Identification and functional prediction of long non-coding RNAs responsive to heat stress in heading type Chinese cabbage

Abstract

Global warming is a devastating force that considerably hinders the growth, quality and yield of heading type Chinese cabbage (Brassica rapa L. ssp. pekinensis). Recent research suggests that long non-coding ribonucleic acids (lncRNAs) play a role in response to abiotic and biotic stresses. In this study, a total of 278 lncRNAs belonging to intergenic, intronic, sense and natural antisense lncRNAs in the heading type Chinese cabbage using RNA-sequencing (RNA-seq) data were identified. Based on the analysis of the differentially expressed lncRNAs, 93 out of 278 lncRNAs were identified as heat-responsive lncRNAs. In total, 65 heat-responsive lncRNAs were predicted as putative targets and target mimics of B. rapa microRNAs (miRNAs). In addition, it was found that some identified lncRNAs play important role in response to heat stress via lncRNA-messenger RNA (mRNA) (lncRNA.Brassica_094-DnaJ protein and lncRNA.Brassica_181-REF4-related 1) co-expression, whereas some lncRNA-miRNA (lncRNA-Brassica_116-bra-miR164a and lncRNA-Brassica_205-bra-miR159) interactions are required for modulation of miRNA action. Taken together, these results provide the starting point for a detailed investigation of the physiological function of the lncRNA-dependent network in heading type Chinese cabbage.