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Indian hand in squashing tomato genome

New Delhi, May 30: Three Indian laboratories participating in an international research consortium have helped decode the tomato genome sequence, and pinpointed 80 per cent of its estimated 35,000 genes.

Scientists hope to use the genome sequence to understand the evolution of the tomato and to accelerate efforts to develop improved varieties of tomatoes and other related fruits such as apples, bananas, and melons.

A research paper by the International Tomato Genome Consortium with a high-quality genome sequence of a domesticated tomato and a draft sequence of its closest wild relative will appear tomorrow in the journal Nature.

“We now have the genome of the second most important horticultural crop worldwide after the potato, and the genome of one of its closest relatives”, said Giovanni Giuliano, a plant biologist in Rome and the Italian coauthor of the paper. “The tomato belongs to a group of plants called the asterids that represent 25 per cent of all land plants,” Giuliano told The Telegraph.

A team of 24 scientists working here at the National Institute of Plant Genome Research, the Indian Agricultural Research Institute, and the University of Delhi, South Campus, decoded the sequence of one of tomato’s 12 chromosomes.

“We also used a whole genome sequencing technique to cover the entire genome five-times to improve sequencing accuracy and remove gaps,” said Akhilesh Tyagi, the NIPGR director, who coordinated the Indian effort.

The Indian team has also identified nearly 80 per cent of the estimated 35,000 genes that are scattered along the entire tomato genome sequence that has an estimated length of 800-million bases, or genetic alphabets.

The analysis of the tomato genome sequence has revealed that it differs from the genome of the potato by more than eight per cent. Both plants belong to the same family called solanaceae.

“About 500 genes appear to be unique to tomato,” Tyagi told The Telegraph .

The sequence has also shown that the tomato plant experienced a whole-genome triplication sometime between 50 million and 70 million years ago. Triplication is a rare biological event in plants and has also been observed in potatoes. The discovery has allowed scientists to understand the evolution of the tomato plant over millions of years.

“Some of the genes that make the tomato fruit what it is today appeared during this triplication event, but they presumably took control of the fruit only a few million years ago,” Giuliano said. “The red and fleshy tomato fruit appeared a few million years ago in the wild, while its sweetness and large size are due to human domestication,” he said.

Scientists believe the tomato genome sequence could be used to improve tomatoes through molecular breeding. “We could now understand through specific genes why certain varieties are resistant to disease,” Tyagi said.

“The genetic information could be used for breeding improved varieties,” he added

Researchers say the tomato shares genes and biochemical pathways with several fruits such as apples, bananas, melons and strawberries and gene information could be used to improve ripening or other traits of such plants.

“We’ve captured virtually all the genes for any characteristic of the tomato, whether it’s taste, natural pest resistance, or nutritional content,” said John Giovannoni, a biologist at Cornell University in the US, and leader of the US sequencing effort, in a statement issued through the university.

The tomato genome consortium began its work nearly eight years ago and involved scientists from Argentina, Belgium, China, France, Germany, India, Israel, Italy, Japan, the Netherlands, South Korea, Spain, the UK, and the US, among other countries.

Tyagi said what triggered the genome triplication event — evident because some genes occur in three copies — is still unclear. But it happened around the time of the mass extinction that wiped out the dinosaurs

“It is possible the environmental changes may have played a role,” he said..