Identification of heat stress-responsive rice microRNAs and their target genes by high-throughput sequencing and degradome analysis

In this study, we identified a set of heat stress-responsive miRNAs and verified their targets through degradome sequencing. Nine libraries (triplicate for 0 h, 12 h and 24 h heat treatment) were constructed and sequenced. Four hundred and nineteen conserved miRNAs and 77 novel miRNAs were identified, of which, 40 conserved and two novel miRNAs were expressed differentially. Quantitative PCR of three selected miRNAs and their targets confirmed that these loci were responsive to heat stress. A total of 1364 target transcripts were identified for 114 conserved miRNA and a total of 65 were identified for 22 novel miRNA families. Gene function and pathway analyses showed that these genes probably play vital roles in rice heat stress tolerance. Overall design: The plant material used in this study was HT54, an Indica breeding line with heat tolerance possibly inherited from its parental variety Guang-Lu-Ai No 4. Previous study have shown that HT54 seedlings could tolerate high temperature up to 48 °C for 79 h. For miRNA library, three-leaf stage rice seedlings were treated by heat shock at 45°C for 0, 12 or 24 h, and triplicate for each data point, thus nine libraries were constructed. For degradome library, one library was constructed at each time point. One miRNA library for each time point was found to be unsuitable for analysis and are not included in this submission.