November 22, 2012
The Tomato Decoded
The tomato, whose genome has been decoded, possesses 31,760 genes. This rich legacy—possibly a reflection of the disaster that killed off the dinosaurs—is some 7,000 more genes than that of a human being, and presents a complex puzzle to scientists who hope to understand its secrets.
A consortium of plant geneticists from 14 countries has spent nine years decoding the tomato genome in the hope of breeding better ones. The scientists sequenced the genomes of both Heinz 1706 (above), a variety used to make ketchup, and the tomato’s closest wild relative, the Currant Tomato (Solanum pimpinellifolium; below) which lives in the highlands of Peru, where the tomato’s ancestors originated. Their results were published recently in the journal Nature.
The tomato, though a fruit to botanists, has been decreed a vegetable since an 1893 United States Supreme Court case. The verdict is not so unreasonable given that the tomato has a close cousin that is a vegetable, namely the potato.
The genomes of the two plants have 92 percent of their DNA in common, the tomato researchers report. The main difference is that the potato is thought to have a handful of genes that direct the plant’s energy away from producing fruit and into the generation of tubers. But even with the genomes of the two plants deciphered, those genes have not yet been identified.
The tomato genome is both of intrinsic interest and a key to understanding the very versatile family of plants to which it belongs. Besides the potato, the Solanaceae family includes the tobacco plant, the pepper, the eggplant and Deadly Nightshade (Atropa belladonna; below).
That the tomato and potato contain so many genes does not mean that they are more sophisticated than people but that they have chosen a different scheme for managing their cells’ affairs. Humans make heavy use of a technique called alternative splicing, which allows the components of each gene to be assembled in many different ways, so that one gene can produce many products. Below: The tomato’s genome.
The Solanaceae family, by contrast, has developed its genetic complexity through gaining more genes. About 70 million years ago, some lucky mishap in the process of cell division led to a triplication of the Solanum genome. The two spare copies of each gene were free to change through mutation. Many were useless and got dropped from the genome, but others developed useful new functions.
The tomato genome team has been able to visualize the result of this triplication by comparing the tomato’s genome with that of the grapevine, a distant relative from which it parted company about 100 million years ago, well before the triplication event. Some of the grape’s genes have a single counterpart in the tomato genome, some have two counterparts and some have three.
Usually the triplication of a genome would be a considerable handicap, saddling a plant with three times as much DNA as it needs. But this event occurred around the time of the catastrophe in which the dinosaurs perished, and the extra genetic versatility may have been a lifesaver. It’s easy to think that in that period, with a lot of volcanic activity and little sunlight, the reservoir of many additional genes would be useful to a plant.
Plant breeders have had more success breeding tomatoes with features of interest to producers, like long shelf life, than with the traits that matter to consumers, like taste and quality. The tomato genome sequence may help remedy the balance, since plant breeders can now rely on DNA as well as physical traits to govern their breeding programs.
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