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Genetically modified tomato puree, which will be available in Safeway and Sainsbury stores, has been produced from fruit which has had the rotting gene removed.
It means the tomatoes remain firmer and last longer than conventionally-grown ones and the puree they produce is subsequently cheaper.
However, supermarket giant Tesco said it would not be stocking the GM puree because the new product did not offer any additional benefits to customers compared to normal puree.
The GM puree has been produced by bioscience company Zeneca, which says the product has a stronger taste and sticks better to pasta than conventional sauces.
The product has taken 10 years to develop from research into the walls of plant cells.
The new tomatoes have been modified to respond in a selective way to a colourless gas, ethylene, which triggers both ripening and rotting processes in fruits.
Fruit importers have used ethylene for 50 years to ensure a regular supply of tropical fruits to Britain. They are picked unripe and then ripened here by exposure to the gas.
However, ethylene also triggers the natural processes which allow plants to shed their leaves and petals and can also start a tomato's decay by activating fungal spores on its surface.
Ripe fruit give off their own ethylene and by modifying them to stop producing it, scientists have found they can delay the rotting process.
Zeneca's Nigel Poole said: "Everybody wins; the farmer has a longer window for delivery, there is less mould damage, the tomatoes are easier to transport and they are better for processing."
The processing requires less energy and water, which helps lower the price.
Consumer groups have called for the mandatory labelling of products which are or contain GM products - at the moment labelling is voluntary.
Prince Charles has been outspoken in his criticism of GM foods. Speaking to an audience of scientists and conservationsists in December he said the implications of some GM crops were "enough to send a cold chill down the spine".
Some critics have dubbed the modified products "Frankenstein foods" and have warned of a consumer boycott.
Opposition to GM foods has remained strong. Critics say the possible health risks are still unknown.
Supporters say GM crops produce increased yields because they can be made insect and herbicide-resistant, which, in turn, would allow more efficient use of farming land and help solve the problem of world hunger.
In 1999 a small-scale study by Arpad Pusztai claimed the internal organs and immune system of rats fed GM-potatoes were altered. Although the study was later shown to be flawed, it triggered a concerted anti-GM food campaign.
By July 1999 Sainsbury and Safeway had been forced to clear their shelves of the GM tomato puree.
In 2005 a Europe-wide blanket ban on planting GM crops was reaffirmed - despite opposition from British ministers. Labelling of GM foods is strictly controlled and there are very few GM products in the shops.
The Department for Environment, Food and Rural Affairs says it does not expect GM crops to be grown commercially in the UK until at least 2008.
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