Genetic Variation in Tomato



Wild and in the Andes

The center of origin/center of diversity for tomato is the Andean region of South America (Equador, Peru, Chile, Bolivia and Columbia).  Domestication of the tomato is thought to have started in Mexico, and then more intensely in Europe after being imported from the New World in the 16^th century.  We know that the path to domestication, far from the center of origin, led to a narrowing of the tomato germplasm base.  Charles Rick, the father of modern tomato breeding (and Mark's Genetics 101 professor at UCD in 1970), estimates that the cultivated tomato contains <5% of the genetic variation found in its various wild relatives.  An excellent review article on domestication of tomato can be found here.



Wild on the Galapagos (photo S. Darwin)


The wild relatives of tomato are almost all small fruited and many are cross pollinated.  The substantial genetic variation within these related species has been a rich source of genes for resistance to various tomato pathogens, and as a source of genetic variation for other traits for which such variation is lacking in cultivated tomato.  The Tomato Genetic Resource Center at UC Davis maintains a vast germplasm collection of wild relatives and other diverse genetic stocks for use by tomato scientists and breeders.  Virtually all modern hybrid tomato cutlivars contain multiple disease resistant genes derived from wild relatives.

The tomato varieties grown in the U.S. trace primarily to the large fruited types developed in Europe over the last 300 years, and brought to America by early settlers.  Family favorites benefitting from additional selection in America for taste and adaptation, and countless generations of seed saving, are today’s heirlooms.


Mutations are the ultimate source of genetic variation in plants, animals and microbes.  The rich genetic diversity within Solanum is the result of many thousands of generations of mutations and genetic recombination, combined with natural selection and speciation.  Although mutations are the foundation for genetic variability on an evolutionary time scale, for a tomato breeder working with thousands of individuals and perhaps a few dozen sexual generations, useful spontaneous mutations at a particular locus (gene) are rare.  The rate of spontaneous mutation can vary by species and by gene, however in maize it is estimated that the average mutation rate in a single gene that causes a visible phenotype is 1/10,000 to 1/100,000 per gamete, per generation.  Mutation rate can be increased significantly by induction with radiation or chemical mutagens.  Induced mutations have been a another valuable source of genetic variation for tomato breeders.  The TGRC germplasm collection contains many such mutant lines that have been selected for specific useful traits.  

Tanksley, 2004

Genetic variation is the “gasoline” that fuels plant breeding.  Although the small amount of genetic variation in tomato has limited breeding progress for some traits, there are a few key genes that together control fruit size, shape and color (Tanksley, 2004) and (Paran and van der Knapp, 2007).  To our delight, these have been used by breeders to develop the substantial phenotypic variation in tomato fruit type available today.  Relatively recent efforts to use the gs gene (green stripe) to create striped patterns on tomato fruit and the Aft gene (anthocyanin fruit) for dark black/purple coloration on tomato fruit add to the kaleidoscope of possibilities ….more on these later.