Transcriptome analysis reveals different responses and tolerance mechanisms of EPSPS and GAT genes in transgenic soybeans

Abstract Background: Glyphosate is a broad-spectrum and non-selective systemic herbicide. Introduction of glyphosate tolerance genes like EPSPS or detoxification genes like GAT could confer glyphosate tolerance to plants. Our previous study revealed that co-expression of EPSPS and GAT genes conferred higher glyphosate tolerance with no “yellow flashing” phenomenon. However, the tolerance mechanisms response to glyphosate at transcriptional level was still unknown. Methods and Results: To investigate glyphosate tolerance mechanisms in different GM soybeans, RNA-seq analysis was conducted using four soybean genotypes, including two non-transgenic (NT) soybeans ZH10, MD12, and two GM soybeans HJ698 and ZH10-6. A total of 90.72 Gb clean reads were generated and differentially expressed genes (DEGs) were identified in these soybeans before and after glyphosate treatments. The similar response of glyphosate in NT soybeans and the different effect of glyphosate to two GM soybeans were identified. The number of DEGs involved in shikimate biosynthetic pathway and herbicide targeted cross-pathways was continuously increased in NT soybeans, and slightly increased in HJ698 as the increasing of treat time. However, it was only significantly increased at 12hpt but tended to recover to levels of 0 hpt at 72 hpt in ZH10-6, which can explain the higher glyphosate tolerance of ZH10-6.Conclusions: All these results suggested that GAT and EPSPS genes associated play a crucial role in response to glyphosate, and the former might work at the early stage of glyphosate exposure while the latter might be activated after the uptake of glyphosate uptake. These findings will provide valuable sights for understanding of the molecular basis underlying glyphosate tolerance.