Profiling the lncRNA-miRNA-mRNA interaction network in the cold-resistant exercise period of grape (Vitis amurensis Rupr.)

Abstract

Background Grape is a plant that is sensitive to low temperature and is vulnerable to low temperature damage. However, little is known about the roles of lncRNAs, miRNAs and mRNAs regulate the hypothermia response mechanism in Vitis amurensis Rupr. Methods In this study, the expression and regulatory network of low-temperature response genes were studied in phloem of grape under different low temperature stress. Results Here, we performed analyses related to RNA-seq and miRNA-seq on grape phloem tissues from five periods of cold resistance campaigns. Three RNA (lncRNAs, miRNAs and mRNAs) obtained by KEGG and GO analyses were used to identify starch and sucrose metabolic pathways associated with cold resistance, and specific changes in BP, CC, and MF were identified in four comparisons. The differentially expressed genes (DEGs) of these pathways were analysed by using Venn diagrams, thermograms and pathway maps respectively, to obtain their specific gene expression during cold exercise. The six DEGs were finally selected, and they were used for qRT-PCR to verify the RNA-seq data. In addition, we found the regulatory networks of miRNAs and lncRNAs correspond to the six DEGs. This study will contribute to further experimental studies to elucidate the cold resistance mechanism of Vitis amurensis Rupr. Conclusions The low temperature response genes of grape are mainly enriched in the metabolic pathways of starch and sucrose, and regulated by miRNA and lncrna, which will provide basic information for further understanding of the cold resistance mechanism of grape in the future.