For years, the life-science companies - Monsanto, Syngenta, Bayer, Pioneer etc - have argued that genetically modified food is the next great scientific revolution in agriculture, and the only efficient and cheap way to feed a growing population in a shrinking world. Non-governmental organisations - including the Foundation on Economic Trends, of which I am president - have been cast as the villains in this agricultural drama, and often categorised as modern versions of the Luddites, accused of continually blocking scientific and technological progress because of our opposition to GM food.

Now, in an ironic twist, new cutting-edge technologies have made gene splicing and transgenic crops obsolete and a serious impediment to scientific progress. The new frontier is called genomics and the new agricultural technology is called marker-assisted selection (MAS). The new technology offers a sophisticated method to greatly accelerate classical breeding. A growing number of scientists believe MAS - which is already being introduced into the market - will eventually replace GM food. Moreover, environmental organisations that oppose GM crops are guardedly supportive of MAS technology.

Rapidly accumulating information about crop genomes is allowing scientists to identify genes associated with traits such as yield, and then scan crop relatives for the presence of those genes. Instead of using molecular splicing techniques to transfer a gene from an unrelated species into the genome of a food crop to increase yield, resist pests or improve nutrition, scientists are now using MAS to locate desired traits in other varieties or wild relatives of a particular food crop, then crossbreeding those plants with the existing commercial varieties to improve the crop. This greatly reduces the risk of environmental harm and potential adverse health effects associated with GM crops. Using MAS, researchers can upgrade classical breeding, and cut by 50% or more the time needed to develop new plant varieties by pinpointing appropriate plant partners at the gamete or seedling stage.

Using MAS, researchers in the Netherlands have developed a new lettuce variety resistant to an aphid that causes reduced and abnormal growth. Researchers at the US department of agriculture have used MAS to develop a strain of rice that is soft on the outside but remains firm on the inside after processing. Scientists in the UK and India have used MAS to develop pearl millet that is tolerant of drought and resistant to mildew. The crop was introduced into the market in India in 2005.

While MAS is emerging as a promising new agricultural technology with broad application, the limits of transgenic technology are becoming increasingly apparent. Most of the transgenic crops introduced into the fields express only two traits, resistance to pests and compatibility with herbicides, and rely on the expression of a single gene - hardly the sweeping agricultural revolution touted by the life-science companies at the beginning of the GM era.

There is still much work to be done in understanding the choreography, for example, between single genetic markers and complex genetic clusters and environmental factors, all of which interact to affect the development of the plant and produce desirable outcomes such as improved yield and drought resistance. Also, it should be noted that MAS is of value to the extent that it is used as part of a broader, agro-ecological approach to farming that integrates new crop introductions with a proper regard for all of the other environmental, economic and social factors that together determine the sustainability of farming.

The wrinkle is that the continued introduction of GM crops could contaminate existing plant varieties, making the new MAS technology more difficult to use. A landmark 2004 survey conducted by the Union of Concerned Scientists found that non-GM seeds from three of America's major agricultural crops - maize, soya beans and oil-seed rape - were already "pervasively contaminated with low levels of DNA sequences originating in genetically engineered varieties of these crops".

Not surprisingly, MAS technology is being looked at with increasing interest within the European Union, where public opposition to GM food has remained resolute. In a recent speech, Stavros Dimas, the EU's environment commissioner, noted that "MAS technology is attracting considerable attention" and said that the EU "should not ignore the use of 'upgraded' conventional varieties as an alternative to GM crops".

As MAS becomes cheaper and easier to use, and as knowledge in genomics becomes more easily available over the next decade, plant breeders around the world will be able to exchange information about best practices and democratise the technology. Already plant breeders are talking about "open source" genomics, envisioning the sharing of genes. The struggle between a younger generation of sustainable-agriculture enthusiasts anxious to share genetic information and entrenched company scientists determined to maintain control over the world's seed stocks through patent protection is likely to be hard-fought, especially in the developing world.

If properly used as part of a much larger systemic and holistic approach to sustainable agricultural development, MAS technology could be the right technology at the right time in history.

· Jeremy Rifkin is the author of The Biotech Century

jrifkin@foet.org