The Small-RNA Profiles of Almond (Prunus dulcis Mill.) Reproductive Tissues in Response to Cold Stress

Abstract

Spring frost is an important environmental stress that threatens the production of Prunus trees. However, little information is available regarding molecular response of these plants to the frost stress. Using high throughput sequencing, this study was conducted to identify differentially expressed miRNAs, both the conserved and the non-conserved ones, in the reproductive tissues of almond tolerant H genotype under cold stress. Analysis of 50 to 58 million raw reads led to identification of 174 unique conserved and 59 novel microRNAs (miRNAs). Differential expression pattern analysis showed that 50 miRNA families were expressed differentially in one or both of almond reproductive tissues (anther and ovary). Out of these 50 miRNA families, 12 and 15 displayed up-regulation and down-regulation, respectively. The distribution of conserved miRNA families indicated that miR482f harbor the highest number of members. Confirmation of miRNAs expression patterns by quantitative real- time PCR (qPCR) was performed in cold tolerant (H genotype) alongside a sensitive variety (Sh12 genotype). Our analysis revealed differential expression for 9 miRNAs in anther and 3 miRNAs in ovary between these two varieties. Target prediction of miRNAs followed by differential expression analysis resulted in identification of 83 target genes, mostly transcription factors. This study comprehensively catalogued expressed miRNAs under different temperatures in two reproductive tissues (anther and ovary). Results of current study and the previous RNA-seq study, which was conducted in the same tissues by our group, provide a unique opportunity to understand the molecular basis of responses of almond to cold stress. The results can also enhance the possibility for gene manipulation to develop cold tolerant plants.

miRNAs play important roles in aroma weakening during the shelf life of ‘Nanguo’ pear after cold storage

“…Additionally, the differentially expressed miRNAs in fruits stored in the cold were identified, and mdm-miR172a-o, mdm-miR167b-g, mdm/ppe-miR395a-i, mdm-miR160a-e, mdm-miR7120a/b, mdm-miR159mdm-miR164b-f, and mdm-miR396b were most significantly differentially expressed in the fruits after LT storage. These low temperature-related miRNAs have also been identified in other plants (Chinnusamy et al, 2007; Josine et al, 2011; Karimi et al, 2016).…”

“…MiRNAs are post-transcriptional regulators of responses to abiotic stresses in plants and have been found to be multi-responsive to multi-environmental conditions individually or together with their target genes (Liu et al, 2008; Zhang et al, 2009; Lee et al, 2010). The miRNA families and their target genes in plants responding to LT stress include miR394, miR399, miR395, miR408, miR169, miR172, miR167, miR160, and miR159 (Cao et al, 2014; Xu et al, 2013; Karimi et al 2016). MiR169 was differentially expressed by the NFYA gene, and the expression of miR160 and miR167 was regulated by auxin-response factors (ARFs) that were related to cold stress (Chen et al, 2012; Karimi et al 2016).…”

“…The miRNA families and their target genes in plants responding to LT stress include miR394, miR399, miR395, miR408, miR169, miR172, miR167, miR160, and miR159 (Cao et al, 2014; Xu et al, 2013; Karimi et al 2016). MiR169 was differentially expressed by the NFYA gene, and the expression of miR160 and miR167 was regulated by auxin-response factors (ARFs) that were related to cold stress (Chen et al, 2012; Karimi et al 2016). MiR156 and miR172 are the most important cold-responsive miRNAs (Xing et al, 2010), and the effect of miR156 and miR172 on LT has been reported in rice, wheat, and peach (Wang et al, 2014; Zhu et al, 2011).…”

“…High-throughput sequencing has identified numerous critical miRNAs, such as miR156, miR159, miR160, miR164, miR172, miR319, miR393, miR394, miR395, miR399, and miR408, that are expressed in response to abiotic stresses in plants (Jones-Rhoades et al, 2006; Schommer et al, 2008; Stief et al, 2014; Sun, et al, 2015; Zhang et al, 2016). MiR156/157 negatively regulates the MADS-RIN to induce the transcription of ripening-related genes in tomato (Dalmay 2010), and the known ripening regulators, the CNR and AP2 TFs, were also identified as targets of miR156 and miR172, respectively (Chung et al, 2008; Karimi et al, 2016). In addition, miRNAs negatively regulate their targets in Arabidopsis roots after infection with cyst nematodes, leading to the downregulation of miRNAs (Xing et al, 2010).…”

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

“…miRNAs bind to complementary mRNA molecules and act as negative regulators of gene expression through endonucleolytic cleavage or translational repression of the cognate mRNA targets [24]. Lately, miRNA regulation of stress response pathway has been established in several plant species [25][26][27][28]. Consistently, a large number of cold stress responsive microRNAs have been identi ed in various plant species with variable results in different reports [27,29,30].…”