Sociology

Grain quality

Japonica

Population

Biology

Storage protein

Gene

Genotype

Demography

Horticulture

Paleontology

Allele

Single-nucleotide polymorphism

Subspecies

Haplotype

Nucleotide diversity

Glutelin

Botany

Genetics

Quantitative trait locus

Nature Communications

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