RNA-sequencing Oryza sativa transcriptome in response to herbicide isoprotruon and characterization of genes involved in IPU detoxification

Abstract

The soil residue of isoproturon (IPU) has become one of the biggest environmental contaminants due to its intensive use in crop production. But how plants respond to IPU and the mechanisms for IPU degradation and detoxification in plants are poorly understood. In this study, we used recent advances in RNA sequencing (RNA-Seq) technology to dissect novel re-programming of transcripts in IPU-exposed rice plants. Four libraries were constructed from shoots and roots with or without IPU exposure. Mapping the clean reads to rice genomic databases generated 31 009–32 118 annotated genes for a single library. Most of the annotated genes were differentially expressed (DEGs) among the libraries. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEGs showed modified biological functions and metabolic pathways associated with the resistance to environmental stress, degradation of xenobiotics and molecular metabolism. Validation of gene expressions by qRT-PCR confirmed the RNA-Seq results. DEGs encoding proteins involved in xenobiotic metabolism, detoxification, transporters, and transcription factors were comprehensively investigated. The activities of several enzymes closely related to xenobiotic metabolism were determined. Notably, the specific cis-elements of degradation-associated DEGs were predicted, and their regulatory networks were analyzed. To evidence the IPU-metabolism in rice, 19 degradations and 5 conjugates were chemically characterized using UPLC-LTQ-MS/MS. Overall, the transcriptome data presented here provide new insight into the molecular and chemical mechanisms of IPU-metabolism in rice.