Systematic identification and characterization of microRNAs with target genes involved in high night temperature stress at the filling stage of rice

Abstract High night temperature stress is one of the main environmental factors affecting rice yield and quality. More and more evidence shows that microRNA (miRNA) plays an important role in various abiotic stresses. However, the molecular network of miRNA regulation on rice tolerance to high night temperatures remains unclear. Here, small RNA, transcriptome and degradome sequencing were integrated to identify differentially expressed miRNAs, genes, and key miRNA‐target gene pairs in rice heat‐sensitive and heat‐tolerant lines at the filling stage suffering from high night temperature stress. It was discovered that there were notable differences in the relative expression of 102 miRNAs between the two rice lines under stress. Meanwhile, 5263 and 5405 mRNAs were differentially expressed in the heat‐sensitive line and heat‐tolerant line, and functional enrichment analysis revealed that these genes were involved in heat‐related processes and pathways. The miRNAs‐mRNAs target relationship was further verified by degradome sequencing. Eventually, 49 miRNAs‐222 mRNAs target pairs with reverse expression patterns showed significant relative expression changes between the heat‐tolerant and the heat‐sensitive line, being suggested to be responsible for the heat tolerance difference of these two rice lines. Functional analysis of these 222 mRNA transcripts showed that high night temperature‐responsive miRNAs targeted these mRNAs involved in many heat‐related biological processes, such as transcription regulation, chloroplast regulation, mitochondrion regulation, protein folding, hormone regulation and redox process. This study identified possible miRNA‐mRNA regulation relationships in response to high night temperature stress in rice and potentially contributed to heat resistance breeding of rice in the future.