Comparative transcriptome profiling reveals key lncRNAs and regulatory mechanisms for salt tolerance in hulless barley

Salt stress poses a significant threat to crop production globally. LncRNAs regulate plant stress responses by interacting with key proteins, affecting gene expression and stress signaling pathways. This study analyzed lncRNAs in the roots of X349 (salt-tolerant) and X66 (salt-sensitive), which differ in biomass accumulation and antioxidant activities. A total of 7,648 novel lncRNAs were identified; among these, 2,210 lncRNAs were characterized as salt-stress responsive lncRNAs, which are associated 4,899 target genes in both genotypes. A total of 139 lncRNAs-mRNA pairs were identified, where 123 were subjects to cis-acting regulation by lncRNAs and the majority (4,776) of target genes were regulated through trans-acting mechanisms. Genotypic comparison revealed 13 unique differentially expressed lncRNAs in X349, which were associated with 27 target mRNAs. Functional enrichment analysis revealed that differentially expressed lncRNAs are significant concentrated in the phenylalanine metabolism, nitrogen metabolism, zeatin biosynthesis and metabolism of alanine, aspartate and glutamate in the salt-tolerant genotype. The salt-responsive lncRNAs and their target genes are primarily associated with chitinases, phenylalanine ammonia-lyases, and wall-associated receptor kinases. Highlighting the potential of salt-responsive lncRNAs and target genes in understanding and improving salt tolerance in hulless barley. Functional validation of lncRNAs and target genes will offer insights into these mechanisms.