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
Dongming Sun A , Ruiqiong Li A , Jinglin Ma A , Shuo Qu A , Ming Yuan B , Zhenhong Yang A , Changjun Zhou C , Junrong Xu A , Yuhang Zhan A , Xue Zhao
A * , Yingpeng Han A * and Weili Teng A *
A
B
C
Handling Editor: Rajeev Varshney
Abstract
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’.
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.
RNA sequencing of Maple Arrow and Hefeng25 generated 75.09 GB and 64.97 GB 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.
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.
These genes may be involved in the relevant pathways of soybean sclerotiniose.
To provide excellent gene resources for further disease-resistance breeding.
Keywords: gene mining, GWAS, haplotype analysis, KEGG enrichment analysis, RNA-seq, sclerotinia stem rot, soybean, transcriptome.
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