Diversity and evolution of rice progenitors in Australia

Abstract

In the thousands of years of rice domestication in Asia, many useful genes have been lost from the gene pool. Wild rice is a key source of diversity for domesticated rice. Genome sequencing has suggested that the wild rice populations in northern Australia may include novel taxa, within the AA genome group of close (interfertile) wild relatives of domesticated rice that have evolved independently due to geographic separation and been isolated from the loss of diversity associated with gene flow from the large populations of domesticated rice in Asia. Australian wild rice was collected from 27 sites from Townsville to the northern tip of Cape York. Whole chloroplast genome sequences and 4,555 nuclear gene sequences (more than 8 Mbp) were used to explore genetic relationships between these populations and other wild and domesticated rices. Analysis of the chloroplast and nuclear data showed 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. Nuclear genome analysis demonstrated that the diverse O. meridionalis populations were sister to all other AA genome taxa while the Australian O. rufipogon‐like populations were associated with the clade that included domesticated rice. 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.

Genetic diversity of Australian wild rice

“…These variants seem to reflect the heterozygous nature of these plants ( Figure 13). This suggests that they have resulted from hybridisation between these populations in agreement with our overall analysis of the nuclear genes (Moner et al, 2018). Figure 45 -57).…”

“…Intermediate location of those accessions (WR-65 and WR-44) and jumping between clades across all starch related genes was interesting ( Figure 12, 13 and Figure 45-57). Read alignment showed two types of reads that are unlikely to be an error and gave strong evidence of hybridisation between Australian wild rice populations taxa A and B (Moner et al, 2018).…”

“…Later studies (Brozynska et al, 2014b;Brozynska et al, 2017;Moner et al, 2018;Wambugu et al, 2015) using NGS data on both the chloroplast and nuclear levels showed the unique characterisation of the Australian wild rice (Figure 2 andFigure 3). The importance of these taxa lies in their having been found in remote areas geographically and far from human intervention and cross pollination with domesticated rice, which kept them as pure as ancient wild rice.…”

Molecular and Morphological Divergence of Australian Wild Rice

“…This showed that the cp genome of Australian O. rufipogon, Jpn1 (taxon A) has a closer relationship to O. meridionalis than to Asian O. rufipogon, although its nuclear type tended to show higher similarity to Asian O. rufipogon. Another perennial species, Jpn2 (taxon B), also shared similarity not only with the cp genome to O. meridionalis but also the nuclear type [14,17,18]. This analysis showed that all Australian wild rice shared some cp genetic similarity with O. meridionalis.…”

Genetic diversity among perennial wild rice Oryza rufipogon Griff., in the Mekong Delta

“…The wild species of genus Oryza is regarded as valuable resource for rice improvement because of its high genetic diversity (Brar, ; Sun, Wang, Li, Yoshimura, & Iwata, ). Application of wild rice to breeding programs can facilitate adaptation to climate change and meet the demand for food security in the face of rapid world population growth (Henry, ; Henry et al, ; Mickelbart, Hasegawa, & Bailey‐Serres, ; Moner et al, ).In this context, Oryza rufipogon and its relatives can provide a rich repository of genes and alleles for potential utilization in rice improvement with the help of genomics‐assisted breeding. Such studies can provide specific insight into natural genetic resources that can be preserved and utilized efficiently.…”