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Ohio State scientists discover gene that controls fruit shape


May 13, 2008
By Mauricio Espinoza

Topics

Ohio State University
crop scientists have cloned a gene that controls the shape of tomatoes,
a discovery that could help unravel the mystery behind the huge
morphological differences among edible fruits and vegetables as well as
provide new insight into mechanisms of plant development.

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Tomatoes with SUN gene turned on and knocked out. Photo courtesy of Ohio State University.

Ohio State University crop scientists have cloned a gene that controls the shape of tomatoes, a discovery that could help unravel the mystery behind the huge morphological differences among edible fruits and vegetables as well as provide new insight into mechanisms of plant development.

The gene – dubbed SUN – is only the second ever found to play a significant role in the elongated shape of various tomato varieties, says Dr. Esther van der Knaap, lead researcher in the study and assistant professor in the Department of Horticulture and Crop Science at Ohio State’s Ohio Agricultural Research and Development Center (OARDC) in Wooster, Ohio.

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The discovery was reported, as the cover article, in a recent issue of the journal, Science.

One of the most diverse vegetable crops in terms of shape and size variations, tomatoes have evolved from a very small, round wild ancestor into the wide array of cultivated varieties – some large and segmented, some pear-shaped, some oval, some resembling chili peppers – available through seed catalogues. However, very little is known about the genetic basis for such transformation in tomatoes and virtually nothing has been discerned about morphological changes in other fruits and vegetables.

“Tomatoes are the model in this emerging field of fruit morphology studies,” Dr. van der Knaap points out. “We are trying to understand what kind of genes caused the enormous increase in fruit size and variation in fruit shape as tomatoes were domesticated. Once we know all the genes that were selected during that process, we will be able to piece together how domestication shaped the tomato fruit – and gain a better understanding of what controls the shape of other very diverse crops, such as peppers and the cucumber and squash family.”

One of the first pieces in Dr. van der Knaap’s fruit-development puzzle is SUN, which takes its name from the Sun 1642 cultivated variety where it was found – an oval-shaped, Roma-type tomato with a pointy end.

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Dr. Esther van der Knaap (left) and an assistant prepare to scan tomato samples. Photo courtesy of Ohio State University.


“After looking at the entire collection of tomato germplasm we could find, we noticed that there were some varieties that had very elongated fruit shape,” explains Dr. van der Knaap. “By genetic analysis, we narrowed down the region of the genome that controls this very elongated fruit shape, and eventually narrowed down that region to a smaller section that we could sequence to find what kind of genes were present at that location.

“In doing that, we identified one key candidate gene that was turned on at high levels in the tomato varieties carrying the elongated fruit type, while the gene was turned off in round fruit. And after we confirmed that observation in several other varieties, we found that this gene was always very highly expressed in varieties that carry very elongated fruit.”

Once SUN was identified, the next step involved proving whether this gene was actually responsible for causing changes in fruit shape. To do so, Dr. van der Knaap and her team conducted several plant-transformation experiments. When the SUN gene was introduced into wild, round fruit-bearing tomato plants, they ended up producing extremely elongated fruit. And when the gene was “knocked out” of elongated fruit-bearing plants, they produced round fruit similar to wild tomatoes.

“SUN doesn’t tell us exactly how the fruit-shape phenotype is altered, but what we do know is that turning the gene on is very critical to result in elongated fruit,” says Dr. van der Knaap. “We can now move forward and ask the question: Does this same gene, or a gene that is closely related in sequence, control fruit morphology in other vegetables and fruit crops?”

Dr. van der Knaap and her team also found that SUN encodes a member of the IQ67 domain of plant proteins, called IQD12, which they determined to be sufficient — on its own — to make tomatoes elongated instead of round during the plant transformation experiments.

IQD12 belongs to a family of proteins whose discovery is relatively new in the world of biology. So new that IQD12 is only the second IQ67 protein-containing domain whose function in plants has been identified. The other one is AtIQD1, discovered in the plant model Arabidopsis thaliana, which belongs to the same family as broccoli and cabbage. In Arabidopsis, AtIQD1 increases levels of glucosinolate, a metabolite that Ohio State food and medical researchers are studying in broccoli for its possible role in inhibiting cancer.
In the process of identifying and cloning SUN, Dr. van der Knaap’s team was also able to trace the origin of this gene and the process by which it came to reside in the tomato genome.

SUN, it turns out, arose as a result of an unusual gene-duplication carried out by a retrotransposon — a type of transposable element or “jumping gene” that can amplify itself anywhere in a genome. Studies showed that the segment of the genome associated with SUN “jumped,” from chromosome 10 to chromosome 7, via this retrotransposon (named Rider).

Such gene duplication, in the end, helped generate a longer tomato fruit that differed significantly from the berry-like fruits that existed before domestication and breeding of this popular modern crop.

Another unique characteristic of the SUN gene is that it affects fruit shape after pollination and fertilization, with the most significant morphological differences found in developing fruit five days after plant flowering. The only other fruit-shape gene previously identified – OVATE, a discovery by Cornell University plant breeder Dr. Steven Tanksley, Dr. van der Knaap’s advisor while she was a post-doctoral associate there – influences the future look of a fruit before flowering, early in the ovary development.

Beyond their contributions to the scientific community’s understanding of plant development, Dr. van der Knaap’s SUN gene discovery and her ongoing research program have important implications for the vegetable- and fruit-production industry. Being able to control and modify fruit shape could lead to the development of new varieties, helping growers to serve specialty markets and processors to reduce costs.

“This discovery will tell us, too, how we can influence the process of fruit formation and facilitate the development of ‘designer fruit,’ ” explains Dr. van der Knaap. “The design or control of fruit shape is especially useful when introducing new varieties. Depending on the goal of the breeding project, the creation of niche markets may require an unusual shape of the product so that consumers are curious to check it out.”

For additional information about Dr. van der Knaap’s fruit morphology research, log on to http://www.tomatoshapes.net .