role by negatively affecting the expression of genes at the post-transcriptional level. Information of miRNAs on some important crops like soybean, Arabidopsis, and rice, etc. are available, but no study on heat-responsive novel miRNAs has yet been reported in wheat (Triticum aestivum L.). In the present investigation, a popular wheat cultivar HD2985 was used in small RNA library construction and Illumina HiSeq 2000 was used to perform high-throughput sequencing of the library after cluster generation; 110,896,604 and 87,743,861 reads were generated in the control (22 °C) and heat-treated (42 °C for 2 h) samples, respectively. Forty-four precursor and mature miRNAs were found in T. aestivum from miRBase v 19. The frequencies of the miRNA families varied from 2 (tae-miR1117) to 60,672 (tae-miR159b). We identify 1052 and 902 mature miRNA sequences in HD2985 control and HS-treated samples by mapping on reference draft genome of T. aestivum. Maximum identified miRNAs were located on IWGSC_CSS_3B_scaff (chromosome 3B). We could identify 53 and 46 mature miRNA in the control and HS samples and more than 516 target genes by mapping on the reference genome of Oryza sativa, Zea mays, and Sorghum bicolor. Using different pipelines and plant-specific criteria, 37 novel miRNAs were identified in the control and treated samples. Six novel miRNA were validated using qRT-PCR to be heat-responsive. A negative correlation was, however, observed between the expression of novel miRNAs and their targets. Target prediction and pathway analysis revealed their involvement in the heat stress tolerance. These novel miRNAs are new additions to miRNA database of wheat, and the regulatory network will be made use of in deciphering the mechanism of thermotolerance in wheat.
KeywordsHeat stress Heat-responsive Illumina HiSeq miRNA Next-generation sequencing qRT-PCR Stress-associated proteins Transcriptome Target genes Triticum aestivum Survey sequence Genome
List of abbreviations
RNA-induced silencing complex
Heat shock factor
Heat shock protein
Calcium-dependent protein kinase
Quantitative real-time PCR
Financial assistance provided by the Indian Council of Agriculture Research (ICAR) under the National Initiative for Climate Resilient Agriculture (NICRA) project (Project 12/115 TG3079) is highly acknowledged. We also thank Director, Indian Agricultural Research Institute (IARI) for providing all the logistic support required for executing the research work.
Conflict of interest
The authors declare that they have no conflict of interest.
Experiments comply with the current laws of the country in which they were performed.
Availability of NGS raw data
The data sets supporting the results of this article are available in the National Center for Biotechnology Information (NCBI) repository [BioProject Database: PRJNA172054; http://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA172054].
- Kumar RR, Singh GP, Goswami S, Pathak H, Rai RD (2014) Proteome analysis of wheat (Triticum aestivum) for the identification of differentially expressed heat-responsive proteins. Aus J Crop Sci 8(6):973–986Google Scholar
- Srivastava N, Chaudhary S, Kumar V, Katudia K, Vaidya K, Vyas MK, Chikara SK (2012) Evaluation of the yield, quality and integrity of total RNA extracted by four different extraction methods in rice (Oryza sativa). Res Rev J Crop Sci Technol 1:1–9Google Scholar