title: Novel and conserved heat-responsive microRNAs in wheat (Triticum aestivum L.).
abstract: 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.
authors.affiliation: Division of Biochemistry, Indian Agricultural Research Institute, New Delhi, 110012, India, ranjeetranjaniari@gmail.com.
authors.forename: Ranjeet Ranjan
authors.initials: RR
authors.lastname: Kumar
authors.forename: Himanshu
authors.initials: H
authors.lastname: Pathak
authors.forename: Sushil Kumar
authors.initials: SK
authors.lastname: Sharma
authors.forename: Yugal Kishore
authors.initials: YK
authors.lastname: Kala
authors.forename: Mahesh Kumar
authors.initials: MK
authors.lastname: Nirjal
authors.forename: Gyanendra Pratap
authors.initials: GP
authors.lastname: Singh
authors.forename: Suneha
authors.initials: S
authors.lastname: Goswami
authors.forename: Raj Deo
authors.initials: RD
authors.lastname: Rai
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping; D017124:Conserved Sequence; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D006358:Hot Temperature; D035683:MicroRNAs / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012275:Oryza / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D045868:Sorghum / Q000235:genetics; D014908:Triticum / Q000235:genetics* / Q000378:metabolism; D003313:Zea mays / Q000235:genetics
chemical_list: D035683:MicroRNAs