The rice genus, Oryza (Poaceae), comprises 23 species and nine recognized genome types. Clarification of phylogenetic relationships of rice genomes is critical for effective utilization of the wild rice germplasm. By generating and comparing two nuclear genes (Adh1 and Adh2) trees as well as a chloroplast gene (matK) tree of all rice species, phylogenetic relationships among the rice genomes were inferred. Origins of the allotetraploid species, which constitute more than one third of rice species diversity, were reconstructed based on the Adh gene phylogenies. Genome types of the maternal parents of allotetraploid species were determined based on the matK gene tree. The phylogenetic reconstruction largely supports the previous recognition of rice genomes. It further revealed that the EE genome species is most closely related to the DD genome progenitor that gave rise to the CCDD genome. Three species of the CCDD genome may have originated through a single hybridization event and their maternal parent had the CC genome. The BBCC genome species had different origins and their maternal parents had either a BB or CC genome. A new genome type, HHKK, was recognized for O. schlechteri and Porteresia coarctata, suggesting that P. coarctata is an Oryza species. Phylogenetic relationship of the AA genome, which contains cultivated rice, is further investigated with additional nuclear gene markers.

Key words: allotetraploid, genome, nuclear gene, Oryza, poaceae, rice