| Non-dormant and mature seeds of plants will germinate and grow up under favorable conditions. Germination is a process that seeds grow up to seedlings from a dry and quiescent statement after a series of complex physiological changes. Germination is under a very comprehensive regulation of many factors, including ambient temperature, light, hormones and etc. Cold stratification can disrupt dormancy and promote germination, and gibberellin and abscisic acid can promote and inhibit germination, respectively. Next-generation sequencing technology provides a more effective way to study the process of germination, enabling us to have a clearer picture of the dynamic changes in seeds during germination. We sampled embryos of rice seeds after Oh,0.5h,1h,3h and5h on imbibition, and analyzed the dynamic transcriptome changes using RNA-Seq technology of Illumina platform.At first we mapped reads to genomic reference sequence, and then calculated levels of gene expression in every sample. Then we identified differential expression genes (DEG) of two adjacent samples. The result showed that the DEG between Oh and1h was much less than that between1h and5h, which indicated massive transcriptome changes occured after1h on imbibition, and implied that1h may be a turning point during rice early development. We also analyzed the gene expression patterns from Oh to5h, and clustered expressed genes into4major classes. Genes in class Cl showed uptrend in expression level, and they mainly involved in the processes of energy metabolism, gibberellin and ethylene metabolism, and response to stress. While genes in class C2and class C3showed downtrend and most of them related to seed storage proteins, light reaction, and abscisic acid metabolism. Finally we analyzed the alternative splicing (AS) events by the information of reads located in junctions. We found15303kinds of AS events, but only3770of them were annotated. That was to say the AS forms of plants were more complex than we have known. |
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