Transcriptome analysis in leaves of rice (Oryza sativa) under high manganese stress

Elucidating molecular mechanisms of rice responses to high manganese (Mn) stress is crucially important to manganese-resistant gene cloning, functional analysis and other research work. In the present study, we analyzed the gene expression in leaves of Mn-sensitive rice (Oryza sativa cv. Xinxiangyou 640) exposed to high Mn stress by high-throughput sequencing. There were about 2831 differently expressed genes [the false discovery rate (FDR) ≤ 0.001 and log2ratio(Mn/CK) ≥ 1] among 21258 genes, in which 1336 appeared to be up-regulated and 1495 appeared to be down-regulated in rice treated with high level of Mn compared with the normal level of Mn. Under high Mn stress, the differentially expressed genes were relating to various transcription factors (TFs), large number of transporters, numerous transferase proteins, catalytic proteins, etc, involving in the major primary and secondary metabolisms. Among the rest, the genes of WRKY family were all significantly up-regulated whereas all the Aux/IAA genes were strongly down-regulated. Potassium transporters were also significantly up-regulated whereas sodium transporters were strongly down-regulated. The expression patterns of representative related genes were further confirmed by fluorescent quantitative real-time reverse transcription-polymerase chain reaction (RT-PCR). Manganese resistance mechanism in rice is very complex and is a consequence of coordinated expression of a large number of genes. This data resource contributed substantially to biological and physiological research on rice genes, and to comparative analysis of Mn-specific responses in plants.