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

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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.