001214-12 10.1038/nsu001214-12 14 December 2000 cells & molecules 'Real' plant genomes not far behind DavidAdam David Adam finds out when Ñ and if Ñ the sequencers will conquer grains, beans and pulses.

When it came to sequencing the genome of a plant, Arabidopsis was, for many, an obvious candidate to tackle first: it is small and simple, and biologists have been studying its genes for years. But to some, this anonymous weed will seem a curious choice for such treatment. Arabidopsis provides an excellent blueprint for understanding and even manipulating plant genetics, but it makes lousy porridge and even worse bread. In the words of one cereal crop researcher: "When are we going to sequence a real plant?"

Rice race

But plants don't come more real than rice, the most important food crop in the world, with half the world's population depending on it. And the complete gene sequence of rice should be available in about four years, thanks to an international public collaboration, the International Rice Genome Project (IRGP), launched two years ago.

The ten-nation IRGP, led by Takuji Sasaki of Japan's Ministry of Agriculture, Fisheries and Food, is decoding all twelve chromosomes from a single rice plant. "We are very optimistic that we can finish by the end of 2004," says Sasaki.

At about 400 million base pairs long, the rice genome is some four times larger than that of Arabidopsis, but it is still small for a grass crop. Its manageable size is one reason to sequence it, and its importance as a food another.

Rice is also an inevitable target for private companies hoping to discover and stockpile genes capable of improving the crop. Novartis and DuPont are heavily involved, and Monsanto caught many plant researchers napping when it announced that it had completed a draft sequence of the rice genome earlier this year. Still more were surprised when the company pledged to turn over all of its hard-won data to the public IRGP project.

Monsanto's draft sequence should shave time and money off the IRGP effort, which was originally budgeted at US$200 million. But Monsanto also stands to benefit. Effectively, the public project will finish off the company's work by improving its accuracy and plugging gaps -- the hardest, most time-consuming stage of any sequencing project. "Monsanto will learn a lot more about the rice genome by putting the information in public hands," Burr says. Staple samples

After rice, most interest lies in other staple food crops such as maize (corn) and wheat. But these plants, especially wheat, have complex genomes, which are even larger than the human genome.

Public and private research teams are racing to identify and patent useful genes from these plants, but most believe that only vastly improved technology will bring the full genome sequences of other crops. And it may not happen at all.

"After rice is finished it would be stupid to sequence maize and wheat," says Benjamin Burr, a plant genome researcher at Brookhaven National Laboratory in New York and an IRGP member. Once the rice genome is completed, he says, it should offer enough clues about the workings of crops such as maize as to make further sequencing unnecessary. But others think it is only a matter of time before plants such as maize and barley are sequenced.

Taking a pulse

Elsewhere, local conditions and interests often dictate which plant species researchers choose to investigate. Randy Shoemaker at Iowa State University is leading projects to improve soy bean crops, in part funded by local soy bean farmers. But he does not expect the plant to be fully sequenced. "It's a lot less expensive to sequence model systems, and soy bean is a poor model for other crops," he explains. Researchers at the National Centre for Plant Genome Research in New Delhi, India, are looking for potentially useful genes in their local crop, chickpea.

Meanwhile, Russel Kohel of the US Department of Agriculture and Texas A&M University is studying cotton. He is finding it difficult to get funding because cotton is not a food crop. "We're not even considering sequencing -- that's far too unrealistic," he says. Instead, he is relying on drawing comparisons with the Arabidopsis sequence. "Cotton gets a lot of press because the transgenic Bt and herbicide-resistant plants have been rushed through, but in reality we're lagging way behind other crops," he says.

Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796-815 (2000). Theologis, A. et al. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana. Nature 408, 816-820 (2000). Salanoubat, M. et al. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana. Nature 408, 820-822 (2000). Tabata, S. et al. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana. Nature 408, 823-826 (2000).