Diversity patterns across 1,800 chloroplast genomes of wild (Oryza rufipogonGriff.) and cultivated rice (O. sativaL.)

Cultivated Asian rice (O. sativa L.) comprises several groups with distinct ecological requirements and culinary uses. While the two subspecies of O. sativa – indica and japonica – have been subjected to a multitude of genetic and genomic analyses, less is known about the origins and diversity of the agronomically marginal groups – aus and aromatic rice. Here we reconstructed complete chloroplast genomes of over 1,800 accessions of wild and cultivated rice, including 240 aus and 73 aromatic varieties, and analysed the haplotype diversity of the taxonomic groups. We confirm the deep phylogenetic divergence between the main chloroplast haplotypes of japonica and indica, and reveal unique profiles of chloroplast diversity in aus and aromatic rice. Our results indicate that the latter two groups are not simple derivatives of indica and japonica, respectively, but originated from independent and/or reticulate domestication processes. Absence of phylogeographic patterns in the wild distribution of chloroplast haplogroups did not allow firm conclusions about geographic origins and the role of inter-group gene flow. Nonetheless, our results suggest that the domestication of indica, japonica, aus and aromatic rice operated on genetically different gene pools and followed different dynamics.