Identification of MicroRNAs that Respond to Soybean Cyst Nematode Infection in Early Stages in Resistant and Susceptible Soybean Cultivars

Soybean cyst nematode (SCN) causes heavy losses to soybean yield. In order to investigate the roles of soybean miRNAs during the early stages of infection (1 dpi and 5 dpi), soybean cultivar Huipizhi (HPZ), which is resistant to a wide range of SCN races, and the susceptible Williams 82 (W82) cultivar were inoculated with 2000 SCN race 3 juveniles. Twenty-four small RNA libraries were then constructed for high-throughput sequencing. By sequencing the small RNA libraries, a total of 643,468,338 sRNA clean reads were obtained, and each library contained at least 19,622,055 clean reads. A total of 634 known miRNAs were identified, and 252 novel miRNAs were predicted. Altogether, 14 known miRNAs belonging to 13 families, and 26 novel miRNAs, were differently expressed may respond to SCN infection in HPZ and W82. Similar expression results were also confirmed by qRT-PCR. Further analysis of the biological processes that these potential target genes of DE miRNAs regulate found that they may be strongly related to plant defense, plant immune systems, and plant-pathogen interactions. In addition, phenylpropanoid biosynthesis, nutrient reservoir activity, signal transducer activity, amino acid biosynthesis, and starch and sucrose metabolism occupied a high percentage in KOG, GO, and KEGG pathway classification. Overall, soybean miRNAs experience profound changes in early stages of SCN infection in both HPZ and W82. The findings of this study can provide insight into miRNAome changes in both HPZ and W82 at the early stages of infection, and may provide a stepping stone for future SCN management.