Rice genome: very early days
Two draft sequences of the genome for rice, one of the most important food staples in the world, were published today. If the numbers are right, a rice plant might have more genes than a human.
Today's issue of Science publishes Oryza sativa genomes by two separate teams one led by Dr Jun Yu of the Chinese Academy of Sciences, and the other by Stephen A. Goff of Swiss-based agribusiness company Syngenta.
Yu and colleagues estimate rice has 46,000 to 55,600 genes whereas Goff and colleagues estimate 32,000 to 50,000. The human genome is estimated to have between 30,000 and 40,000 genes.
But at this stage, the figures are rubbery.
"I wouldn't take the numbers too strictly," commented Dr Liz Dennis of CSIRO's Division of Plant Industry, director of the New South Wales Centre for Agricultural Genomics.
"These are huge ranges and there is more than 50 per cent error in them."
Yu and colleagues acknowledge the computer program they used was not trained to recognise rice genes specifically, and it is possible that that it may have counted some genes twice.
Estimates for the human genome may need to be revised upwards too, argued Dennis, because some human genes seemed to have more than one protein product whereas there is no widespread evidence of this phenomenon in plants.
"I think that the number of genes in rice will end up being in the same order as humans," she said.
Where does that leave mere humans? Aren't we supposed to be the head of the evolutionary tree and thus have the most complex genome? Dennis suspects there might be just a touch of anthropocentrism here.
"We don't photosynthesise, and we can run away from adverse circumstances whereas plants have to stay and adapt to the situation," she said.
In fact most plants including rice have tremendous duplication of genes which scientists think may be a sign that plants copy their genes and then modify them as a strategy for coping with selective pressures.
Scientists hope the genomic information will ultimately boost the productivity of grain crops. This is the first cereal genome to be sequenced, and is a model for other cereals which have the same genes in the same order.
The advantage of the rice genome, Dennis pointed out, is that it is the smallest of the cereal genomes and is therefore easier to work with.
The genomes of other cereals contain much more non-gene DNA, often called 'junk' DNA. Only 50 per cent of the rice genome is non-gene DNA, whereas 'junk' makes up 95 per cent of the human genome.
Rice shares about 20 per cent of its genes with other organisms, and 30 per cent with other plants. Fifty per cent of rice genes are apparently unique to cereals.
Dennis said the next step is to focus on the function of the genes what proteins they produce and how they are controlled.
"We have the dictionary, now we need to find out the meaning."
Genes perform differently in different contexts, according to factors such as what genes they are next to, interaction with environmental factors, and possibly even interaction with 'junk' DNA.
It is possible, acknowledged Dennis, that we've written off such non-gene DNA as 'junk' far too soon.
Restrictions on Syngenta data
Yu and colleagues, who sequenced the genome for the O. sativa indica subspecies commonly grown in China, have made their data fully available on the publicly searchable GenBank database.
Goff's team's work, however, on the japonica subspecies, will remain on the Syngenta website with certain restrictions on its use by researchers.
Twenty genome researchers, including two Nobel Prize winners, have complained about the restrictions.
Dennis said she unsure whether CSIRO would be restricted in its use of Syngenta's data, but the availability of the Chinese data may mean they don't have to rely on it.
The ETC Group (formerly RAFI) which campaigns on agricultural issues, argues Syngenta's actions are unacceptable.
"Any attempt to privatise the genetic blueprint of the world's most important food crop is a threat to food security especially for poor farmers and consumers in Asia," said Director, Hope Shand.
"Syngenta says that it will make data available to the academic community through 'collaboration agreements'. This doesn't sound so bad. But the reality is that material transfer agreements (contracts) could be used to give Syngenta first rights to any commercial results and/or prohibit the sharing of resulting materials with third parties."
The group plans to award Syngenta a "Captain Hook Award" for biopiracy and anti-food security at the United Nations Convention on Biological Diversity meeting next week in The Hague.