Identification and functional prediction of salt stress-related long noncoding RNAs in grapevine roots

•A total of 1661 lncRNAs responded to salt stress in grapevine roots.•Target genes of salt-induced grapevine lncRNAs were predicted.•A total of 815 lncRNAs and 608 mRNAs were linked through 75 shared miRNAs.•lncRNAs might regulate salt resistance through multiple pathways including ion binding. Long noncoding RNAs (lncRNAs) are a widespread RNA molecules of more than 200 bp that lack coding potential and have been proven to function in response to abiotic stresses. In this study, we identified salt stress-induced lncRNAs in grapevine roots and predicted their intricate regulatory roles. A total of 3952 novel lncRNAs that were distributed across all 19 grape chromosomes, more than 70 % of which were located in intergenic regions. Compared with mRNAs, lncRNAs exhibit short ORFs, a high SNP density and low expression. A total of 1661 differentially expressed lncRNAs (DElncRNAs) were detected in salt-treated roots in comparison to the control, and the greatest number of DElncRNAs were produced in the roots at 12 h after salt treatment. We predicted that 546, 771, and 608 mRNAs could be directly or indirectly regulated by DElncRNAs in cis-, trans-, and miRNA-mediated patterns. Multiple target genes of DElncRNAs were found to be involved in transcriptional regulation, the ubiquitin-proteasome pathway, multiple ion binding, and electron carrier activity. Furthermore, a large number of NB-ARC domain proteins are potential targets of DElncRNAs. These findings provide a comprehensive view of potentially functional lncRNAs, providing insight into the molecular mechanism of salt resistance in grape.