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.
Highlights
The Oryza genus has two cultivated species and about 21 wild relatives and based on chromosome paring, these Oryza species are divided into 10 genome types namely AA, BB, CC, BBCC, EE, FF, GG, CCDD, HHJJ and HHKK1
The resultant phylogenetic tree had two main distinct clades where the primary division was into a clade including O. glumaepatula and O. longistaminata which formed the basal clade and one containing all the other species
This study shows that the basal clade consists of O. longistaminata and O. glumaepatula which are found in Africa and South America respectively
Summary
Be attributed to a relatively rapid diversification of the AA genome, differential choice of genes, use of insufficient data, incomplete lineage sorting, misidentification of accessions and introgression. This study shows that the basal clade consists of O. longistaminata and O. glumaepatula which are found in Africa and South America respectively This divergence could be as a result of long distance dispersal through movement of animals especially birds, followed by ecological differentiation. Though chloroplast genomes may have particular advantages in resolving phylogenetic relationships, Middleton et al.[17], noted that their use in divergence dating may be problematic especially in species with short evolutionary times. This is due to the fact that presence of multiple chloroplast haplotypes may not correspond with species divergence since they may have diverged long before actual species divergence.
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