Unveiling The Origin of Sacred Red Rice Preserved in Japanese Shrines

Pericarp color is a key trait selected during rice domestication. Although most modern cultivars have a white pericarp, ancestral rice likely had a red pericarp, as extant wild rice retains this trait and the 14-bp deletion in the Rc gene, which confers white pericarp, is prevalent among modern cultivars. In Japan, several red rice accessions have been preserved in geographically separated shrines for ritual use. Here, we investigated the genomic origin and evolutionary history of the sacred red rice accessions preserved in four shrines across three regions of Japan, together with a red rice landrace from Kokubunji, Tokyo. Genome-wide analyses showed that all the shrine accessions belong to temperate japonica, whereas the Kokubunji landrace is tropical japonica. In addition, we found that the Rc region among all the GJ accessions belongs to a major haplotype cluster regardless of the Rc function, consistent with the reduced genetic diversity surrounding the Rc locus in GJ. Further analyses of the Rc region revealed that three shrine accessions belong to a haplogroup derived from the lineage associated with white pericarp origin, while one accession belong to another haplogroup in the haplotype cluster. The Kokubunji landrace showed introgression in the Rc flanking region. In addition, analyses of heading date-related genes suggest that shrine-preserved red rice retains ancient genetic features and has been minimally influenced by modern breeding. Overall, sacred red rice preserved in Japanese shrines represents a valuable genetic resource that has maintained ancient diversity in temperate japonica over a long period.