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Background  The perennial,  Oryza rufipogon  distributed from Asia to Australia and the annual  O. meridionalis  indigenous to Australia are AA genome species in the  Oryza . However, recent research has demonstrated that the Australian AA genome perennial populations have maternal genomes more closely related to those of  O. meridionalis  than to those found in Asian populations of  O. rufipogon  suggesting that the Australian perennials may represent a new distinct gene pool for rice.    Results  Analysis of an  Oryza  core collection covering AA genome species from Asia to Oceania revealed that some Oceania perennials had organellar genomes closely related to that of  O meridionalis  (meridionalis-type).  O. rufipogon  accessions from New Guinea carried either the meridionalis-type or rufirpogon-type (like  O. rufipogon ) organellar genomes. Australian perennials carried only the meridionalis-type organellar genomes when accompanied by the rufipogon-type nuclear genome. New accessions were collected to better characterize the Australian perennials, and their life histories (annual or perennial) were confirmed by field observations. All of the material collected carried only meridionalis-type organellar genomes. However, there were two distinct perennial groups. One of them carried an rufipogon-type nuclear genome similar to the Australian  O. rufipogon  in the core collection and the other carried an meridionalis-type nuclear genome not represented in the existing collection. Morphologically the rufipogon-type shared similarity with Asian  O. rufipogon . The meridionalis-type showed some similarities to  O. meridionalis  such as the short anthers usually characteristic of annual populations. However, the meridionalis-type perennial was readily distinguished from  O. meridionalis  by the presence of a larger lemma and higher number of spikelets.    Conclusion  Analysis of current accessions clearly indicated that there are two distinct types of Australian perennials. Both of them differed genetically from Asian  O. rufipogon . One lineage is closely related to  O. meridionalis  and another to Asian  O. rufipogon . The first was presumed to have evolved by divergence from  O. meridionalis  becoming differentiated as a perennial species in Australia indicating that it represents a new gene pool. The second, apparently derived from Asian  O. rufipogon , possibly arrived in Australia later.

Molecular relationships between Australian annual wild rice, Oryza meridionalis, and two related perennial forms