Transcriptome analysis showed the metabolic pathway of differentially expressed genes (DEGs) in resistant and susceptible soybean (Glycine max) to sclerotinia stem rot (SSR) and candidate gene mining

Context Sclerotinia stem rot (SSR) is one of the diseases that seriously affect soybean yield, leading to heavy losses all over the world. A well-known SSR resistant variety is ‘Maple Arrow’.Aims In this study, transcriptome sequencing analysis of resistant variety ‘Maple Arrow’ and susceptible variety ‘Hefeng25’ was conducted to understand the resistance mechanism of resistant and susceptible soybean varieties to SSR and to look for candidate genes.Methods RNA sequencing of Maple Arrow and Hefeng25 generated 75.09GB and 64.97GB clean readings, respectively. In total, 417 differentially expressed genes (DEGs) were found among the different comparable groups. Gene ontology enrichment, Kyoto Encyclopedia of Genes and Genomes analysis and haplotype analysis were performed for genes with different expression levels in Maple Arrow and Hefeng25.Key results It was found that DEGs from Maple Arrow and Hefeng25 were involved in the regulation of ‘oxidation–reduction process’, ‘regulation of transcription’, ‘amino acid metabolism’, ‘methylation’ and ‘membrane’, ‘integral component of membrane’ and ‘epidermal growth-factor receptor substrate 15’. In total, 31 haplotypes of 12 genes were screened out with significant or extremely significant differences among soybeans with different levels of SSR resistance.Conclusions These genes may be involved in the relevant pathways of soybean sclerotiniose.Implications To provide excellent gene resources for further disease-resistance breeding.