Comparative Transcriptome Analyses between Resistant and Susceptible Varieties in Response to Soybean Mosaic Virus Infection

Abstract

Soybean mosaic virus (SMV) is a worldwide and hardly controlled virus disease in soybean. Kefeng-1 is an elite variety resistant to SMV in China. In order to discover resistance genes and regulation networks in Kefeng-1, we analyzed transcriptome data of resistant (Kefeng-1) and susceptible (NN1138-2) soybean varieties in response to infection of the SMV strain SC18 at 0, 6, and 48 hours post-inoculation (hpi) and 5 days post-inoculation (dpi). Many differentially expressed genes (DEGs) were identified with Kefeng-1 and NN 1138-2. Based on the enrichment analysis for gene ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, we found that 48 hpi was the best time point for the defense response of the two soybean varieties in response to the SMV infection. The expression of seven candidate genes was further verified by qRT-PCR and was relatively consistent with the results of RNA-Seq. The expression of genes for Glyma.11G239000 and Glyma.18G018400, members of the ethylene-insensitive 3/ethylene-insensitive3-like (EIN3/EIL) protein family involved in ETH, were downregulated in NN1138-2 but not in Kefeng-1 and the expression of Glyma.14G041500 was upregulated in Kefeng-1 at 5 dpi. The expression of jasmonic acid repressor genes (TIFY/JAZ) was downregulated in NN1138-2 but not in Kefeng-1. NPR1 involved in the salicylic acid signaling pathway was downregulated in NN1138-2 at 48 hpi but upregulated in Kefeng-1. It shows that ethylene, jasmonic acid, and salicylic acid signaling pathways may be involved in the disease resistance process to the SMV strain SC18. Our findings would help to understand the molecular mechanism of soybean resistance to SMV.