Transcriptomic analysis reveals regulatory mechanisms of LncRNAs and mRNAs in hulless barley in response to cold...

In this study, RNA-seq analysis of 36 samples from two varieties at six temperature gradients detected a total of 101,193 expressed transcripts, including 25,809 lncRNAs and 75,384 mRNAs. Using 24 °C, 12 °C, and 5 °C as the cold group and 0 °C, -5 °C, and - 8 °C as the freezing group, 2719 CT_24°C_vs_5°C differentially expressed lncRNAs were detected in the cold group, of which 581 were up-regulated and 2138 were down-regulated, and 2,563 differentially expressed lncRNAs were detected in the freezing group, of which 601 were up-regulated and 1962 were down-regulated. In the group CT_0°C_vs_-8 °C, differentially expressed lncRNAs were 1,415, of which 250 were up-regulated and 1,165 were down-regulated, and in CS_0°C_vs_-8 °C, differentially expressed lncRNAs were 1,301, of which 228 were up-regulated and 1,073 were down-regulated.In the cold-damaged group, the total number of predicted paired lncRNA-mRNA pairs was 1904, of which 1152 pairs were paired by cis, and 752 pairs were paired by tran. In the freezing group, 922 pairs of lncRNA-mRNA pairs were predicted, of which 473 pairs were in the cis mode and 449 pairs were in the tran mode. In the cold group, 656 differential lncRNA target genes intersected with differentially expressed mRNAs in the CT_24℃_vs_5℃ comparison, and 668 in the CS_24℃_vs_5℃ comparison. In the freezing group, 187 differentially expressed mRNAs intersected with differentially expressed lncRNA target genes in the CT_0°C_vs_-8 °C comparison, and 146 in the CS_0°C_vs_-8 °C comparison. GO enrichment analysis indicated significant enrichment in the metabolic process and response to stimulus pathways in both the cold and freezing groups. KEGG enrichment analysis revealed significant enrichment in the Nucleotide excision repair (ko03420) and DNA replication (ko03030) pathways in the cold-damaged group, and in the Ascorbate and aldarate metabolism (ko00053) pathway in the freeze-damaged group. This suggests that the Ascorbate metabolic pathway plays a significant role in the barley response to frost damage.