Heterosis is a common phenomenon in which the hybrids exhibit superior agronomic performance than both parents such as biomass production, grain yield, and stress tolerance. Although heterosis breeding is one of the main techniques in rice breeding, the molecular mechanisms responsible for this basic biological phenomenon are not well understood. To further get an insight into the molecular mechanisms of rice heterosis, comparative root proteomic analysis between a super-hybrid rice LYP9 and its parental cultivars 9311 and PA64S at seedling stage were performed. Total proteins were extracted and subjected to two-dimensional gel electrophoresis. The scatter plots analysis results showed that the LYP9’s expression profiles were more similar to 9311 than PA64S. A total of 11 differentially expressed protein spots were detected and identified by matrix-assisted laser desorption/ionization-time of flight/time of flight mass spectrometry, corresponding to 10 unique proteins. These proteins were identified to be involved in several cellular processes, including metabolism, secondary metabolism, Transcription regulation, energy metabolism, signal transduction, disease and defense. Moreover, based on our present data, the differentially expressed proteins could work together to play a major role in the induced defense response. In addition, we observed that phenylalanine ammonia-lyase, Os12g0440200 and putative PrMC3 proteins had higher expression in LYP9 than its parents. These proteins can be strongest candidates for further functional research.
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