Transcriptome-based discovery of genes and networks related to RSC3Q-mediated resistance to Soybean mosaic virus in soybean

Abstract

Soybean mosaic virus (SMV) is a worldwide disease of soybean (Glycine max (L.) Merr.) that can cause serious reduction in yield and seed quality. Soybean cv. Qihuang-1 is an important source of resistance to SMV in China, carrying a resistance gene (RSC3Q) against SMV strain SC3. In order to discover genes and networks regulated by RSC3Q-mediated resistance in Qihuang-1, we analysed transcriptome data of a pair of near-isogenic lines, R (RSC3Q) and S (rSC3Q), from the cross Qihuang-1 × Nannong 1138-2 (rSC3Q), after SC3 inoculation. Many differentially expressed genes (DEGs) were identified in the R and S lines at 6, 20 and 48 h post-inoculation. Based on pathway-enrichment analysis of DEGs, three genes encoding calmodulin-like protein (Glyma03g28650, Glyma19g31395 and Glyma11g33790) with downregulated expression in the S line were identified in the plant–pathogen interaction pathway at 6 h post-inoculation. Analyses by quantitative real-time PCR were performed to verify that these three genes were not beneficial for SMV infection. Our results also revealed a complex plant-hormone signal network in RSC3Q-mediated resistance during the early stage of SMV infection. Expression of jasmonic acid repressor genes (TIFY/JAZ) and abscisic acid-induced genes (PP2C3a) was upregulated in the R line but not the S line. More DEGs related to indole-3-acetic acid were found in the R line than the S line, and no salicylic acid-related DEGs were identified. These results suggest that suppression of jasmonic acid or promotion of abscisic acid is important for RSC3Q-mediated resistance against SC3, and that salicylic acid may not act as a main regulator of RSC3Q-mediated resistance during early stages of SC3 infection. Growth and development were greatly affected through RSC3Q-mediated resistance responses after SC3 infection. Our understanding would be enhanced by identification of factors associated with RSC3Q that help to trigger the resistance response.

WGCNA Reveals Hub Genes and Key Gene Regulatory Pathways of the Response of Soybean to Infection by Soybean mosaic virus

“…Conventional transcriptome analysis has been applied to the analysis of molecular regulatory networks of soybean resistance to SMV. Although the plant-pathogen interaction pathway, MAPK signaling pathway, and plant hormone signal transduction pathway have been showed to respond to SMV infection, this response was mainly due to the role of some individual genes in the pathways [35][36][37][38][39]. The WGCNA method can identify the relationship between module eigengenes and hub genes with sample traits.…”

“…The transcriptome analysis revealed a downregulation of NBS-LRR family genes in the susceptible variety Hefeng25 when infected with SMV N1 [36]. Potential genes related to ABA, plant-pathogen interaction, and jasmonic acid (JA) pathways related to Rsc3Q-mediated resistance to SMV strain SC3 were identified via transcriptome analysis between the R (RSC3Q) and S (rSC3Q) lines from the cross Qihuang-1 (which carries the resistance gene RSC3Q) × Nannong1138-2 (which carries the susceptible gene rSC3Q) [37]. Transcriptome analysis of the response of the resistant variety Kefeng-1 to SMV strain SC18 and the susceptible variety NN1138-2 also revealed that several genes related to the ethylene (ETH), jasmonic acid (JA), and salicylic acid (SA) signaling pathways may be involved in the disease resistance to SC18 [38].…”

Major viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration

“… Yuan et al. (2020) used transcriptomic analysis of R and S isogenic lines developed from Qihuang-1 Nannong 1138-2 × Soybean cv.…”

“…Recent advances in RNA-seq-based transcriptome sequencing have offered novel insights into the molecular mechanisms of disease resistance and identified possible candidate gene(s) conferring resistance against various viral diseases in grain legumes (Martin et al, 2016;Dasgupta et al, 2021). Yuan et al (2020) used transcriptomic analysis of R and S isogenic lines developed from Qihuang-1 Nannong 1138-2 × Soybean cv. Qihuang-1 subjected to SMV infection at 6, 20, and 48 h post-inoculation (hpi) to elucidate the underlying candidate gene(s) conferring SMV resistance.…”

RNA-seq Gene Profiling Reveals Transcriptional Changes in the Late Phase during Compatible Interaction between a Korean Soybean Cultivar (Glycine max cv. Kwangan) and Pseudomonas syringae pv. syringae B728a

“…Recently, (molecular) components of soybeans associated with biotic stress response have been identified ( Cooper et al, 2013 ; Delgado-Cerrone et al, 2018 ; Helm et al, 2019 ; Liu et al, 2015b ; Pottinger et al, 2020 ; Russell et al, 2015 ; Wei et al, 2020 ; Yuan et al, 2020 ). Thus, we felt it is necessary to fill the knowledge gap in a Korean soybean accession.…”