Tomato genome is sequenced

30 May 2012

One of the world's most important crops, the tomato, has had its genome sequenced, scientists report in the journal Nature today.

The Tomato Genome Consortium (TGC) includes more than 300 scientists from 14 countries. Sequencing the genome of the crop Solanum lycopersicum and its closest wild relative Solanum pimpinellifolium allowed them to identify the 35,000 genes of the cultivated tomato, and to show how these differ from its wild progenitor.

Identifying which genes are linked to which characteristics means scientists will be able to focus more accurately on beneficial traits and deliver new tomato varieties more quickly and efficiently. New varieties could include tomatoes with improved taste and higher nutrient concentrations, or those better equipped for combating disease and drought.

Tomato relative benefits

The tomato genome sequence will also help identify beneficial genes in other plant relatives of the tomato, such as potato, pepper and aubergine, the team says. All these crops are members of the Solanaceae or nightshade family, one of the world’s most important vegetable plant families in terms of both economic value and production volume.

Food security

Developing better tomatoes will also contribute to the quest for global food security, the team says.

As well as using this new genome information to develop a wider variety of beneficial traits, scientists can also investigate more deeply the processes by which humans have been able to domesticate some plants and not others.

Dr Sandra Knapp, botanist at the Natural History Museum who worked with the genome sequencing research, explains, 'Knowledge of the tomato genome could perhaps one day help us to domesticate and use more than just the very few plant species upon which we depend for food'.

Globally, humans rely on fewer than 10 species of flowering plants for about 80% of their caloric intake, Knapp says. 'More detailed knowledge of how people have changed plant species like the tomato through domestication and breeding will directly address the pressing problems of food security humankind faces.'

Chromosome number 4

The UK contribution to the project began with a focus on chromosome 4, one of the tomato's 12 chromosomes.

The UK team produced high quality sequences, which set the standard for other chromosomes being sequenced around the world.

Thanks to international collaboration and the adoption of new technologies the final assembled sequence is of outstanding quality and coverage making it a powerful and readily accessible tool for crop improvement says the team.

Other genetic clues

The tomato sequence research will also reveal insights into how the tomato and its relatives have diversified and adapted to new environments as they have evolved.

They show that the genome of the group to which the tomato belongs expanded abruptly about 60 million years ago by doubling. Subsequently, much of this genetic redundancy created by the doubling was lost, but some genes remained and were used for new functions by the plant.

Some of the genes generated during that expansion were involved in the development and control of the ripening process. Understanding the process of fruit ripening is important because it influences the health promoting properties of fruits like the tomato.

Other crop genomes

The tomato now joins other crop plants with genome sequences available for plant researchers, including rice, maize, sorghum, poplar, potato, soybean, strawberry, cucumber and grape.

 

The UK effort was led by Imperial College London and the University of Nottingham in collaboration with The Genome Analysis Centre, the James Hutton Institute, the University of East Anglia (UEA) and the Natural History Museum. The project was funded in the UK by the Biotechnology and Biological Sciences Research Council (BBSRC), Defra and the Scottish Government and the sequencing was undertaken by the Wellcome Trust Sanger Institute.

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