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Exploring microRNA (miRNA) expression patterns in  Hemerocallis  under low-temperature stress helps understanding the mechanisms of miRNA-mediated stress responses. Here, eight separate libraries were generated from the leaves and roots of two different varieties, cold-tolerant ‘Jinyan 7’ and cold-sensitive ‘Lucretius 4’, which were exposed to 20°C and −4°C for 8 h. In total, 333 cold-responsive miRNAs, including 85 putative novel and 248 conserved miRNAs, were identified during different temperature treatments. Under cold-stress conditions, two miRNAs were down-regulated and one was up-regulated in the roots, and no differentially expressed miRNAs were detected in the leaves in ‘Lucretius 4’. In ‘Jinyan 7’, there were two novel and one conserved differentially expressed miRNAs in leaves, whereas three conserved and two novel miRNAs were differentially expressed in roots. The target genes were mainly involved in metabolic processes and cellular components. The differential expression levels of 10 miRNAs were validated using quantitative RT–PCR. Some candidate miRNAs (e.g. ath-miR165a, ath-miR166a, ath-miR395a and novel-miR67) may be involved in plant response-related processes to low-temperature.

Identification and differential expression of cold-stress-responsive microRNAs in cold-tolerant and -susceptible Hemerocallis fulva varieties