Search Results (10)

The domestication syndrome is defined as a collection of domestication-related traits that have undergone permanent genetic changes during the domestication of cereals. Australian wild rice populations have not been exposed to gene flow from domesticated rice populations. A high level of natural variation of the sequences at domestication loci (e.g., seed shattering, awn development, and grain size) was found in Australian AA genome wild rice from the primary gene pool of rice. This natural variation is much higher than that found in Asian cultivated rice and wild Asian rice populations. The Australian Oryza meridionalis populations exhibit a high level of homozygous polymorphisms relative to domesticated rice, inferring the fixation of distinct wild and domesticated alleles. Alleles of the seed shattering genes (SH4/SHA1 and OsSh1/SH1) present in the shattering-prone O. meridionalis populations are likely to be functional, while the dysfunctional alleles of these seed shattering genes are found in domesticated rice. This confirms that unlike Asian wild rice populations, Australian wild rice populations have remained genetically isolated from domesticated rice, retaining pre-domestication alleles in their wild populations that uniquely allow the impact of domestication on the rice genome to be characterized. This study also provides key information about the domestication loci in Australian wild rice populations that will be valuable in the utilization of these genetic resources in crop improvement and de novo domestication. Full article

The composition and nutritional properties of rice are the product of the expression of genes in the developing seed. RNA-Seq was used to investigate the level of gene expression at different stages of seed development in domesticated rice (Oryza sativa ssp. japonica var. Nipponbare) and two Australian wild taxa from the primary gene pool of rice (Oryza meridionalis and Oryza rufipogon type taxa). Transcriptome profiling of all coding sequences in the genome revealed that genes were significantly differentially expressed at different stages of seed development in both wild and domesticated rice. Differentially expressed genes were associated with metabolism, transcriptional regulation, nucleic acid processing, and signal transduction with the highest number of being linked to protein synthesis and starch/sucrose metabolism. The level of gene expression associated with domestication traits, starch and sucrose metabolism, and seed storage proteins were highest at the early stage (5 days post anthesis (DPA)) to the middle stage (15 DPA) and declined late in seed development in both wild and domesticated rice. However, in contrast, black hull colour (Bh4) gene was significantly expressed throughout seed development. A substantial number of novel transcripts (38) corresponding to domestication genes, starch and sucrose metabolism, and seed storage proteins were identified. The patterns of gene expression revealed in this study define the timing of metabolic processes associated with seed development and may be used to explain differences in rice grain quality and nutritional value. Full article

Wild Oryza species are being targeted for commercial cultivation due to their high nutritional grain profile, and their association with Aboriginal people in many regions. Australian wild Oryza species have potential as high-value, low-volume, culturally identified, and nutritious food, especially in gourmet food, tourism, restaurants, and value-added products. However, the basic agronomic protocols for their cultivation as a field crop are unknown. In this review, we identify the major factors supporting the commercial production of wild Oryza, including their stress-tolerant capacity, excellent grain quality attributes, and Indigenous cultural identification of their grains. The key challenges to be faced during the development of a wild rice industry are also discussed which include management barriers, processing issues, undesirable wild traits, and environmental concern. This manuscript proposes the use of agronomic research, in combination with breeding programs, as an overarching framework for the conceptualization and implementation of a successful wild rice industry, using the North American wild rice industry as a case study. The framework also suggests an integrated system that connects producers, industry, and government stakeholders. The suggested procedures for developing a wild rice industry in Australia are also applicable for other wild Oryza species. Full article

Proline has been reported to play an important role in helping plants cope with several stresses, including salinity. This study investigates the relationship between proline accumulation and salt tolerance in an accession of Australian wild rice Oryza australiensis Domin using morphological, physiological, and molecular assessments. Seedlings of O. australiensis wild rice accession JC 2304 and two other cultivated rice Oryza sativa L. cultivars, Nipponbare (salt-sensitive), and Pokkali (salt-tolerant), were screened at 150 mM NaCl for 14 days. The results showed that O. australiensis was able to rapidly accumulate free proline and lower osmotic potential at a very early stage of salt stress compared to cultivated rice. The qRT-PCR result revealed that O. australiensis wild rice JC 2304 activated proline synthesis genes OsP5CS1, OsP5CS2, and OsP5CR and depressed the expression of proline degradation gene OsProDH as early as 1 h after exposure to salinity stress. Wild rice O. australiensis and Pokkali maintained their relative water content and cell membrane integrity during exposure to salinity stress, while the salt-sensitive Nipponbare failed to do so. An analysis of the sodium and potassium contents suggested that O. australiensis wild rice JC 2304 adapted to ionic stress caused by salinity by maintaining a low Na⁺ content and low Na⁺/K⁺ ratio in the shoots and roots. This demonstrates that O. australiensis wild rice may use a rapid accumulation of free proline as a strategy to cope with salinity stress. Full article

Drought often compromises yield in non-irrigated crops such as rainfed rice, imperiling the communities that depend upon it as a primary food source. In this study, two cultivated species (Oryza sativa cv. Nipponbare and Oryza glaberrima cv. CG14) and an endemic, perennial Australian wild species (Oryza australiensis) were grown in soil at 40% field capacity for 7 d (drought). The hypothesis was that the natural tolerance of O. australiensis to erratic water supply would be reflected in a unique proteomic profile. Leaves from droughted plants and well-watered controls were harvested for label-free quantitative shotgun proteomics. Physiological and gene ontology analysis confirmed that O. australiensis responded uniquely to drought, with superior leaf water status and enhanced levels of photosynthetic proteins. Distinctive patterns of protein accumulation in drought were observed across the O. australiensis proteome. Photosynthetic and stress-response proteins were more abundant in drought-affected O. glaberrima than O. sativa, and were further enriched in O. australiensis. In contrast, the level of accumulation of photosynthetic proteins decreased when O. sativa underwent drought, while a narrower range of stress-responsive proteins showed increased levels of accumulation. Distinctive proteomic profiles and the accumulated levels of individual proteins with specific functions in response to drought in O. australiensis indicate the importance of this species as a source of stress tolerance genes. Full article

There are a few wild species belonging to genus Oryza in Australia. Taxon A and Taxon B have been characterized genetically and ecologically. We have backcrossed the Taxon B carrying larger seed size with Japonica type cultivated rice, Taichung 65 (T65). BC4F1 seeds selected the seed size of BC4F2 showed that Taxon B type subgroup carries 21.5% larger seeds size than T65. The heterozygous group showed incomplete dominance in seed size. Introgressed segments suggested that the causal gene could be a single and located on chromosome 3. By using BC4F2, we characterized agronomical traits to show how the large seed size gene affects to yield. The larger seed size did not show any correlation to number of panicles and panicle length. However, it affected negative effect on number of spikelets. It is explained as Trade-off relation. The negative effect will be resolved to introduce genetic factor related to number of tillers or spikelets per panicle, or they may be tried improved ways of cultivation. The seed size is attractive to improve new varieties as “Australian native rice” to be adopted with a variety of cooking style which prefer large grain size or a variety of application of the size. Japanese Sake is another way because it generally requires larger grain size to expect white core. We are generating pure lines carrying only the gene involving to the seed size with other negative traits for cultivation. Full article

Two types of perennial wild rice, Australian Oryza rufipogon and a new taxon Jpn2 have been observed in Australia in addition to the annual species Oryza meridionalis. Jpn2 is distinct owing to its larger spikelet size but shares O. meridionalis-like morphological features including a high density of bristle cells on the awn surface. All the morphological traits resemble O. meridionalis except for the larger spikelet size. Because Jpn2 has distinct cytoplasmic genomes, including the chloroplast (cp), cp insertion/deletion/simple sequence repeats were designed to establish marker systems to distinguish wild rice in Australia in different natural populations. It was shown that the new taxon is distinct from Asian O. rufipogon but instead resembles O. meridionalis. In addition, higher diversity was detected in north-eastern Australia. Reproductive barriers among species and Jpn2 tested by cross-hybridization suggested a unique biological relationship of Jpn2 with other species. Insertions of retrotransposable elements in the Jpn2 genome were extracted from raw reads generated using next-generation sequencing. Jpn2 tended to share insertions with other O. meridionalis accessions and with Australian O. rufipogon accessions in particular cases, but not Asian O. rufipogon except for two insertions. One insertion was restricted to Jpn2 in Australia and shared with some O. rufipogon in Thailand. Full article

Domestication syndrome, i.e. seed shattering, seed dormancy and plant architecture have been selected during the domestication of wild rice around 10,000 years ago. These traits evolved through a series of genomic modifications, including selection of nucleotide polymorphisms resulting from spontaneous mutations, recombination, and fixation of alleles and were incorporated into cultivated rice by hybridization or introgression. The Australian wild rice populations are geographically and genetically distinct and free from genetic exchange with cultivated rice unlike the wild populations in Asia. Furthermore, recent studies reveal they have numerous traits of value and unique alleles. Therefore, these populations seem to be suitable to use to investigate the genetic basis of domestication traits as well as other important traits. In this study, we aim to determine the origin and role of domestication loci using two Australian wild populations: Taxa A (like Oryza rufipogon) and Taxa B (like Oryza meridionalis) endemic near Cairns, Northern Queensland. To do so, firstly, we will analyse the variation of domestication loci in these two wild populations by the comparison with cultivated rice (Oryza sativa spp. japonica cv. Nipponbare) using the whole genome sequencing. Secondly, we will look at the gene expression of the domestication loci at different seed development stages using transcriptomics. Thirdly, we will determine the variation of starch synthesis related genes using whole genome sequencing. Next generation sequencing along with a set of bioinformatics tools will be applied. This research may enlighten our understanding about the domestication process as well as provide insights into how to domesticate these species through genetic manipulation for commercial purpose. Full article

Wild rice relatives having the same AA genome as domesticated rice (Oryza sativa) comprise the primary gene pool for rice genetic improvement. Among them, O. meridionalis and O. rufipogon are found in the northern part of Australia. Three Australian wild rice strains, Jpn1 (O. rufipogon), Jpn2, and W1297 (O. meridionalis), and one cultivated rice cultivar Taichung 65 (T65) were used in this study. A recurrent backcrossing strategy was adopted to produce chromosomal segment substitution lines (CSSLs) carrying chromosomal segments from wild relatives and used for trait evaluation and genetic analysis. The segregation of the DNA marker RM136 locus on chromosome 6 was found to be highly distorted, and a recessive lethal gene causing abortion at the seed developmental stage was shown to be located between two DNA markers, KGC6_10.09 and KGC6_22.19 on chromosome 6 of W1297. We name this gene as SEED DEVELOPMENT 1 (gene symbol: SDV1). O. sativa is thought to share the functional dominant allele Sdv1-s (s for sativa), and O. meridionalis is thought to share the recessive abortive allele sdv1-m (m for meridionalis). Though carrying the sdv1-m allele, the O. meridionalis accessions can self-fertilize and bear seeds. We speculate that the SDV1 gene may have been duplicated before the divergence between O. meridionalis and the other AA genome Oryza species, and that O. meridionalis has lost the function of the SDV1 gene and has kept the function of another putative gene named SDV2. Full article

African para grass (Urochloa mutica) is an invasive weed that has become prevalent across many important freshwater wetlands of the world. In northern Australia, including the World Heritage landscape of Kakadu National Park (KNP), its dense cover can displace ecologically, genetically and culturally significant species, such as the Australian native rice (Oryza spp.). In regions under management for biodiversity conservation para grass is often beyond eradication. However, its targeted control is also necessary to manage and preserve site-specific wetland values. This requires an understanding of para grass spread-patterns and its potential impacts on valuable native vegetation. We apply a multi-scale approach to examine the spatial dynamics and impact of para grass cover across a 181 km² floodplain of KNP. First, we measure the overall displacement of different native vegetation communities across the floodplain from 1986 to 2006. Using high spatial resolution satellite imagery in conjunction with historical aerial-photo mapping, we then measure finer-scale, inter-annual, changes between successive dry seasons from 1990 to 2010 (for a 48 km² focus area); Para grass presence-absence maps from satellite imagery (2002 to 2010) were produced with an object-based machine-learning approach (stochastic gradient boosting). Changes, over time, in mapped para grass areas were then related to maps of depth-habitat and inter-annual fire histories. Para grass invasion and establishment patterns varied greatly in time and space. Wild rice communities were the most frequently invaded, but the establishment and persistence of para grass fluctuated greatly between years, even within previously invaded communities. However, these different patterns were also shown to vary with different depth-habitat and recent fire history. These dynamics have not been previously documented and this understanding presents opportunities for intensive para grass management in areas of high conservation value, such as those occupied by wild rice. Full article