Genome-wide characterization of drought stress responsive long non-coding RNAs in Tibetan wild barley

Abstract

Drought is the most common and frequently occurring abiotic stress limiting crop yield and quality. Long non-coding RNAs (lncRNA) play crucial roles in regulating expression of genes in plants under various abiotic stress. The participation of lncRNAs in plant drought tolerance in barley is largely unknown. Here, we compared the lncRNA transcriptome in roots of two Tibetan wild barley genotypes XZ5 (drought-tolerant) and XZ54 (drought-sensitive), and one drought tolerant cv. Tadmor in response to polyethylene glycol-induced drought stress. In total, 23,651 novel lncRNAs were identified, among which 535 were characterized as drought responsive according to their different expression profile among XZ5, and XZ54 and Tadmor in response to drought stress. LncRNA target prediction revealed 1279 potential lncRNA-messenger RNA (mRNA) pairs, among which 503 pairs function in cis-acting mode and 776 in trans. Functional enrichment analysis showed that the targets were significantly enriched in molecular functions related to plant hormone signal transduction, diterpenoid biosynthesis, and ascorbate/aldarate metabolism. Multiple promising targets of drought-responsive lncRNAs were discovered, including the SPL3, BRI1 gene. Further analysis of genotypic difference in transcriptome we identified 10 drought-tolerance associated lncRNAs in XZ5, being exclusively induced by drought stress in XZ5 among the three genotypes, and sequencing data were confirmed by RT-qPCR. The lncRNA-mRNA interaction-based functional role showed these lncRNAs mediated the regulation of kinase mediated signal transduction, a serine/threonine-protein kinase SMG1 is likely responsible for drought tolerance in XZ5. These findings extend our knowledge of lncRNAs as important regulators in drought tolerance.