The average Italian eats 16.5 kilograms of fresh tomatoes a year — the average American consumes even more.

Many of these people will no doubt fondly remember tomatoes as being tastier in years gone by — but nostalgia plays tricks. Over the past five years a European Union collaboration has grown and analysed 7,000 heirloom and modern varieties of tomato and shown that modern tomatoes actually taste better. That is not just a question of subjective perception, either — they contain more of the sugar and acids that make up flavour than the ancestral strains do. And that is all thanks to conventional plant breeders.

The scientists have analysed many more traits in these variants than just taste. They have built up a phenotypic resource that details all the desirable (and undesirable) properties you might want to see in a tomato — from pest-resistance to speed of ripening. The resource will be extremely valuable for those who want to exploit the tomato genome, the sequence of which we publish this week (see page 635). The paper reports the sequences of both the inbred tomato strain Heinz 1706 — generated by the company whose founder Henry Heinz changed the world of tomato ketchup — and its wild ancestor Solanum pimpinellifolium. (Among the many aphorisms ascribed to Heinz is this fitting one: to improve the product in glass or can, you must improve it while it is still in the ground.)

Plant genomes are more challenging to sequence than those of animals because they tend to be larger and more complicated. But at around 900 megabases — just over one-quarter of the size of the human genome — the tomato genome proved manageable. Still, more than 300 scientists from 90 institutes across 14 countries have been slaving away at the task since 2003. It is a fabulous effort that has the potential to radically advance plant science. First, however, the biology behind the genome needs to be understood.

Understanding the basis of tomato genomics is important for three reasons. First, it will help scientists to unravel the extraordinary diversity of the tomato plant, and of the natural world in general. The tomato belongs to one of the planet's most diverse plant genera — Solanum, which includes more than 1,000 species ranging from the potato (Solanum tuberosum) to woody nightshade (Solanum dulcamara). Comparing sequences may help researchers to understand evolutionary processes.

The skills of traditional plant breeders will have to come back into fashion in the world of science.

Second, the tomato genome will teach scientists more about some basic plant mechanisms. It has already revealed, for example, previously unknown genes involved in the molecular pathways that make some tomatoes red. Deep-red tomatoes may be in high demand, but the colour is actually quite unusual in nature, even among tomatoes.

Third, the genome will help scientists and growers to improve the quality of tomatoes. Tomatoes destined for sauces, for example, need to be viscous. Fresh tomatoes must be able to travel distances without bruising or rotting. Farmers would like all tomatoes to be resistant to disease and pests, and to ripen at the same time for convenient harvesting. Attempts in the 1990s to market genetically modified tomatoes with a single improved trait failed, in large part because of the public's fear of 'Frankenfoods'.

It is not necessary to go down the genetic-modification path again, at least for tomatoes. The genome should help plant breeders to make clever crosses between variants with desirable traits. In this way, they should be able to create products that can be firm and disease-resistant without compromising on taste. It is a question of knowing which genes sitting on what part of the genome control which traits — because this helps to avoid undesirable knock-on effects of interbreeding for a particular characteristic. The tomato community has a real start on this with its well-planned phenotype resource.

This means, of course, that the skills of traditional plant breeders — who have a feel for the whole organism — will have to come back into fashion in the world of science. In the past, breeders were the vanguard of plant sciences, just as physiologists — also masters of the whole organism — led work on mammalian biology. But the failure of both fields to understand the molecular elements of the systems they were studying limited their scientific progress. Molecular biology and genomics ousted them from their thrones, but molecular tools now give them an opportunity to make triumphant returns.