Molecular dissection of atrazine-responsive transcriptome and gene networks in rice by high-throughput sequencing.

The residue of atrazine (a herbicide) has become hazards in environments due to its intensive use. However, its molecular toxicity to on plants and human beings is not fully understood. In this study, we performed high-throughput sequencing of atrazine-exposed rice (Oryza sativa) to analyze global expression and complexity of genes in the crop. Four libraries were constructed from shoots and roots with or without atrazine exposure. We sequenced 5,751,861, 5,790,013, 5,375,999 and 6,039,618 clean tags that corresponded to 220,806, 111,301, 248,802 and 114,338 distinct tags for Root-Atr (root control, atrazine-free), Shoot-Atr (shoot control, atrazine-free), Root+Atr (root treated with atrazine) and Shoot+Atr (shoot treated with atrazine) libraries, respectively. Mapping the clean tags to gene databases generated 18,833-21,007 annotated genes for each library. Most of annotated genes were differentially expressed among the libraries. The most 40 differentially expressed genes were associated with resistance to environmental stress, degradation of xenobiotics and molecular metabolism. Validation of gene expression by quantitative RT-PCR confirmed the deep-sequencing results. The transcriptome sequences were further subjected to Gene Orthology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and showed modified biological functions and metabolic pathways. Our results not only highlight the transcriptional complexity in rice with atrazine but also represent a major improvement for analyzing transcriptional changes on a large scale in xenobiotics-responsive toxicology.