A de novo evolved gene contributes to rice grain shape difference between indica and japonica

Genome-wide association study

We carried out GWAS for grain shape using the panel of both indica and japonica varieties, which were obtained from the germplasm band or breeders in central China. We rephenotyped the grain shape-related traits, such as grain length (GL) and grain width (GW) of 289 rice varieties, including 158 japonica varieties genotyped previously²³ and 131 indica resequencing varieties. Tremendous variation in GL and GW was observed in these 289 rice varieties. A total of 2,269,131 single-nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) ≥ 0.01…