Genetic diversity of Australian wild rice

Abstract

Rice (Oryza sativa) is the most important crop in the world. Two thirds of the world population consume rice as main part of their daily diet. Crop wild relatives are essential to provide new genetic resources in order to improve crops to meet food demand and cope with environmental changes. Domestication of rice led to loss of many important genes through application of strong selection for the traits favoured by humans. Australian wild rice has unique features and is found growing in areas isolated from domesticated rice. This avoids the risk of contamination by gene flow from domesticated rice into the wild rice populations as in Asia where wild rice is mixed with cultivated rice in the same areas. These populations retain the genetics of rice prior to domestication.We took the advantage of next generation sequencing to study the Australian and Asian wild relatives of rice. We assembled high quality chloroplast sequences and used them to investigate the phylogeny of these populations, providing more details on the biogeography of the major groups of wild AA genome rices globally. Interestingly, the Australian chloroplast type was distinct from all others and was found to extend north to the Philippines. The groups of Asian wild relatives had substantially overlapping distributions across the area studied. This suggested a complex evolutionary history of the rice progenitors leading to the domestication of rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, Analysis of the chloroplast and nuclear data demonstrated very clear evidence of distinctness from other AA genome Oryza species with significant divergence between Australian populations. Phylogenetic analysis suggested the Australian populations represent the earliest-branching AA genome lineages and may be critical resources for global rice food security. Populations of apparent hybrids between the taxa were also identified suggesting ongoing dynamic evolution of wild rice in Australia. These introgressions model events similar to those likely to have been involved in the domestication of rice.Starch quality and quantity are crucial for rice consumers and the rice industry. Starch properties have been linked directly to impact on human health. Many genes have been involved in determining rice starch properties. The genetic relationship of the starch related genes: ISA2, ISA3, PUL, SBE1, SBE3, SBE4, SSI, SSII-1, SSII-2, SSII-3, SSIII, SSIV and GBSSI in the Australian wild rice populations of Cape York were studied. Many SNPs/FNPs were recorded in the UTRs and exonic regions of these genes that could possibly impact on their expression and function. CDS prediction of the GBSSI gene showed an extra 120bp in some populations. This was due to a change in the predicted splicing site that would lead to intron retention and add 40 amino acid to the predicted protein. It seems that this addition would not affect the active site, however this may explain the differences in starch properties of this taxa reported previously. Australian wild rice populations have potential as a novel source of starch related genes which may help to improve the health of rice consumers.