Molecular genetic basis of determining subspecies of ancient rice using the shape of phytoliths

The presence of phytoliths derived from motor cells of rice (Oryza sativa L.) in archaeological sites could provide strong evidence for cultivation of rice in ancient times. The shape of phytoliths is now considered an effective criterion for determining subspecies of ancient rice. To understand the molecular genetic basis of determining subspecies of ancient rice based on the shape of phytoliths, and to analyze the quantitative trait loci (QTLs) controlling the shape of the silica body, which is the predecessor of phytoliths, we used 68 recombination inbred lines (RIL) from progeny of a combination of a cross between japonica variety, Asominori and indica variety, IR24. Knowledge of the positions of QTLs for the shape of the silica body would contribute to the study on the differentiation and evolution of rice at the molecular level. A total of 16 QTLs associated with the shape of the silica body were detected. Of these, five QTLs for vertical length of the silica body were mapped to chromosome 2, 3, 4, 8 (two QTLs) and accounted for 7.1–10.7% of the total phenotypic variation. Six QTLs for the horizontal length were detected on chromosome 1, 2, 3, 4 (two QTLS), 8 and accounted for 8.1–10.7% of the total phenotypic variation. Five QTLs controlling the lateral length on chromosome 1 (two QTLs), 2, 11 (two QTLs) were detected and explained 7.3–8.6% of the phenotypic variation. The genetic linkage relationships between QTLs for the shape of the silica body and taxonomic traits for classifying subspecies of rice showed feasibility of classifying subspecies of rice based on the shape of phytoliths in archaeological sites.