The dark pigment, known as anthocyanin, is intended to give tomatoes the same potential health benefits as fruit such as blueberries.
Anthocyanin is an antioxidant which studies on animals show could help fight cancer.
Scientists say the new tomatoes, first developed in Britain, could improve the nutritional value of everything from ketchup to pizza topping.
The tomatoes were developed at the John Innes Centre in Norwich where Prof. Cathie Martin hopes the first delivery of large quantities of juice will allow researchers to investigate its potential.
They are part of a new generation of GM plants designed to appeal to consumers – the first types were aimed specifically at farmers as new tools in agriculture.
The purple pigment is the result of the transfer of a gene from a snapdragon plant – the modification triggers a process within the tomato plant allowing the anthocyanin to develop.
Although the invention is British, Prof. Cathie Martin says EU restrictions on GM encouraged her to look abroad to develop the technology.
Canadian regulations are seen as more supportive of GM and that led to a deal with an Ontario company, New Energy Farms, which is now producing enough purple tomatoes in a 5,000sq ft greenhouse to make 440 gallons of juice.
The first 1,200 litres are due to be shipped to Norwich shortly – and because all the seeds will have been removed, there is no genetic material to risk any contamination.
The aim is to use the juice in research to conduct a wide range of tests including examining whether the anthocyanin has positive effects on humans. Earlier studies show benefits as an anti-inflammatory and in slowing cancers in mice.
A key question is whether a GM product that may have health benefits will influence public opinion.
A major survey across the EU in 2010 found opponents outnumbered supporters by roughly three to one. The last approval for a GM food crop in the EU came in 1998.
Prof. Cathie Martin hopes that the purple tomato juice will have a good chance of being approved for sale to consumers in North America in as little as two years’ time.
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