Global rice research meets up in Canberra

By Graeme O'Neill
Friday, 15 November, 2002


With its long hours of sunlight, the Murrumbidgee Irrigation Area of NSW produces the highest yields of any rice-growing region in the world, but the water-hungry crop requires around 20 megalitres of water to produce a tonne of rice.

CSIRO Plant Industry molecular geneticist Dr Liz Dennis believes new rice varieties bred for cold tolerance could reduce that figure by 30 per cent, yielding substantial savings for the Murray-Darling system's over-extended water reserves.

Dennis' colleague Dr Narayana Upadhyaya convened a two-day international workshop at the division's headquarters in Canberra this week, titled 'Towards building a global rice gene machine'. The workshop attracted around 30 overseas researchers, from Australia, Japan, France, Korea, Taiwan and Brazil, to review progress in the fast-evolving field of rice functional genomics.

Rice ranks behind wheat and ahead of maize in terms of global production, but is the world's most important human food. A substantial volume of the world's wheat and maize production goes to feeding livestock.

Dennis says that two draft genomes have already been produced for the two main types of rice grown in the world today.

In April this year, the International Rice Research Institute published the first draft genome for Oryza sativa ssp indica, while European life sciences company Syngenta published a draft genome for the japonica subspecies, the main type grown in Japan.

Both will be combined with a complete rice genome sequence being compiled by the public International Rice Genome Sequencing Project (IRGSP), coordinated by the Japan Rice Genome Program, which is expected to be published before year's end.

'Green rat' genes

The function of many rice genes is already known, but most of the estimated 35,000 to 55,000 genes are just anonymous DNA sequences of unknown function -- the massive task of determining what each of these genes actually does in rice is just beginning.

Molecular geneticists hope to have a full catalogue the function of the 15,000 genes in their 'green rat', the tiny cabbage relative Arabidopsis thaliana, by 2010. Dennis believes it could take several decades to do the same for rice, which has a genome some four times larger.

The Canberra workshop was organised to review developments in genetic tools for exploring gene function.

Gene knockout methods are the most common exploration tool for functional plant genomics, says Dennis. They use a various approaches to inactivate genes, and the resulting changes in the plant's appearance or performance provide clues to the inactivated gene's normal function.

The most common way of making knockout varieties has been to introduce mobile DNA elements called retrotransposons into the plant's genetic blueprint. These 'jumping genes' occasionally insert themselves into genes, silencing or otherwise modifying their activity.

Geneticists than look for a gene with an embedded transposon tag -- the transposon serves additionally as a hook that allows molecular geneticists to fish out the affected gene, so its function can be investigated.

The approach is laborious and inefficient because scores to hundreds of transposons may end up scattered across the plant's chromosomes. If multiple genes are silenced, it becomes difficult to determine which gene controls what.

Hairpin technology

CSIRO molecular geneticist Dr Chris Helliwell described to this week's workshop a new, high-throughput technique for targeting and silencing genes in a non-random manner.

Called 'hairpin' technology, it was pioneered by Dr Peter Waterhouse's team. Hairpin gene constructs can be used to target and inactivate any gene in a plant, with great precision -- hairpin genes call also protect plants against viral infections.

Helliwell's team has developed a one-pass technique that copies the RNA recipes of active genes in plant cells and converts them automatically into hairpin molecules, pre-packaged for the standard Agrobacterium gene-delivery system.

Cuttings of the plant are simply dipped in a solution containing the Agrobacterium vector, which inserts the hairpin gene as it infects the plant's cells.

The plants that develop from the transfected cells are knockouts for that specific gene and no other -- hairpin technology is exciting interest among molecular geneticists as potentially the most powerful and precise tool yet developed for exploring gene function in plants.

Dennis says the Canberra workshop was not about rice breeding, but about functional genomics tools. It provided information that geneticists -- both conventional and GM -- can use for their own breeding programs.

Each knockout technique has certain advantages -- the most rapid progress in functional plant genomics will probably come from a combination of old and new techniques, Dennis says.

Cold genetics

Australian rice breeders want to improve the cold tolerance of the varieties grown in the Murrumbidgee Irrigation Area -- growers currently use water as a thermal blanket to protect their crops when temperatures fall below about 18 degrees, which can disrupt flowering and reduce yields.

Even an improvement of a few degrees in chilling tolerance would allow growers to reduce their water use by around 30 per cent, says Dennis.

Australia is also interested in producing varieties with starch composition tailored to various industrial uses.

The Australian rice crop is worth around $800 million a year -- about a fifth the value of wheat -- and most production is exported.

Dennis says there will be spin-off benefits for wheat breedings from functional genomics studies in rice.

Rice has a compact genome that is a 'mini-me' for the monster genomes of wheat, in particular, and maize, which arose through multiple duplications of an ancestral set of genes common to all grasses.

With a genome some 100 times larger than that of rice, wheat is a formidable challenge for functional genomics. But because the genes on rice's chromosomes are arrayed in essentially the same order as in wheat and maize, and there are strong homologies between the genes, what is true of gene function in rice should be informative about the function corresponding genes in other cereal crops.

Australia is a small player in the international rice market, but, Dennis says, "If we do a 10th of the genome, we'll get 100 per cent back."

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