Published online 10 December 2008 | Nature | doi:10.1038/news.2008.1294

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Soya genome sequenced

Biofuel potential spurs US consortium to map DNA of nutritious bean.

Dry soya podJGI sequenced the soya bean because of its biodiesel potential.USDA-ARS

The soya bean has been sequenced at last. Glycine max is an important human and animal food crop, rich in oil and protein. But it is as a feedstock for biodiesel — in which vegetable oil is chemically altered to power diesel engines — that it attracted the notice of the US Department of Energy's Joint Genome Institute (JGI) in Walnut Creek, California.

Scientists at JGI and partner institutions released a complete draft of the genome on 8 December at the International Conference on Legume Genomics and Genetics in Puerto Vallarta, Mexico. The sequencing took three years and cost somewhere in the neighbourhood of US$20 million, including all the initial research, the researchers estimate.

Soya lags behind rice, which was sequenced in 20051, but wheat and maize are still to come. The genomes of many crop plants are very large and highly duplicated – which is part of the reason that plant biologists work with simpler genomes like that of thale cress (Arabidopsis thaliana) as models. Many other plant genomes contain the confounding traces of interspecies hybridizations and doubling events, in which the entire genome of the plant is duplicated and the two copies then wander off on separate evolutionary trajectories.

Double trouble

"Soy doubled 10 million or so years ago," says Dan Rokhsar of JGI, one of the project's leaders, "but if you look carefully, you can see at least two other doubling events." The result is that each gene in the genome is likely to have up to three very similar cousins, and this made many plant biologists sceptical that soy could be sequenced using the so-called 'shotgun' approach pioneered by Craig Venter.

In this method, the genome is blasted into fragments each about 700 base pairs long. These are sequenced, and then the whole genome is put back together again, like a puzzle. With all the similar genes floating around, says Rokhsar, "it is as if there are two puzzles very similar that are all mixed up."

Randy Shoemaker, based at the US Department of Agriculture in Iowa, and a team leader on the soya bean project, is now eating his own sceptical words. He was quoted in a 2000 Nature News story predicting that soy would never be sequenced, in part because of its complexity (See 'Real' plant genomes not far behind).

Despite the doubts, "it came together relatively easily" says Gary Stacey of the University of Missouri in Columbia, another team leader. The sequence was checked against previously known soy genes, and according to Rokhsar at least 98% are found in the sequenced genome.

Cash crop

The sequence will be used by both biofuel designers and farmers as a tool for improving soy to their own specifications. "Now we can identify all the genes involved in the oil synthesis in the seed," says Stacey, which should help to boost oil production. And, stresses Rokhsar, boost production efficiently. "Ideally you use no water, no fertilizer, and the lousiest soil possible," he says.

Farmers who grow soya for human or livestock consumption may want to use the genome information to breed higher-yielding plants or varieties with higher protein content.

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The US United Soybean Board, a farmer's group funded by a small tithe on each bushel of soy sold in the United States, funded early work that "caught the eye of JGI", according to Rick Stern, a soya bean farmer from Cream Ridge, New Jersey, and production committee chairman for the board. "Right now it takes 15-20 years to get a new variety; we are hoping to make that five to seven" with the help of the genome.

Markers identifying genes that breeders want can be used to find those plants that contain the genes without having to grow the plant to maturity. Or biotechnology can slot hot genes straight into plant cells.

Soya bean is grown on about 95 million hectares around the world, principally in the Americas, although it originates in Asia. Production of soya has increased more than 200% over the past 30 years, according to the Paris-based European Association for Grain Legume Research. 

  • References

    1. International Rice Genome Sequencing Project Nature 436, 793–800 doi:10.1038/nature03895 (2005).
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