The Significance of Heat Responsive Long Noncoding RNAs in Rice Discovered by Integrating Expression, Network and Genetic Analyses

Abstract Long noncoding RNAs (lncRNAs) play vital roles in plant responses to environments. However, the systematic identification of lncRNAs in rice under heat stress remains to be fully performed. We performed steady-state strand-specific RNA-seq for rice seedlings under heat stress to predict lncRNAs. In total, 2743 lncRNAs were predicted, and their expression profiles in response to heat treatments were provided. We identified 231 differentially expressed lncRNAs (DELs) in their steady-state level under heat stress, including 31 DELs common to both varieties and 103 and 97 specific to ZS97B and SYD2, respectively, all defined as heat-responsive lncRNAs (HRLs). The target-coding genes of HRLs were predicted through cis-action, ceRNAs, precursors of miRNA, antisense modes and other trans-action targets. GO and KEGG enrichment analyses of HRL targets revealed functions in which HRLs were involved. The interaction network between HRLs, target genes and relevant miRNAs was constructed. The HRLs and their targets were integrated with publicly available QTLs for rice seedling growth under heat stimulus, and 10 HRLs and 12 target genes were co-localized with 5 heat-relevant QTLs. Sequence motif analysis found a few significant motifs enriched in 231 HRL sequences, and the differential significance of enriched motifs between HRLs and background sequences was tested. Our findings provide new insights into the characterization of lncRNAs in terms of the heat response and resources for further investigations of plant heat tolerance improvement.