Molecular and Morphological Divergence of Australian Wild Rice

A large deletion within intron 20 sequence of single-copy PolA1 gene as a useful marker for the speciation in Oryza AA-genome species

Oryza AA-genome complex comprises five wild species, O. rufipogon, O. barthii, O. longistaminata, O. glumaepatula, and O. meridionalis. Evolutionary relationships among these five wild species have remained contentious and inconclusive. We found that intron 20 of PolA1, a single-copy nuclear gene, was short (S-type: 141-142 bp) in O. rufipogon, O. barthii, and O. glumaepatula, while long (L-type: ca. 1.5 kb) introns were apparent in O. longistaminata and O. meridionalis. Because Oryza species containing BB, CC, EE, FF, and GG genome showed L-type introns, the S-type intron was probably derived from the L-type intron by the deletion of a 1.4 kb fragment through intramolecular homologous recombination between two tandem TTTTGC repeats. Excluding the large deletion sequence, intron 20 sequence of O. barthii was identical to that of O. longistaminata. As more than 3,470 accessions of O. rufipogon and O. sativa also contained the same intron 20 sequence with O. longistaminata except for single T-nucleotide deletion, which was shared with O. glumaepatuala, the deletion of the T-nucleotide probably occurred in the L-type intron 20 of O. logistaminata. Deletions of a large 1.4 kb fragment and single T-nucleotide within the intron 20 of PolA1 gene were considered as useful DNA markers to study the evolutionary relationships among Oryza AA-genome species.

New Hybrid Spikelet Sterility Gene Found in Interspecific Cross between Oryza sativa and O. meridionalis

Various kinds of reproductive barriers have been reported in intraspecific and interspecific crosses between the AA genome Oryza species, to which Asian rice (O. sativa) and African rice (O. glaberrima) belong. A hybrid seed sterility phenomenon was found in the progeny of the cross between O. sativa and O. meridionalis, which is found in Northern Australia and Indonesia and has diverged from the other AA genome species. This phenomenon could be explained by an egg-killer model. Linkage analysis using DNA markers showed that the causal gene was located on the distal end of chromosome 1. Because no known egg-killer gene was located in that chromosomal region, this gene was named HYBRID SPIKELET STERILITY 57 (abbreviated form, S57). In heterozygotes, the eggs carrying the sativa allele are killed, causing semi-sterility. This killer system works incompletely: some eggs carrying the sativa allele survive and can be fertilized. The distribution of alleles in wild populations of O. meridionalis was discussed from the perspective of genetic differentiation of populations.