RNA-Seq transcriptome analysis of fresh-eating maizes sensitive and tolerant to mesotrione in the seedling stage

Postemergence applications of mesotrione can cause great damage to maize inbred lines and hybrids. Variation among different responses to mesotrione may be attributed to differential rates of herbicide metabolism. In this study, field and pot experiments were conducted using two fresh-eating maize inbred lines with different response to mesotrione. After mesotrione treatment, the accumulation of ROS in susceptible maize inbred line were significantly increased. The photosynthesis was severely inhibited, and the susceptible plant eventually died. We employed RNA-Seq analysis to compare transcriptome responses between mesotrione-treated and untreated in both tolerant and susceptible maize inbred lines. A total of 7985 differentiation expressed genes (DEGs) were identified. There were 4020 up-regulated genes and 3450 down- regulated genes in susceptible maize, and only 526 up-regulated genes and 495 down-regulated genes in tolerant maize. Gene oncology (GO) enrichment analysis showed that the majority of differentiation expressed genes were concentrated in molecular function, cellular components and biological processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that the differentiation expressed genes were mainly involved in photosynthesis, carbohydrate, amino acid and lipid metabolism pathways. Based on gene expression and function annotation, 9 genes were selected as the candidates most likely involved in herbicide metabolism, and quantitative real time RT-PCR validated the RNA-Seq results. The candidate genes were Zm00001d042099, Zm00001d044157, Zm00001d007462, Zm00001d002436, Zm00001d021804, Zm00001d042541, Zm00001d040764, Zm00001d032828 and Zm00001d020544.