Rice gene machine rolls on

It may seem like an odd world to those more interested in the human and animal genetic field, but the humble rice plant must not be underestimated.

Not only does it feed most of the world, but rice can tell us wheat-dependent Australians an enormous amount about other cereals that are crucial to our economy.

Much progress has been made in the field since the completion of the rice and Arabidopsis genome sequences, CSIRO Plant Industry's principal research scientist Dr Narayana Upadhyaya says. Now the task is to understand the functions of the estimated 56,000 genes, just under half of which are thought to be coding.

To discuss the challenges, progress and prospects of this new era in plant science, Upadhyaya has managed to assemble a stellar cast for the workshop he is convening at ISPMB in late August, deep in the wheat belt that is South Australia.

"Plant functional genomics is now a major driving force of change and a great challenge to the scientific community," Upadhyaya says.

"There is so much information in the Arabidopsis area and so much information on rice. Not only are findings important for rice but also for other cereals."

Upadhyaya says rice has been chosen as a model cereal for functional genomics not only because it is a major food crop but also because of its small genome, the ease with which it can be transformed, its well-understood genetics, and because of the existence of great similarities in gene sequence, structure, order and function among all the cereals and grasses.

"It's fine to talk about rice but we have to relate it to other cereals, so that will be one of the talks at the workshop," he says.

Stellar line-up

Confirmed speakers include Takuji Sasaki from Japan's National Institute of Agrobiological Sciences, who will give a short introduction to genome sequencing; Emmanuel Guiderdoni from CIRAD in France will talk about transfer DNA (T-DNA) insertion and mutagenesis as a source for functional genomics; and Upadhyaya himself will speak on transposon insertion and tagging, along with Venkatesan Sundaresan from the University of California, Davis.

"There will also be one talk on gene targeting by homologous recombination by Rei Tarada from Japan; Bal Antonio from RGP Japan will talk on bioinformatics; Alex Johnson from Mark Tester's group at Adelaide (ACPFG) will speak about activation tagging; and Michel Delseny (University of Perpignon) on comparative genomics," he says. "Some of the leading scientists in the world will be there."

In addition to speaking at the workshop, most are contributing a chapter to a book on rice functional genomics that Upadhyaya is editing. It is expected to be published in October by Springer Life Sciences.

Rice functional genomics

Through CSIRO, Upadhyaya is also the Australian representative on the International Rice Functional Genomics Consortium, a voluntary group of international researchers working to make as many resources in the form of mutants publicly available.

"Mutants offer one way to relate a gene to its function," he says. "Using insertional mutants, it is possible to uncover regions of the genome controlling or enhancing the expression of genes determining developmental processes, productivity and quality."

Upadhyaya's team at CSIRO Plant Industry is producing rice insertional mutants as a resource for the functional genomics project. The team is now performing seedling vigour and grain yield trait-targeted insertional mutagenesis using specially designed gene-tagging constructs.

He is also a member of the Australian Genome Alliance, dedicated to raising local awareness in the power of the rice gene machine. The difficulty is, of course, in spreading an understanding of the use of the project to politicians and public alike.

"The idea here is to make rice-growing in Australia more sustainable. We have to have the research projects so that we can address the issues of water efficiency, of cold (rice is really susceptible to cold during flowering) - that's the area we can push. And what we have to do is take the best information about rice and relate it to wheat and barley."