Comparative Quantitative Proteomic Analysis Reveals Differentially Expressed Proteins Involved in Grain-Filling Rate of Rice at the Early Ripening Stage

Abstract Background Grain-filling ability is a determinant factor of rice potential yield. Grain filling is a biological process of starch accumulation involved a large number of major enzymes implicated in carbohydrates metabolism in developing rice endosperm and is governed by a complex balance between the sink (grains) and the source (assimilates). This study was carried out to analyze the proteomic profile of rice grains and to identify proteins associated with high grain-filling rate during the early ripening period in rice. Results TMT and LC-MS/MS were employed in analyzing proteomic profile of grains from two rice cultivars possess contrasting phenotypes in grain filling rate to identify proteins associated with high grain-filling rate during the early ripening stage. The two cultivars differed significantly in grain-filling rate during the period of 0–3 days after full heading, indicating the appropriacy of cultivars selection for quantitative proteomic analysis. A total of 219 differentially expressed proteins in grains between the two cultivars were identified, providing a database for quantified proteomics in rice grains during grain filling stage. Elevated expression of many enzymes involved in starch and sucrose metabolism during rice grain filling was observed. GO and KEGG analyses revealed that the largest portion of differentially expressed proteins during grain filling associated with carbohydrate metabolism and transportation, suggesting a more specific function of those protein in rice grain development. Starch, sucrose, fatty acids and amino acids biosynthesis and metabolism were significantly enriched pathways. Conclusions Analysis of protein-protein interactions indicated the implication of the same proteins in several biological processes such as carbohydrate transport and metabolism, fatty acid metabolism, energy production and conversion and secondary metabolites biosynthesis. The data provide valuable information about the roles of biosynthesis, transport and metabolism of carbohydrate and amino acids in rice grain filling and development. The results represent a valuable foundation for further studies of the roles of differentially expressed proteins in underlying grain filling stage in rice and their potential impacts on rice productivity.