Genome-wide analysis of miRNAs and Tasi-RNAs in Zea mays in response to phosphate deficiency

Abstract

Globally important cereal crop maize provides important nutritions and starch in dietary foods. Low phosphate (LPi) availability in the soil frequently limits the maize quality and yield across the world. Small non-coding RNAs (Snc-RNAs) play crucial roles in growth and adaptation of plants to the environment. Snc-RNAs like microRNAs (miRs) and trans-acting small interfering RNAs (Tasi-Rs) play important functions in posttranscriptional regulation of gene expression, which controls plant development, reproduction, and biotic/abiotic stress responses. In order to identify the miR and Tasi-R alterations in leaf and root of maize in response to sufficient phosphate and LPi at 3LS and 4LS, the snc-RNA population libraries for 0th, 1st, 2nd, 4th, and 8th day were constructed. These libraries were used for genome-wide alignment and RNA-fold analysis for possible prediction of potential miRs and Tasi-Rs. This study reported 174 known and conserved differentially expressed miRs of 27 miR families of maize plant. In addition, leaf and root specific potential novel miRs representing 155 new families were also discovered. Differentially expressed conserved as well as novel miR functions in root and leaf during early stage of Pi starvation were extensively discussed. Leaf and root specific miRs as well as common miRs with their target genes, participating in different biological, cellular, and metabolic processes were explored. Further, four miR390-directed Tasi-Rs which belong to TAS3 gene family along with other orthologs of Tasi-Rs were also identified. Finally, the study provides an insight into the composite regulatory mechanism of miRs in maize in response to Pi deficiency.

Transcriptomic Analysis of Soil Grown T. aestivum cv. Root to Reveal the Changes in Expression of Genes in Response to Multiple Nutrients Deficiency

“…Since past one and half decade several transcriptome analysis were performed in different plant species in response to diverse micronutrient deficiency to mine the important genes along with their role in different metabolic pathways (Wasaki et al, 2003, 2006; Li et al, 2010a,b; Cai et al, 2012; Ma et al, 2012; Park et al, 2012; Takehisa et al, 2013, 2015; Yu et al, 2016; Forieri et al, 2017; Gupta et al, 2017). In continuation, the current study reports 398 differentially expressed genes through a comparative transcriptomic study of micronutrient deficient samples grown in soil having environment growth conditions.…”

“…Under abiotic stress, the ND affect majorly in the quality and quantity of the crop. Identification and understanding of the cellular mechanism of signaling, sensing and adaptation in response to ND is crucial to enhance productivity and quality of the wheat (Gill et al, 2016; Gupta et al, 2016b, 2017). Considering the complexity of above said mechanisms and processes, it is crucial to understand the functional elements and molecular constituents involved during these NDs at transcriptome level.…”

MicroRNAs in model and complex organisms

“…Considering the importance of miRNAs, this special issue focuses on some exciting research questions associated with functional roles of miRNAs both in animals and plants with the contribution of 18 valuable papers Azevedo-Pouly et al 2016;Baddela et al 2016;Deniz and Erman, 2016;Esmaeili et al 2016;Ferdous et al 2016;Giusti et al 2016;Gu et al 2016;Gupta et al 2017;Liu et al 2016;Qiu et al 2016;Reis et al 2016;Soltani et al 2016;Wang et al 2017;You et al 2017;Zhang et al 2016;Zhao et al 2016): How are the miRNAs involved in drought tolerance in plants? What is the role of miRNAs under biotic stress conditions?…”

“…In this special issue, Alptekin and colleagues reviewed the current progress about abiotic stress associated miRNAs and their targets as well the potential application of miRNA-based biotechnology on improvement of crop tolerance to abiotic stresses Zhang 2015), particularly in wheat and barley ). In addition, six research papers explore the miRNA response to abiotic stress as well as hormone treatment in several plant species (Esmaeili et al 2016;Ferdous et al 2016;Giusti et al 2016;Liu et al 2016;Gupta et al 2017;Zhao et al 2016) and detected miRNAs have shown that they play important roles in plant response to environmental adaptation. Liu and colleagues surveyed the miRNAs responsive to water-deficiency stress in four type of durum wheat (Liu et al 2016).…”

“…In addition to the cereals, drought and osmotic stress associated miRNAs are also characterized in peach and almond (Esmaeili et al 2016;Giusti et al 2016). Also, Gupta and colleagues were analyzed and identified miRNAs and tasiRNAs under phosphate deficient conditions (Gupta et al 2017). Furthermore, the miRNAs from grapevine berries in response to ethylene hormone treatment were surveyed by Zhao and colleagues .…”