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

Abstract

BackgroundThe 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.ResultsAnalysis 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.ConclusionAnalysis 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.

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

“…(2016)]. Based on the previous finding that Taxon B shares numerous molecular markers with O. meridionalis (Sotowa et al ., 2013) and that they descended from a common ancestor (this study), this genome was evaluated as well. QUAST results showed higher O. meridionalis genome fraction aligning to Taxon B assemblies than Nipponbare genome, 62.4% and 56.3% to hybrid and PacBio, respectively.…”

“…The first individual, referred to here as Taxon A, was collected from Abattoir Swamp Environmental Park near Julatten and was described by Sotowa et al . (2013) as Oryza rufipogon ‐like taxon (r‐type) collected from Jpn1 site. The second individual, referred to here as Taxon B, was collected from a small wetland beside the Peninsula Developmental Road and in Sotowa et al .…”

“…The second individual, referred to here as Taxon B, was collected from a small wetland beside the Peninsula Developmental Road and in Sotowa et al . (2013) was called Oryza meridionalis ‐like (m‐type) taxon collected from Jpn2 site. Specimens of these wild rice populations were collected from their natural habitats and are now kept and maintained in glasshouse conditions at The University of Queensland in Brisbane, Australia.…”

Genomic characterisation of Australian wild rice species

“…The main objectives of having more rice reference sequences are (1) facilitating MAS in breeding programmes, (2) finding new valuable wild alleles with agronomic significance and (3) studying the evolution of the entire genus. (Sotowa et al 2013). Both of them exhibit a perennial life history and belong to the AA genome group.…”

“…Identification of potentially new species was carried out by field observation and molecular analysis and distinction was made based on molecular and morphological traits (Sotowa et al 2013). Taxon A was characterised as perennial wild rice, morphologically similar to…”