The size, shape, skin thickness, color and taste of tomatoes are all traits determined by their genes. Now, scientists from 14 nations, including the U.S., have sequenced the tomato genome ¿ the order and location of the tomato's 35,000 genes. "Science Behind the News" is produced in partnership with the National Science Foundation.
Science Behind the News- Tomato-DECODED
ANNE THOMPSON, reporting:
It was a mystery that took genetics 'detectives' from 14 nations to solve-decoding the tomato genome, the sequence and location of each of its 35,000 genes. Yes, the tomato is, botanically, a fruit, grown or imported by almost every nation and culture on Earth. Tomatoes are a $40 billion annual industry worldwide, and a $2 billion a year crop in the US. Genes determine what traits all these tomatoes have, and over time there’s been something of a split between commercial tomato sellers and the average tomato buyer over what those traits should be.
JIM GIOVANNONI (USDA-ARS, Boyce Thompson Institute): Breeders have selected for traits that will give long shelf life, long storability and firmness, all important for shipping a tomato, say, across the country or half way around the world.
THOMPSON: Traits like thick skins and delayed ripening, so tomatoes can be picked green, often trucked by the ton to warehouses, where they might sit for days or weeks before being treated with ethylene, a natural gas, to turn them a uniform bright red – which doesn’t always mean fully ripe, or tasty.
GIOVANNI: The question I always get is “where’s the flavor gone?” Anyone who’s grown a tomato knows that tomato could taste much better.
THOMPSON: How to make a tomato that ships and stores well, but still tastes vine-ripened? Or make tomato plants, say, more naturally resistant to disease, or able to grow in a greater range of climates, with less water? With plant breeding, which even now is done pretty much the way the Aztecs, early cultivators of the tomato, did it.
BRUCE ROE (University of Oklahoma): You take this plant and you take another plant next to it and you shake the pollen from this plant on to another plant, that’s a slightly different variety. How many genes are you transferring from this plant to the other one? Are they going to do harm Are they going to do good?
GIOVANNI: Working without a genome sequence is working somewhat blind.
THOMPSON: Wait, let’s hit pause here. What is a genome?
ROE: That’s the information that’s going to make that tomato plant a tomato plant.
THOMPSON: The tomato has 12 chromosomes. So, think of a 12 volume set of books, and inside each of those chromosome books is a sequence of DNA, short for deoxyribonucleic acid (that’s a minimum of 33 points in Scrabble, by the way), a sequence written with genetic code, using an alphabet of four molecules. To crack that code, the 14 nations of the International Tomato Genome Sequencing Consortium, split up the task. In the US, specialists in genetics, biology, and bioinformatics set to work, with funding from the National Science Foundation and the USDA Agricultural Research Service. Researchers put DNA from tomatoes into a gene sequencer, which identify the order of molecules in tiny sections of the chromosomes.
ESTER VAN DER KNAAP (Ohio State University): Nowadays, it’s very easy to generate short sequences. But it’s putting them in the right order that is the difficulty.
THOMPSON: That assembly takes thousands of hours of high speed computing, and high intelligence data analysis.
ROE: We look for overlaps between the little pieces to give us larger pieces. And then we look for overlaps between the larger pieces.
THOMPSON: Until you finally get something that looks like this- Chromosome 1, decoded. Chromosome 10, decoded. All the tomatoes chromosomes decoded; the order and location of every gene in the tomato. Now that they know what gene is where, the scientists are working to identify what each gene does. For example, the so called “SUN gene” on Chromosome 7, produces oblong tomatoes, just the right shape for efficient commercial harvesting.
VAN DER KNAPP: We took a tomato plant that makes a round fruit. We put the SUN gene in and then we got a very elongated fruit.
THOMPSON: Now, breeders or growers who want a particular trait, can cross bread parent plants that have that trait, and do DNA tests on the offspring at the seedling stage. Because they know just where in the sequence to look, they can see which seedlings have inherited the desired gene, keep those, and discard the rest.
DAVID FRANCIS (Ohio State University): We’re still using traditional breeding or making crosses, but we’re selecting very precisely for what we want.
THOMPSON: And discoveries about the tomato can apply to a whole range of other fruits and vegetables.
ROE: Everything in nature is there for a reason, and the job of a scientist is to figure out why.
THOMPSON: Mysteries of nature to be investigated, solved, by this and the next generation of data masters and code breakers.
EXCELSIOR, Minn. — On a crisp late fall afternoon, David Bedford plucks an apple from a young tree, chomps into the fruit and chews thoughtfully.
Tomato, Tomatoes, Genome, Genes, Sequence, Sequencing, Sequencer, Selection, Pollen, Pollination, Cross Pollination, Plant, Seedling, Breeding, Traits, Shape, Taste, Flavor, Disease, Shelf Life, Storability, Shipping, Ripening, Ripen, Vine-Ripened, Warehouse, Greenhouse, Ethylene, DNA, Deoxyribonucleic Acid, Cell, Chromosome, Chromosomes, Base Pair, Assembly, Gene Function, Domesticated, Crop, Crop Plant, Food, Fruit, International Tomato Genome Sequencing Consortium, SOL Genomics Network, National Science Foundation, USDA, U.S. Department of Agriculture, ARS, Agricultural Research Service, Advanced Center for Genome Technology, ACGT, University of Oklahoma, Bruce Roe, Boyce Thompson Institute, James Giovannoni, The Ohio State University, Esther van der Knaap, David Francis, Computer Analysis, Genetics, Biology, Bioinformatics, Data Analysis