Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots

Abstract

BackgroundNitrate is the major source of nitrogen available for many crop plants and is often the limiting factor for plant growth and agricultural productivity especially for maize. Many studies have been done identifying the transcriptome changes under low nitrate conditions. However, the microRNAs (miRNAs) varied under nitrate limiting conditions in maize has not been reported. MiRNAs play important roles in abiotic stress responses and nutrient deprivation.Methodology/Principal FindingsIn this study, we used the SmartArray™ and GeneChip® microarray systems to perform a genome-wide search to detect miRNAs responding to the chronic and transient nitrate limiting conditions in maize. Nine miRNA families (miR164, miR169, miR172, miR397, miR398, miR399, miR408, miR528, and miR827) were identified in leaves, and nine miRNA families (miR160, miR167, miR168, miR169, miR319, miR395, miR399, miR408, and miR528) identified in roots. They were verified by real time stem loop RT-PCR, and some with additional time points of nitrate limitation. The miRNAs identified showed overlapping or unique responses to chronic and transient nitrate limitation, as well as tissue specificity. The potential target genes of these miRNAs in maize were identified. The expression of some of these was examined by qRT-PCR. The potential function of these miRNAs in responding to nitrate limitation is described.Conclusions/SignificanceGenome-wide miRNAs responding to nitrate limiting conditions in maize leaves and roots were identified. This provides an insight into the timing and tissue specificity of the transcriptional regulation to low nitrate availability in maize. The knowledge gained will help understand the important roles miRNAs play in maize responding to a nitrogen limiting environment and eventually develop strategies for the improvement of maize genetics.

Constitutive Expression of Rice MicroRNA528 Alters Plant Development and Enhances Tolerance to Salinity Stress and Nitrogen Starvation in Creeping Bentgrass

“…1). This suggests that miR528 is regulated by abiotic stress, consistent with observations in rice, maize, and sugarcane (Ding et al, 2009;Xu et al, 2011;Ferreira et al, 2012;Nischal et al, 2012). …”

“…Responds to Salt, Drought, and N Deficiency Stresses miR528 has previously been implicated in plant responses to drought, salt, and N deficiency in annual species (Ding et al, 2009;Xu et al, 2011;Ferreira et al, 2012;Nischal et al, 2012). To study its role in perennial grass species, we first examined its expression in response to various abiotic stresses in creeping bentgrass.…”

“…Recently, an evolutionarily conserved monocotspecific miRNA, miR528, was identified to respond to multiple stresses, including salt, drought, low-temperature, submergence, nitrate starvation, and arsenite and arsenate stresses in maize (Zea mays), sugarcane (Saccharum officinarum), phalaenopsis orchid (Phalaenopsis aphrodite), and rice (Oryza sativa; Zhang et al, 2008;Xu et al, 2011;Ferreira et al, 2012;Nischal et al, 2012;Sharma et al, 2015). In addition, deep sequencing analysis shows that miR528 responds to diazotrophic bacteria in maize and might be involved in cytoplasmic male sterility in rice anther (Thiebaut et al, 2014;Yan et al, 2015).…”

The miRNA-mediated post-transcriptional regulation of maize response to nitrate

“…39,40 In a our recent paper, 38 a Zea mays miRNAs-microarray platform was used to identify six mature miRNAs putatively involved in the maize root response to nitrate. Concurrently, a parallel study 41 reported a list of nitrate regulated miRNAs, partially overlapping with those identified in our research. qPCR and ISH results then pointed out that the response to nitrate starvation may be at least partially regulated post-transcriptionally through the downregulation of specific miRNAs.…”

A Wheat CCAAT Box-Binding Transcription Factor Increases the Grain Yield of Wheat with Less Fertilizer Input

“…The microRNA169 (miR169) family is known to be regulated by both N and P starvation (Pant et al, 2009;Lundmark et al, 2010;Xu et al, 2011Xu et al, , 2013Zhao et al, 2011;Liang et al, 2012). Different members of this microRNA family show distinct response patterns to N or P starvation (Pant et al, 2009;Liang et al, 2012;Xu et al, 2013).…”