Genome-Wide Identification of Vegetable Soybean (Glycine max L.) microRNAs and their Targets Under Chilling Stress by High-Throughput Sequencing and Degradome Analysis

MiRNAs play an important regulatory function by cleaving or inhibiting the translation of target gene transcripts in plants. Chilling stress is a major factor limiting the yield and quality of vegetable soybean (Glycine max L.) on a global scale. Systematic identification and function analysis of miRNA under chilling stress could be helpful to clarify the molecular mechanism of chilling resistance. In the present study, two independent small RNA libraries from leaves of vegetable soybean were constructed, and sequenced with the high-throughput Illumina Solexa system. Based on sequence similarity and hairpin structure prediction, we identified a total of 434 known miRNAs and three novel miRNAs, which belong to 136 miRNA families. Moreover, the expression patterns of these miRNAs have been verified by qRT-PCR analysis. Furthermore, we identified their gene targets by high-throughput degradome sequencing. A total of 898 transcripts were targeted by 54 miRNA families. These transcripts were identified and attributed to five categories, involving in the regulation of plant growth and development. More importantly, we identified 55 miRNAs that differentially expressed between chilling stress and the control. The targets of these miRNAs were enriched in oxidation-reduction, signal transduction, and metabolic process functional categories. The qRT-PCR confirmed that there was a negative relationship among the miRNAs and their targets under chilling stress. Our work provides comprehensive molecular evidence for the possible involvement of miRNAs in the process of chilling-stress responses in vegetable soybean.