Evolutionary History of GS3, a Gene Conferring Grain Length in Rice

Abstract

Unlike maize and wheat, where artificial selection is associated with an almost uniform increase in seed or grain size, domesticated rice exhibits dramatic phenotypic diversity for grain size and shape. Here we clone and characterize GS3, an evolutionarily important gene controlling grain size in rice. We show that GS3 is highly expressed in young panicles in both short- and long-grained varieties but is not expressed in leaves or panicles after flowering, and we use genetic transformation to demonstrate that the dominant allele for short grain complements the long-grain phenotype. An association study revealed that a C to A mutation in the second exon of GS3 (A allele) was associated with enhanced grain length in Oryza sativa but was absent from other Oryza species. Linkage disequilibrium (LD) was elevated and there was a 95.7% reduction in nucleotide diversity (theta(pi)) across the gene in accessions carrying the A allele, suggesting positive selection for long grain. Haplotype analysis traced the origin of the long-grain allele to a Japonica-like ancestor and demonstrated introgression into the Indica gene pool. This study indicates a critical role for GS3 in defining the seed morphologies of modern subpopulations of O. sativa and enhances the potential for genetic manipulation of grain size in rice.

Natural variation of rice strigolactone biosynthesis is associated with the deletion of two MAX1 orthologs

“…The fact that the Indica low-SL allele is present in ∼33% of the tropical japonica varieties in the Diversity Panel is consistent with introgression from indica and aus varieties into tropical japonica varieties growing sympatrically in tropical environments. This pattern of allele divergence and introgression in Oryza sativa has been documented in other studies (31)(32)(33)(34). SLs regulate overall plant architecture.…”

Linking differential domain functions of the GS3 protein to natural variation of grain size in rice

“…The predicted protein of Zhenshan 97, whose coding region was identical to Guangluai 4, was 231 aa in length. Relative to Zhenshan 97, Minghui 63 had a C→A substitution at 165 bp downstream from the predicted translation start site (ATG), causing premature termination of the predicted protein and resulting in long grain, which was also observed in several studies (8,22,23). Chuan 7 had a 1-bp deletion at 357 bp (C) downstream from the predicted translation start site, which caused a frameshift mutation in the C terminus that yielded a truncated 149-aa protein (Fig.…”

“…It was neither found with additional sequences of 60 accessions of Oryza rufipogon and Oryza nivara from Bangladesh, China, India and Myanmar, Nepal, Sri Lanka, and Thailand, nor observed among the 54 diverse accessions published previously (22). Database searching of the predicted polypeptide sequence of the frameshift C terminus found no match with any conserved motif.…”

“…By comparative sequencing analysis, they found a nonsense mutation in the second exon of the putative GS3 shared among all of the large-grain varieties tested in comparison with varieties with smaller grains. This mutation caused a 178-aa truncation in the C terminus of the predicted protein, which was widespread in the global rice germplasm collections (22,23), indicating that this mutation had an ancient origin and played an important role in grain size variation and domestication of the cultivated rice.…”

A map of rice genome variation reveals the origin of cultivated rice

“…2c). For example, at the causal SNP site for GS3 (a major QTL for grain shape 33,34 ), the null allele mainly existed in the wild rice populations in the Guangxi and Guangdong provinces of southern China. This allele rapidly extended to become the major …”