Identification of Co-Expression Gene Related to Tea Plant Response to Glyphosate Based on WGCNA

Abstract

[Objective] This study aimed at analyzing both expression patterns and regulatory pathways of tea plants in response to glyphosate stressing, which could revealed the effect of glyphosate herbicides on tea plants at transcriptional level and identify key genes of tea plants. [Method] C. sinensis cv Jin-guanyin was applied as material plant. A recommended concentration of glyphosate was irrigated to test plants. The leave samples were collected at different time intervals (0, 0.25, 1, 3 and 7 d). The samples were sequenced by transcriptome, the content of shikimic acid was also quantified. The WGCNA method was used to jointly analyze transcriptome and shikimic acid content data, to identify co-expressed gene modules related to glyphosate response, and to screen out key regulatory genes. [Result] The content of shikimic acid in tea leaves reduced gradually during first 3 days. However, it suddenly reached a peak on the 7th day (6.99 times compared with no glyphosate treated sample). A total of 12 568 differential expression genes (DEGs) were also identified, which mainly enriched in phenylpropane, flavonoid biosynthesis and plant hormone signal transduction pathways. In addition, the glyphosate treatment induced 24, 52, 31 and 69 genes respectively which related to shikimic acid metabolism, phenylpropane, flavonoid biosynthesis and hormone signal transduction pathways. A total of 19 modules were screened out by WGCNA method. The correlation analysis of transcriptome and shikimic acid content indicated two key modules, including 2 024 and 2 305 genes, respectively. The top 50 genes with the highest connectivity in the key modules were selected for co-expression analysis, and 6 key response genes were obtained, including 2 resistance genes (SHMT and RPM), 1 drug resistance gene (PDR), 1 ion transport gene (At), 1 membrane transport gene (GPT), and 1 transcription factor gene (ERF). [Conclusion] Glyphosate could affect downstream genes transcription of phenylpropane, flavonoid biosynthesis and hormone signal transduction pathways by interfering shikimic acid metabolism of tea plants. In addition, this study also identified two co-expression modules closely related to glyphosate response, and found that multiple potential candidate genes and transcription factors could resist glyphosate stress, such as SHMT, RPM, At, PDR, ERF and GPT.