Relationships of wild and domesticated rices (Oryza AA genome species) based upon whole chloroplast genome sequences

Abstract

Rice is the most important crop in the world, acting as the staple food for over half of the world’s population. The evolutionary relationships of cultivated rice and its wild relatives have remained contentious and inconclusive. Here we report on the use of whole chloroplast sequences to elucidate the evolutionary and phylogenetic relationships in the AA genome Oryza species, representing the primary gene pool of rice. This is the first study that has produced a well resolved and strongly supported phylogeny of the AA genome species. The pan tropical distribution of these rice relatives was found to be explained by long distance dispersal within the last million years. The analysis resulted in a clustering pattern that showed strong geographical differentiation. The species were defined in two primary clades with a South American/African clade with two species, O glumaepatula and O longistaminata, distinguished from all other species. The largest clade was comprised of an Australian clade including newly identified taxa and the African and Asian clades. This refined knowledge of the relationships between cultivated rice and the related wild species provides a strong foundation for more targeted use of wild genetic resources in rice improvement and efforts to ensure their conservation.

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

“…Given this root age, the A genome group diverged in the last 3 million years and the divergence of the japonica and indica clades dated at about 990 000 years ago (Figure 3). The chloroplast genomes appear to have diverged more recently (Wambugu et al ., 2015) possibly due to some degree to the sharing of maternal genomes across this group.…”

“…Figure adapted and modified from Wambugu et al . (2015). Taxa marked in green represent Asian rice species, in blue: African, in orange: South American and in red: Australian.…”

Genomic characterisation of Australian wild rice species

“…This approach proved to be valid for phylogeny of closely related species and was subsequently used to resolve the entire AA genome rice species tree with addition of African and South American species (Wambugu et al 2015). …”

“…The wild relatives of rice provide a gene pool that allows for the expansion of diversity (Krishnan et al 2014) An understanding of genetic relationships and diversity between and within these Asian and Australian populations will guide the effective use of wild genetic resources for global rice improvement. The phylogenetic relationships between all of the A genome taxa have recently been estimated using whole chloroplast genome sequences Wambugu et al 2015). In this phylogeny the Australian A genome taxa form a distinct clade, which is a sister to the Asian domesticated rice clade ( Figure 5.2A).…”

“…The phylogeny of the Oryza genome groups has been widely studied and is now well known (Ammiraju et al 2010a;Ge et al 1999;Lu et al 2009). The relationships between the most recently diverged A genome diploids, that include domesticated rice, has been more challenging and only lately has their phylogeny been more fully described, using both chloroplast (Wambugu et al 2015) and nuclear genomes (Stein et al, personal communication).…”