A Closed Panicle Regulated by OsLG1 was a Selected Trait during Rice Domestication

Prior to the domestication of cereals, hunter-gatherers harvested seeds from their wild relatives. A reduction in seed-shattering degree played a most crucial role in separating the domesticated cereals from their wild ancestors. In rice (Oryza sativa L.), two loci, qSH1 and sh4, have a strong influence on the seed-shattering habit. The wild progenitor O. rufipogon Griff. has functional alleles at both loci that enhance the formation and development of an abscission layer between the pedicel and spikelet. However, the non-shattering phenotype was not obtained through a single non-functional mutation at either locus in the genetic background of wild rice. In this study, we show that a simple morphological change in panicle shape, controlled by the SPR3 locus, had a large impact on seed-shattering and pollinating behavior. In the genetic background of wild rice, we discovered that plants with a cultivated type of closed panicle had significantly reduced seed shattering through seed retention. Additionally, their long awns in closed panicles disturbed free exposure of anthers and stigmas on the flowering spikelets, resulting in a significant reduction of the outcrossing rate. The SPR3 locus was localized in a 9.3-kb genomic region, and a complementation test suggested that this region regulates the liguleless gene (OsLG1). A sequence analysis revealed a selective sweep around the SPR3 genomic region in cultivated rice. These results demonstrate that a closed panicle was a selected trait in the early phase of rice domestication and that rice was destined to become a self-pollinating crop.