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Grain protein content (GPC) affects rice nutrition quality. Here, we identify two stable quantitative trait loci (QTLs),  qGPC-1  and  qGPC-10 , controlling GPC in a mapping population derived from  indica  and  japonica  cultivars crossing. Map-based cloning reveals that  OsGluA2 , encoding a glutelin type-A2 precursor, is the candidate gene underlying  qGPC-10 . It functions as a positive regulator of GPC and has a pleiotropic effect on rice grain quality. One SNP located in  OsGluA2  promoter region is associated with its transcript expression level and GPC diversity. Polymorphisms of this nucleotide can divide all haplotypes into low ( OsGluA2   LET  ) and high ( OsGluA2   HET  ) expression types. Population genetic and evolutionary analyses reveal that  OsGluA2   LET  , mainly present in  japonica  accessions, originates from wild rice. However,  OsGluA2   HET  , the dominant type in  indica , is acquired through mutation of  OsGluA2   LET  . Our results shed light on the understanding of natural variations of GPC between  indica  and  japonica  subspecies.

Natural variation of OsGluA2 is involved in grain protein content regulation in rice