Genome-Wide Identification of Soybean microRNA and siRNA Responsive to Soybean Cyst Nematodes Infection By Deep Sequencing

The soybean cyst nematode (SCN), Heterodera glycines, is one of the most important pests limiting soybean production worldwide. It is known that small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), play central roles in growth and development, defense against pathogens, and responses to environmental changes in plants. In this study, we sequenced 24 small RNA libraries including three biological replicates from two soybean cultivars (SCN susceptible KS4607; and SCN HG Type7 resistant KS4313) that were grown under SCN-infested and noninfested soil at two different time points (SCN feeding establishment; and egg production). Several hundred conserved and putative novel miRNAs in soybean were identified from a total of 0.3 billion reads (average about 13.5 million reads for each sample) with the programs of Bowtie and miRDeep2 mapper. Differential expression analyses were carried out using DESEQ to evaluate significant differences among miRNAs involving in soybean and SCN interaction. Comparative analysis of miRNA profiling indicated some known miRNAs with similar expression pattern as the previous report, plus an additional10 families of miRNA candidates might be specifically related to cultivar responses to SCN. Correlated gene expression analysis of differentially expressed miRNAs will be conducted to confirm these miRNAs expression and reveal the correlations of potential target genes. These findings suggest that miRNAs are likely to play important roles in soybean response to SCN. Recently, new technology such as short tandem target mimic (STTM) has been successfully applied to demonstrate many miRNA functions. The present work could provide a framework for miRNA identification and the development of novel approaches for improving soybean SCN resistance in future studies.