Genome-Wide Identification of Phytophthora sojae-Associated microRNAs and Network in a Resistant and a Susceptible Soybean Germplasm

Phytophthora root rot, caused by Phytophthora sojae (P. sojae), is one of the most devastating diseases limiting soybean production worldwide. microRNAs (miRNAs) play major roles in regulating plant defense against pathogens. To understand the roles of soybean miRNAs during P. sojae infection, we analyzed four small RNA libraries from two soybean germplasms before and after P. sojae isolate JS08-12 infection. The cultivar Nannong 10-1 was resistant to JS08-12, whereas the 06-070583 line was susceptible to JS08-12. In total, 528 known and 555 putative novel miRNAs in soybean were identified from 97 million reads; 74 known miRNAs and 75 novel miRNAs that might be specifically related to Nannong10-1 responses to P. sojae; and 55 known and 43 novel miRNAs expressed before and after infection in the susceptible line 06-070583. qRT-PCR provided similar miRNA expression patterns to those obtained by the small-RNA sequencing of the four libraries. Then, the potential target genes of these differentially expressed miRNA were predicted, which encoded transcriptional factors, resistance proteins and transporters. Finally, we focused on the targets of the three legume-specific miRNAs (gma-miR1508, gma-miR1509, and gma-miR1510) and charted the miRNA-target interactions and networks based on the published degradome data.