Chloroplast genome sequence indicates Australian wild rice represents a source of diversity for rice improvement

Rice (Oryza sativa Japonica) was probably domesticated from wild populations of Oryza rufipogon in Asia. Relative to cultivated rice, O. meridionalis, from Australia is the most genetically distant Oryza species with an A genome (some level of inter breeding with O. sativa is possible) O. rufipogon and O. meridionalis are found in widespread populations across northern Australia. Massively parallel sequencing was used to determine the sequence of the chloroplast genomes of O. rufipogon from Asia and Australia and O. meridionalis and O. australiensis (a very distant member of the genus) from Australia and to compare them with the chloroplast genome sequence of domesticated rice. O. australiensis differed in more than 850 places (SNP or indel) from each of the other samples. The other wild rices had only around 100 differences relative to cultivated rice. O. meridionalis and O. rufipogon in Australia had closely related chloroplast genomes with only 32 differences. The Asian O. rufipogon chloroplast was much closer to that of O. sativa with only 68 differences. The chloroplast sequences emphasize the genetic distinctness of the Australian populations and their potential value as a source of novel germplasm for rice.