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Bioscience Issues

Revealing tomato’s secrets

Sharon Schmickle award-winning MinnPost writer

What is your idea of a dream tomato? Women selling the juicy globes in the markets, no doubt, would wish for a slow-spoiling variety so that today’s leftovers would sell tomorrow.  Buyers, of course, would want luscious flavor. Growers would hope for fortification against yield-stealing pests.

The day when all of those wishes could come true has been advanced by news published online in the journal Nature: tomato’s genome has been decoded. Now that scientists have the full genetic code of a common tomato, they have an unprecedented view of some 35,000 genes that make the tomato what it is.

With tomato’s genetic sequence in hand, scientists can deploy computer programs to identify genes associated with important traits and spot variations that will stand as landmarks for breeding programs. The sequence also opens the door to a far better understanding of how tomato plants interact with field conditions – say, with drought – to determine the crop’s health, viability and eventual taste.

Taste + nutrition = importance for Africa
Tomato is one of the most important vegetable crops in Africa, according to the AVRDC-World Vegetable Center which works from a research station in Arusha, Tanzania, to help combat threats to the crop across Africa.

Tomato has a wealth of culinary friends on African tables. Sure you can eat it alone, sliced or diced. But you also can stir it into a spicy peanut soup. You can boil it for West African-style Jollof Rice. You can steam it – wrapped in banana leaves along with spices and fish or meat. The recipe list goes on and on, with subtle variations across the continent.

It’s no wonder then that tomato is a best-seller in African markets. And it poses the rare case in which a food we love to eat also is nutritious.

Tomato is rich in pro-vitamin A and antioxidants, making it a vital remedy for widespread deficiencies of the crucial vitamins and minerals known as micronutrients, said Roland Schafleitner, who heads molecular genetics for the Vegetable Center.

Thanks to its popularity, tomato also is an important source of cash income for smallholder farmers – often women whose incomes go directly to feed, clothe and educate their children.

New varieties “urgently needed”
However, diseases have been relentless in their attacks on tomatoes in Africa, compounding the stresses of heat and drought. Further, too many tomatoes rot before reaching markets because transportation is so difficult.

Research by the Vegetable Center and other organizations has led to major advances against destructive pests such as tomato mosaic virus, fusarium wilt and late blight. The Center conducted extensive surveys to find resistant genes in local varieties, some over 70 years old.

Even so, “new improved varieties are urgently needed by tomato farmers in Africa if they are to exploit the full potential of tomato growing and marketing for income generation and nutrition,” Schafleitner said.

While progress has been made against diseases, breeding a tomato that tolerates extreme heat and/or drought is more difficult because many, many genes are involved. The same is true for boosting the concentration of nutrients in tomato.

This is where the genome sequence comes in to play.

The full-length sequence will make it far easier for tomato breeders to use a modern technique called marker-assisted breeding, Schafleitner said.

Simply put, the technique involves finding DNA sequences that are in, or very near to, genes conferring desired traits. Let’s say a high-vitamin tomato is crossed with another one that resists blight. Using modern tools, the breeder should be able to quickly screen the offspring’s DNA. If the DNA includes the genetic landmarks for both traits, the cross was successful.

“This method already has been used in tomato for several years to select for relatively simple traits encoded by one or a few genes, but has not been as successful for complex traits involving many genes,” Schafleitner said.

He was describing conventional breeding assisted by modern tools – not the genetic engineering process that introduces new and novel genes into a plant’s DNA lineup. The genome could be useful for both approaches.

With the full-length genome sequence in hand, tomato breeders also can save time and money by deploying other new, more efficient, breeding methods. One, called genomic selection, makes is possible to improve complex traits involving hundreds of thousands of genes.

Revealing tomato’s secrets
An international team of more than 300 scientists from 14 countries spent nine years deciphering the genome of the tomato known as Heinz 1706, a variety commonly used to make ketchup. The team also sequenced the genome of tomato’s closest wild relative, Solanum pimpinellifolium.

Their work added tomato to a select group of crop plants for which genomes have been sequenced. The others include rice, corn, sorghum, poplar, potato, soybean, grape and Arabidopsis thaliana, a plant widely studied as a model organism.

Because tomato is a member of the Solanaceae or nightshade family, its sequence is expected to help identify important genes in related plants. Tomato’s well-known relatives include potato, pepper and eggplant.

The genome sequences also reveal new chapters in the Solanaceae family history. It had long been known that tomato originated in South America. Spanish explorers are believed to have carried it to Europe and also to far-flung colonies from where it spread across Asia and Africa.

Now, the genome sequence spells out a fascinating new chapter, set some 60 million years ago about time of the mass extinction of the dinosaurs. The tomato genome expanded abruptly during that period, raising intriguing questions about its adaptation and survival.

Some of the genes tomato took on during that otherwise disastrous time survive today and account for traits we value in our many uses of tomatoes.

“The genome sequences of tomato and S. pimpinellifolium also provide a basis for understanding the bottlenecks that have narrowed tomato genetic diversity: the domestication of S. pimpinellifolium in the Americas, the export of a small number of genotypes to Europe in the 16th century, and the intensive breeding that followed,” said the report in Nature.

Schafleitner of the World Vegetable Center explained further: “Many genes are present in the genome in multiple copies or in the form of families of genes with similar DNA sequence and function, making the identification of genes acting in a certain pathway at a specific developmental stage difficult. The full-length tomato genome sequence, for the first time, provides records for every single gene and overcomes this bottleneck.”

The genome will enable plant breeders to dissect biochemical pathways and identify the factors that affect everything from plant growth to fruit set to yield.

“Plant scientists and breeders, and ultimately farmers and consumers, will strongly benefit from this new insight,” Schafleitner said.

For consumers worldwide, the upshot could be improvements in nutrition and taste at the same time sellers and growers get their wish for longer-lasting tomatoes. Some genes that enhanced nutrition and taste were silenced over the years as breeders selected plants that resisted diseases or ripened slowly.

Now, scientists can mine the genome for those muted genes and learn how to turn them on again – hopefully, simultaneously so that flavor and shelf life could be enhanced at the same time. Indeed, the rich reservoir of information about tomato’s ripening could serve as a model for understanding the ripening process in a range of fruits and vegetables.

Fruit or vegetable?
One riddle the sequence may not resolve is the longstanding question of whether tomato is a fruit or a vegetable.

“Scientifically speaking, a tomato is definitely a fruit,” says the Oxford Dictionaries.

Botanists agree, based on the tomato’s arrangements of ovaries and seeds.

But those of us who insist on calling it a vegetable now can point to the considerable DNA tomato shares with potato, defined by the Oxford Dictionaries as a tuber eaten as a vegetable.