Evolution of Fruit Shape in Tomato

Written by Matt DiLeo

Someday you’ll be able to use CAD software to draw up what you want a plant to look like and the software (containing detailed growth models) will tell you what genetic constructs you need to bring it into the world…

But for now we barely understand how natural morphological variation is controlled. So I was excited to see this paper out of the van der Knaap and Francis labs. In it, they review some of the known levers by which tomato plants control fruit shape and investigate their historical appearance.

Many species of wild tomatoes grow along the western coast of South America, from above the snowline in the Andes to the cloud forests and desert valleys below. Despite this great ecological diversity, most of them produce little, green fruit (that are often covered with fur). These wild species are generally bitter and inedible, but a few species make sweet, red ripe fruit. Some have suggested that Solanum lycopersicum var. cerasiforme (the cherry tomato) is the ancestral domesticated tomato. More recently, others have suggested it is a feral mix of domestic and wild tomatoes. One way or another, the few centuries of domestication since have witnessed and enormous diversification of fruit shape (and flavor!) as it was tracked from the Americas to Europe and back – with each culture adapting it to their unique cultures and cuisines.

Today, tomatoes come in all shapes and sizes from small round cherries to large, lumpy, many-loculed heirlooms. The authors worked to track the morphological history of this fruit by looking for associations between alleles with known impacts on fruit shape and germplasm of known origins.

They began by assembling 368 heirloom, modern and wild genotypes from Europe and the Americas, which they then classified into 8 fruit shape categories: flat, rectangular, ellipsoid, obovoid, round, oxheart, long and heart. 4 genes (SUN, OVATE, FAS and LC) have so far been discovered to make major contributions to these differences in fruit shape. The SUN mutation creates elongated fruit, apparently due to a misregulation of the phytohormone auxin (thanks to the influence of a retrotransposon). The OVATE mutation (an early stop codon) creates pear shaped fruit. FAS (FASCIATED) and LC (LOCULE NUMBER) both contribute to tomato size and locule number.

The authors looked for associations among these alleles and the shape classifications in their diverse germplasm collection. They found the SUN mutation in 88% of long and 83% of oxheart-shaped fruit. The OVATE mutation was present in 83% of ellipsoid, 59% of rectangular and 48% of oxheart-shaped fruit. 82% of flat fruit had the LC mutation and 28% had the FAS mutation. 63% of long fruit also had LC.

While all 4 gene mutations are present in both modern and heirloom fruit, their presence in older varieties is indicative of their evolution. Little is known about what tomatoes looked like when Columbus first encountered them, but we know his compatriots tracked them from Mexico to Spain and Italy soon after they were discovered. The first written account of these fruit in 1544 describes them as flat and segmented, and soon after as fasciated – suggesting that LC and FAS were already present in Latin American varieties by this time. The next novel tomato fruit shape (pear) wasn’t mentioned until 1813, possibly indicating that OVATE was brought to Europe in a later wave of germplasm. This allele proliferated in Italy and is now present in 71 out of 109 elongated accessions, where it’s responsible for the classic Italian paste tomato shape.

SUN arose much later than OVATE and FAS and can now be found in half of US heirlooms (especially those of northern European origin) and Spanish regional accessions with elongated fruit shapes (but not Latin American or wild accessions). This suggests that SUN originated in Europe rather than the Americas – Northern Europe to be specific, as only 6 of 109 Italian fruit varieties contain it. SUN probably first appeared in an LC background because older heirloom and regional varieties with SUN also have LC except for recent exceptions like Banana Legs.

It’s exciting to witness these early steps towards understanding how plants work, but I’m really looking forward to that CAD software…

Rodríguez GR, Muños S, Anderson C, Sim SC, Michel A, Causse M, Gardener BB, Francis D, & van der Knaap E (2011). Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity. Plant physiology, 156 (1), 275-85 PMID: 21441384
Xiao, H., Jiang, N., Schaffner, E., Stockinger, E., & van der Knaap, E. (2008). A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit Science, 319 (5869), 1527-1530 DOI: 10.1126/science.1153040
Liu, J. (2002). A new class of regulatory genes underlying the cause of pear-shaped tomato fruit Proceedings of the National Academy of Sciences, 99 (20), 13302-13306 DOI: 10.1073/pnas.162485999

Written by Guest Expert

Matt DiLeo has a PhD in Plant Pathology from UC, Davis. During his postdoctoral research at Boyce Thompson Institute, he researched unintentional effects of genetic engineering. Matt builds R&D teams and biotech platforms: genome editing, gene discovery, microbials, and controlled environment agriculture.


  1. But… isn’t coexistance of different types due to single gene differences an impossibility?
    (Sorry… this is an awesome post and I felt it deserving of at least one response… alas that was the best I could come up with after toying with multiple CAD related wossnames)

  2. Ah I see where you’re going… if only Bt and RR were simply associated with insect resistance and herbicide tolerance!
    Now if only I knew exactly which genes were responsible for all the tomato plants in my garden dying horrifically.
    I have a feeling they’re carried on my own chromosomes sadly.

  3. I have 3 plants, two of which are volunteers from last year and hence terrible (one fruit which rotted on the vine, and one coming in now which appears to be about to collapse the plant… but then all that needs is a staking), one of which is the only one of my many cherry tomatoes that made it – I got one set of toms off the cherry before the heat hit the 100’s at which point flowering shut down, and now have a bunch more appearing – I believe I got the hint here at Biofortified to go around flicking all my flowers as I had the same zero fruiting issue last year (insects apparently are on a Monsanto boycott)

  4. My tomatoes this year taught me the difference between knowing something and seeing it. I planted mostly heirlooms. I harvested mostly hybrids. I got a handful of White Tomesol, which were pretty cool being white and all, a couple Ananas Noire (though they weren’t nearly as big as the ones I had last year). Slugs & bugs ate the few Carbon & Kellogg’s Breakfast I had (I forgot to spray them…bugs sure do love pesticide-free tomatoes). The Yellow Ping Pongs threw off a few tomatoes, but the Green Zebras hardly even tried. A lot of them went from green to mush before I could make it to my garden (which was not at home). But by and large, what I got most of was these Rome type I was given (which I assume were hybrids, though I don’t really know). Got bunches of them. The heirlooms, well, last year they did pretty good, but this time, don’t know if it was the heat or the new spot or my own plentiful screw-ups, but it wasn’t a good year. I always knew what heterosis was but I really know it now. Hopefully next year will be better; I want to try to make some white salsa.

  5. Anastasia,
    I don’t know if rationality affects emotions, but I always prefer more-coloured to less-.
    The anthocyanins and carotenoids and betalains are supposed to be GOOD for you (though I’ve heard of a carrot that makes tocopherols instead of carotenoids), so I RATIONALLY prefer colourful produce, except as sparse novelties: brown bread, properly-yellow-fleshed peaches, purple cabbage, etc. Maybe I never graduated toddlerhood? (I didn’t get a certificate or anything.)
    I was disappointed that the purple in “Black Krim” was so heat-labile. Why do some anthocyanins survive? Concentration? Is there a way to stabilize them (without weird metals or a bunch of quercetin)? What happens to them anyway (chemistry)? Can we splice-in betalains?

  6. You can make white pasta sauce too. It’s a cool novelty but the white tomatoes I’ve eaten have pretty weak flavor. Same goes for Green Zebra, though it supposedly makes awesome fried tomatoes.

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