Whole Genome Sequencing of Australian A Genome Wild Rice Reveals Valuable New Alleles for Rice Breeding

Wild crop relatives are a source of variation which is of significant value for crop improvement. Australian A genome wild rice, Oryza rufipogon and O. meridionalis, retain a high level of genetic diversity compared to modern cultivated rice and its wild Asian counterparts due to their geographical isolation in Northern Australia. Australian A genome wild rices were sequenced and analysed for polymorphisms across the genome. High rates of polymorphism were observed in the Australian wild rice with up to 2.5 times the SNP frequency compared to cultivated rice and Asian O. rufipogon. The mean SNPs per kb of genes relative to O. sativa cv. Nipponbare was 8.06 and 7.84 in O. rufipogon and O. meridionalis respectively compared to 2.13 in O. rufipogon from Asia and 2.12 in cultivated rice. The mean number of non-synonymous SNPs per kb of gene sequence was up to three fold higher in the Australian A genome wild rice. An analysis of polymorphisms around genes selected during rice domestication shows the Australian A genome wild rice retains significant variability that could be highly valuable for improvement of rice.