CSIRO scientists isolate semi-dwarfing rice gene

Researchers at CSIRO Plant Industry have used the publicly available rice genome sequence to isolate the semi-dwarfing gene in varieties responsible for the 'green revolution' and develop 'perfect' markers for it.

The results, published in the Proceedings of the National Academy of Science, will speed up the breeding of new rice varieties as well as other cereals, said team leader and co-author of the paper, Dr Wolfgang Spielmeyer.

Spielmeyer explained that the approach combined previous mapping studies, which had localised the semi-dwarfing trait to a specific chromosomal region, with sequence information obtained from the Japanese consortium's International Rice Genome Sequencing Project, to identify the semi-dwarfing gene sd-1.

"Conventional methodologies usually take a lot more time and effort. With the rice genome sequence in front of you, you can essentially walk through it," he said.

The scientists also had a good idea of what they were looking for - a fault in a gene involved in the synthesis or metabolism of gibberellins, a major plant hormone deficient in semi-dwarfed plant varieties.

"We focused our search for sd-1 on the genes involved in gibberellins production that were located within the previously identified region. That's when we found that the sd-1 gene was defective, restricting the synthesis of gibberellins, creating a semi-dwarf rice plant," said Spielmeyer.

"It's a great example of how information from the publicly available rice genome sequence can be used to isolate genes that are important to agriculture."

The sd-1 gene discovered by the team has been used to design a 'perfect' marker, one that is specific to the gene sequence. Now the marker can be used for marker assisted breeding programs, which Spielmeyer says will speed up rice breeding programs.

Spielmeyer and his group are also using the rice sd-1 gene to search for the equivalent gene in other cereal plants, the main goal of their project.

"Although the information is important for rice breeders, the real focus for our work is to look at similar genes in wheat. The Australian wheat industry is very interested in these kinds of genes, which play a critical role in wheat production," he said.

"The rice genome gives us enough data to start fishing through the wheat genome. We need to tie the data together between gene markers discovered using the rice gene and finding semi-dwarfing genes."

He said that the group hoped to have concrete data within the next 12 months.

"The rice work is a wonderful stepping stone," Spielmeyer said. "We are increasingly utilising the rice genome as a halfway house to understanding wheat. It's a really wonderful resource."

The CSIRO researchers are using the same approach to look for other important genes, such as those involved in transpiration efficiency.

While Spielmeyer said that the sd-1 gene and its associated markers would remain in the public domain, it would be a different story for wheat genes discovered by the group, as wheat breeding is a commercial business both in Australia and overseas.

The project has been funded by Graingene, a strategic alliance between CSIRO, the Australian Wheat Board and the Grains Research and Development Corporation.

• For more information see the PNAS paper: Wolfgang Spielmeyer, Marc H Ellis, and Peter M Chandler. Semidwarf (sd-1), 'green revolution' rice, contains a defective gibberellin 20-oxidase gene PNAS 2002 99: 9043-9048