Lorne Genome: True blue genomics

Across the Australian research landscape, small genome projects are pushing their heads above the ground.

Following is a selection of the current and future plans for large-scale genome mapping and sequencing projects in Australia.

Cow

One of the first international genome projects that Australian researchers have been involved in is the Bovine Genome Sequencing Project. One of a number of genomes sponsored by the US NIH's National Human Genome Research Institute (NHGRI), the cow genome was the third major sequencing effort to be put together after the human and the mouse genome, and has been funded by an international public-private consortium including the NHGRI, which contributed US$25 million to the US$53 million project; the US Department of Agriculture; the State of Texas; Genome Canada; Australia's CSIRO Livestock Industries; and, New Zealand's Agritech Investments, Dairy Insight and AgResearch. CSIRO contributed AUD$1.5 million to the project, but has been unable to interest livestock industry groups in providing any funding. The draft sequence of the bovine genome, from the Hereford breed of cattle, was published in September 2004, and the project is scheduled for completion in 2005.

Wallaby

Early in 2003, Australian marsupial genome researchers, led by Prof Jenny Graves at the Canberra-based ARC Special Research Centre for Kangaroo Genomics, resigned themselves to the fact that the NHGRI had chosen the US opossum species for sequencing over an Australian marsupial. It seemed that Australia had missed its chance to be involved in sequencing the genome of a national icon. But following NHGRI chief Francis Collins' visit to the International Congress of Genetics, held in Melbourne in July 2003, the researchers received a ray of hope -- while the US would push forward with its plans to sequence the opossum genome, the NHGRI would match funds raised in Australia in order to obtain a 2 X coverage of the tammar wallaby genome. After a concerted effort to raise the AUD$6 million required for the project to go ahead, led by the AGRF's director Sue Forrest, the Australian group raised $4.5 million from the Victorian government, and a further $1.5 million as in kind support from Applied Biosystems. The project, which will be supported by the Human Genome Sequencing Centre at Baylor College of Medicine headed by expat Australian Richard Gibbs, is expected to take two years to complete.

Sheep blowfly

In November 2004, wool industry group Australian Wool Innovations announced it was providing AUD$1.4 million to a consortium of Australian and New Zealand researchers, led by the University of Melbourne's Phil Batterham, to map the genome of the sheep blowfly Lucilia cuprina, in a bid to better control and prevent flystrike in sheep, a $160 million problem for Australian farmers. While not a full-scale sequencing project, the researchers plan to create BAC libraries and produce a detailed physical map of the genome, and also to sequence around 30,000 ESTs, specifically focusing on life cycle stages crucial to the parasitic life cycle, says Batterham. Microarray studies of gene expression will be performed and transformation technologies will be developed and refined to allow transgenic expression and knockouts of genes of interest. The project is expected to run for three years, and by the end of it Batterham hopes to have a better understanding of what causes the development of insecticide resistance, and to have identified and validated a number of genetic targets for the rational design of new insecticides. According to Batterham, AWI is the first industry group to invest in a genome project designed to target a problem facing its industry. "Hats off to AWI, because they've really shown the way," he says.

Cotton bollworm moth

Batterham is also lobbying for funding for the genome sequencing of the cotton bollworm moth Helicoverpa armigera, a global pest of cotton and other crops that costs Australian farmers alone $225 million annually, and globally costs more than $2 billion. The pest is particularly devastating in China and India, where farmers spend more than half of their annual income on insecticides. And the cotton bollworm is highly resistant to the arsenal of chemicals used against it. As with the sheep blowfly, the initial goals would be to understand the genetic basis of insecticide resistance and identification of suitable genetic targets for rational insecticide design. But Batterham wants to go further than simply generating a BAC library and collection of ESTs, which are already underway in Australia and other locations -- he says the missing piece of the puzzle is the genome sequence. "The genome of Helicoverpa would be quite informative for other moth pests such as the diamond back moth, which is not a big pest in Australia but important overseas," Batterham says. "This would provide a fabulous research infrastructure." At present, Batterham is working with other Australian researchers with an interest in the cotton bollworm genome, and is looking at options to raise funding for the project. "Everyone we've talked to thinks it is important and a good idea, and they want to see a business plan, so we're putting that together now," he says.

Brassica

At the Victorian Department of Primary Industries' Plant Biotechnology Centre (PBC) at La Trobe University, researchers are working to sequence a chromosome from the Brassica rapa A genome as part of the Multinational Brassica Genome Project (MBGP), joining other researchers from the US, Europe, Canada, China and Korea who are working on the other chromosomes. The genome under study, from Brassica rapa (Chinese cabbage), is not the only commercially relevant species in the brassica group, and the consortium hopes the genome sequence will assist in the study and breeding of other brassica crops including canola. According to Dave Edwards, the statewide leader for computational biology and discovery technologies at the PBC, stage one of the project -- the sequencing of the BAC ends -- is almost complete. "It's made easier by the relationship between Brassica and Arabidopsis," he says. "We're collating the data at the moment." In fact, one of the major roles played by the PBC is in bioinformatics, including the development of new tools and the distribution of databases among members of the consortium. The next step will be to start mapping the BACs and the whole genome sequence is expected to be available by the end of 2007. Edwards says the project, which has been supported by funding from the Grains Research and Development Corporation, Horticulture Australia and the Victorian state government, has really raised the profile of both Victoria and Australia as a player in brassica genomics research. And it stands to substantially benefit Australia's canola industry, as well as other brassica crop industries. "Unless we're a player in these things... if we weren't part of the project, we'd be left on the sidelines," he says.

Eucalyptus

Earlier this year, a group of international scientists attending the 2nd Symposium on Eucalyptus Molecular Genetics in Tasmania voted to form a consortium to map and sequence the genome of the southern blue gum, Eucalyptus globulus, a species important as a forestry species in a number of countries. To date, the consortium comprises scientists from several Australian universities, the CSIRO, various government departments and the AGRF, as well as from South Africa, Brazil, France and the USA. A strategy for the project is being formulated and funding sought. But it's still unclear what the scope of Australia's participation will be in the project, or whether it will go overseas.