Jump to Content

Projects

Cereal Genome Mapping

Sequencing of crop genomes provides deep insights into plant evolution and new tools for crop improvement. The sequencing of giant and repetitive genomes such as wheat and barley can be a challenge which requires worldwide collaborative efforts.

A preliminary step to genome sequencing is the physical mapping, the construction of a scaffold of DNA segments where genes are positioned. Our project is working towards development of a physical map and ultimately a full genome sequence for barley chromosome 7H and wheat chromosomes 7A, 7B and 7D. These chromosomes carry loci controlling important traits including yield, quality, disease resistance and abiotic-stress tolerance. We evaluate the physical distance between markers along these chromosomes, assess their gene content and analyse how the genes recombine between parental lines for breeding of new varieties. Ultimately new genes will be discovered in wheat by shotgun sequencing of isolated chromosome arms using next-generation sequencing technologies.

We also aim to develop computational models describing relationships between genomes of wheat, barley and other cereals. This would enable the use of simpler genomes such as barley to accelerate assembly of the maps in corresponding regions of the more complex wheat genome.

PBRC researchers

Collaborators

top^

Cereal Plant PhenomicsPlant phenomics

The Australian Plant Phenomics Facility (APPF) provides state-of-the-art capabilities for plant phenotyping, offering controlled environments, field-based plant growth monitoring using high throughput robotics, and automated imaging and computing technologies that will generate up to 50 TB of data per year.

We will develop phenotyping software suitable for two vital food crops: wheat and barley.  Datasets will be generated for diverse sets of germplasm covering collections of wild, landrace and cultivated lines in addition to genetic populations, mutant populations, and transgenic lines where particular genes have been silenced or over-expressed. For many of the lines, notably the genetic populations, additional datasets will also be available. These will include data from field trials covering yield and components of yield under a wide range of environmental conditions, maturity, and many other characteristics. In addition to these phenomic datasets, we will obtain transcriptomic and metabolomic datasets.

From the combined datasets, the ultimate objective is to develop models of the plant's response to environmental and developmental stimuli that can be traced back to specific biochemical or molecular events.

PBRC researchers

Collaborators

top^

Enabling High-Resolution Mapping of in vivo Protein-DNA Interactions

Next-generation sequencing technologies are revolutionizing biology and medicine by allowing us to probe genetic structure and function and its effect on disease states at a hitherto unknown level.  In particular, next-generation sequencing technologies permit ChIP-seq—an assay for observing in vivo protein-DNA interactions, which are vital for cellular functions and are involved in the mechanisms for many diseases, including cancer, genetic diseases, and infectious diseases.  Thus, ChIP-seq is an important technology that is likely to have a profound impact on human health and, with the falling cost of sequencing, it is a technology that is likely to become more and more accessible.  There is, however, a barrier to the accessibility of ChIP-seq: bioinformatics tools for analysis of ChIP-seq data are not yet at a stage that would allow them to be widely and easily used by biologists and clinicians for fast, easy, and high-quality analysis.

We aim to develop robust and efficient computational and statistical methods that allow accurate and reliable identification of genomic loci associated with protein-DNA interaction from ChIP-seq data, leading ultimately to a user-friendly computational tool for ChIP-seq analysis that will be distributed for free for non-profit use through the World Wide Web, enabling fast, easy, and high-quality analysis for biologists and clinicians.

PBRC researchers

Collaborators

top^

Making Fuel-Producing Microbes

The production of cheap, clean, renewable energy is one of the world's most pressing problems. And microbes are a potential solution.

Microbes, such as blue-green algae, are capable of taking solar energy and storing it as a chemical fuel, thus allowing us to make use of the solar energy that continually bathes our planet in 10,000-fold abundance to our consumption. In contrast to the traditional solution of photovoltaic cells, solar microbial biofuel does not require expensive batteries for energy storage and, since microbes self-replicate, the capturing apparatus itself is potentially cheaper. Unfortunately, naturally-occurring microbes are not optimised for biofuel production from solar energy and must be engineered for this purpose.

We aim to engineer microbes that are useful for biofuel production using an approach that is grounded in mathematical modelling and computational design. We aim to engineer, in particular, a blue-green algae that converts solar energy and carbon dioxide into petroleum.  Our activities include using and developing flux-balance metabolic models and their extensions, developing efficient algorithms for computational design and optimisation, and constructing engineered strains.

PBRC Researchers

Collaborators

top^