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.

Characterization of drought- and heat-responsive microRNAs in switchgrass

“…Sequencing profiles revealed that most miRNA families responded similarly to both the stressors (drought or heat) while a fewmiRNA families showed stress-specific response, i.e., induced or repressed only under drought or heat in switchgrass ( Table 2). The altered expression of several miRNAs following drought or heat in this study was largely in agreement with several earlier reports that studied miRNA responses to stress conditions ingrasses[40,41, [53][54][55][56][57][58][59][60][61][62][63][64][65][66].Nevertheless, there are alsoinstances in which our study did not correspond with some of the earlier reports. For instance,drought stress repressed the expression of miR166 in wheat [53], rice [57] and sugarcane [63] while we found it is induced in switchgrass.Drought downregulated the expression of miR167 and miR168 in switchgrass [40] andmiR168 in rice [57]butthese miRNAs are found to be up-regulated by drought in this study.The miR396 levels were repressed in wheat [53],rice [57] and sugarcane [63]under drought but it is up regulated under drought in the present study.…”

“…For example, miR167 and miR529expression was downregulated in response to heat in rice [56], whereas we found upregulation in switchgrass. Likewise, miR393 was down regulated by heat in wheat [65]whereas it was upregulated in this study. Such discrepancies between different species or even within switchgrass could be attributed to a variety of factors such as differences in stress imposition,stress intensity, stress duration, age of the treated plants andtissue sources (leaves vsseedlings) or even speceis-specific responses.…”

Harnessing Next Generation Sequencing in Climate Change: RNA-Seq Analysis of Heat Stress-Responsive Genes in Wheat (Triticum aestivum L.)

“…Predictions on yield reductions in wheat on account of the climate change are frightening. However, it is difficult to identify novel SAGs, when the genomic information is not available (Kumar et al, 2014b). High-throughput NGS is, however, currently contributing significantly in the identification of novel genes associated with the biotic and abiotic stresses.…”

Using Biotechnology-Led Approaches to Uplift Cereal and Food Legume Yields in Dryland Environments

“…Drought-associated miRNAs include 11 in cowpea (Barrera-Figueroa et al, 2011), five in maize (Sheng et al, 2015), 18 each in rice (Barrera-Figueroa et al, 2012) and sorghum (Katiyar et al, 2015), and 71 in durum wheat (Liu et al, 2015). In contrast, the heat stress responsive miRNAs include eight in common bean (Jyothi et al, 2015), 11 and 26 in rice (Liu et al, 2017; Mangrauthia et al, 2017), and 6 and 12 in wheat (Xin et al, 2010; Kumar et al, 2015). Changes in miRNAs under stress correlate well with increased expression of stress-related genes in tolerant genotypes.…”

“…For example, Liu et al (2017) reported eight target genes that correspond with 26 miRNAs within the four QTL regions associated with heat stress in heat-tolerant rice. This relationship of miRNAs with their target genes, however, may not be one-to-one (i.e., negative or positive) and may vary between miRNAs of the same gene family or even for the same target miRNAs at various development stages (Lopez-Gomollon et al, 2012; Zhang et al, 2012; Kumar et al, 2015). Identification of differentially abundant miRNAs in stress-tolerant germplasm may thus provide molecular evidence that miRNAs contribute to stress tolerance and so are good candidates for enhancing stress tolerance in crops by transgenic breeding.…”