Genome-wide Gene Expression Profiling Of Salinity Responsiveness And Spatial And Temporal Profiling Of DNA Methylation Induced By Drought And Salinity In Rice

Abiotic stresses such as drought and salinity are very important factors limiting rice growth and productivity around the world. Affymetrix rice genome array containing 48,564 japonica and 1,260 indica sequences was used to analyze the gene expression pattern of rice responsive to salinity stress, try to elucidate the difference of genome-wide gene expression profiling of two contrasting rice genotypes in response to salt stress and to discover the salinity related genes and gene interaction and networks. Epigenetic mechanisms such as DNA methylation, plays a crucial role in regulating gene expression in plant responses to environmental stresses. The objectives of this study were:(1) to characterize the phenotypic and physiological traits associated with salinity tolerance (ST) pyramiding lines, (2) to understand the expression pattern of salinity tolerance pyramiding line and its recurrent parent IR64, (3) to understand the roles of DNA methylation in the epigenetic regulation of gene expression in rice responses and adaptation to drought and salinity stresses.A set of pyramiding lines with significantly improved salinity tolerance were selected by salinity screening of pyramiding population and phenotypic confirmation. The genetic background, morphological and yield traits of those ST pyramiding lines were highly similar with IR64. Most of the salinity tolerance pyramiding lines can improve their salinity tolerance through lower shoot Na+ concentration and lower root to shoot Na+ translocation et al, but there were two pyramiding lines 177-71 and 183-33 may have different mechanisms for salinity tolerance.A ST pyramiding line 177-103 and its recurrent parent IR64 were used for phenotypic and gene expression analysis under salinity and salinity +ABA conditions. We found that exogenous ABA under salinity condition improved rice salinity tolerance by increasing leaf relative water content, decreasing shoot Na+ concentration and root to shoot Na+ translocation. Under salinity condition, the number of differentially expressed genes (DEGs) in 177-103 was more than that in IR64, and most of up-regulated DEGs in 177-103 are response to stress. But in IR64, most of up-regulated DEGs are transcription related genes. The DEGs under salinity showed very strong tissue specificity, the number of DEGs in leaf was more than that in root. A lot of genes differentially expressed by exogenous ABA treatment under salinity condition, such as Leaf senescence protein,1-deoxy-D-xylulose 5-phosphate synthase 2 precursor and Protein of unknown function DUF26 were induced by ABA and contributed to salinity tolerance.We also found some important genes related with salinity in intrgression DNA regeions, such as Annexin, SDR (Short-chain dehydrogenase/Reductase) and plant liqid transferase proteion (LTP) et al.MSAP results indicate that drought and salinity could induce genomewide changes in DNA methylation/demethylation. Most of drought induced methylation/demethylation sites were of two major types distinguished by their reversibility, including 70% of methylation/demethylation sites at which drought induced epigenetic changes were reversed to their original status after recovery, and 29% of sites at which the drought induced DNA demethylation/methylation changes remain even after recovery. Significant decrease of DNA methylation induced by salt stress was specifically detected in roots at seedling stage, and the decreasing extent of DNA methylation in IR29 was more than that in FL478. The drought and salinity induced DNA methylation/demethylation alteration showed a significant level of developmental and tissue specificity.