Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

Abstract

In addition to regulating growth and development, the most important function of microRNAs (miRNAs) in plants is the regulation of a variety of cellular processes underlying plant adaptation to environmental stresses. To gain a deep understanding of the mechanism of drought tolerance in rice, genome-wide profiling and analysis of miRNAs was carried out in drought-challenged rice across a wide range of developmental stages, from tillering to inflorescence formation, using a microarray platform. Among the 30 miRNAs identified as significantly down- or up-regulated under the drought stress, 11 down-regulated miRNAs (miR170, miR172, miR397, miR408, miR529, miR896, miR1030, miR1035, miR1050, miR1088, and miR1126) and eight up-regulated miRNAs (miR395, miR474, miR845, miR851, miR854, miR901, miR903, and miR1125) were revealed for the first time to be induced by drought stress in plants, and nine (miR156, miR168, miR170, miR171, miR172, miR319, miR396, miR397, and miR408) showed opposite expression to that observed in drought-stressed Arabidopsis. The most conserved down-regulated miRNAs were ath-miR170, the miR171 family, and ath-miR396, and the most conserved up-regulated miRNAs were ptc-miR474 and ath-miR854a. The identification of differentially expressed novel plant miRNAs and their target genes, and the analysis of cis-elements provides molecular evidence for the possible involvement of miRNAs in the process of drought response and/or tolerance in rice.

Analysis of biochemical variations and microRNA expression in wild (Ipomoea campanulata) and cultivated (Jacquemontia pentantha) species exposed to in vivo water stress

“…Approximately two-dozen miRNA families are highly conserved in diverse plant species indicating their essential roles in plant growth and development as well as other processes (Axtell and Bartel 2005;Sunkar and Jagadeeswaran 2008). Several conserved and species-specific miRNAs responsive to drought have been identified in Arabidopsis thaliana , Oryza sativa , Triticum dicoccoide, Medicago truncatula, Phaseolous vulagris and Populus trichocarpa (Sunkar and Zhu 2004;Liu et al 2008;Zhao et al 2007;Zhou et al 2010;Kantar et al 2011;Trindade et al 2010;Arenas-Huertero et al 2009;Lu et al 2008).…”

“…Upregulation of miRNAs in response to water deficit has been reported in several plant species (Kantar et al 2011;Trindade et al 2010;Arenas-Huertero et al 2009). miR169 was observed to respond to only Polyethanol Glycol (PEG)-mediated water deficit in rice while several miRNAs were observed to respond (both up and downregulated) to field like water deficit (Zhao et al 2007;Zhou et al 2010). miRNA expression also varies between closely related species differing in their ability to withstand stress (Kulcheski et al 2011).…”

In silico identification of candidate microRNAs and their targets in potato somatic hybrid Solanum tuberosum (+) S. pinnatisectum for late blight resistance

“…This miR821 family is known for boron-deficiency-responsive microRNAs in Citrus sinensis roots (Lu et al, 2014), low-N tolerance in rice genotypes (Nischal et al, 2012) and play a similar regulatory mechanism in Asiatic cotton (Wang et al, 2012b). Whereas, third miR1030 family may play important roles in growth and development of Solanaceae (Kim et al, 2011), down regulated under drought stress in rice (Zhou et al, 2010), adaptive response to abiotic stress in cotton (Boopathi and Pathmanaban, 2012) and cold-responsive miRNAs in peach (Barakat et al, 2012). The fourth miR1510 family has been identified for various plant developmental process including biotic and abiotic stress response in potato (Din et al, 2014); and resistance to the soybean cyst nematode in root (Xu et al, 2014) and RNA populations of seed and vegetative tissues in soybean (Zabala et al, 2012).…”

Ascorbate oxidase is the potential conductor of a symphony of signaling pathways

“…19 It is noteworthy by miRNA. 13,14 Further studies will be necessary to unravel the apparently complex regulation of AO expression.…”