Origins and Adaptations:
Evolutionary History of the Tomato
This is where tomatoes came from, and there are still wild relatives living there to this day. (the little shapes on the map) For any plant it is useful to know where it came from, it’s original environment, the conditions it evolved in, adapted to. How much sun exposure, how much precipitation and how is that precipitation distributed throughout the year (for instance many CA natives evolved to have a summer dry period). Tomatoes originated in Peru and Ecuador over 80,000 years ago, where it is warm and relatively dry. The genes evolved from that place, from those conditions; an interplay between the plants and their environment, and so that is where a discussion of the genes begins. Pease et al. (2016). Phylogenomics Reveals Three Sources of Adaptive Variation During a Rapid Radiation. PLOS Biology Journal.
Pease et al. (2016). Phylogenomics Reveals Three Sources of Adaptive Variation During a Rapid Radiation. PLOS Biology Journal.
This diagram illustrates what the fruit of many of those wild relatives look like, and indicates whether that species is able to interbreed with the tomato (Solanum lycopersicum). The closest relatives are the three on top. All tomatoes are derived from Solanum pimpinellifolium (Currant Tomato). Du, M. et al. (2025). Molecular breeding of tomato: Advances and challenges. J. Integr. Plant Biol. 67: 669–721.
As these research papers show, tomatoes are related to other species of Solanums, some more closely related and able to interbreed with tomatoes. The closest related is called Solanum pimpinellifolium (Currant tomato) which phylogenetic studies show is the common ancestor of all cultivated tomatoes. Pease et al. (2016). Phylogenomics Reveals Three Sources of Adaptive Variation During a Rapid Radiation. PLOS Biology Journal.
Li et al. 2023 Super-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species. Nature Genetics. 55: 852-860.
Solanum pimpinellofolium compared to heirloom type, through domestication, and selecting for certain traits allowed to become bigger, but also lost diversity “genetic bottleneck” Tanksley SD. 2004. The Plant Cell 16 S181-S189
This shows the tomato's journey of domestication. Flores et al. 2023. The Tomato's Tale: Exploring Taxonomy, Biogeography, Domestication, and Microbiome for Enhanced Resilience. Phytobiomes journal 8: 5-20
So heart tomatoes have (sun) gene elongating them (developed post-European domestication) and (fas) gene combining their carpels. Rodriguez et al. 2011. Distribution of SUN, OVATE, LC, and FAS in the Tomato Germplasm and the Relationship to Fruit Shape Diversity. Plant Physiology, Volume 156, Issue 1, Pages 275–285,
Charles Rick really opened the door to incorporating wild species genes into tomatoes and to understanding tomato genetics. He went out and collected those wild relatives and helped figure out how to cross-breed their genes into tomatoes.
His collection is maintained as a resource for tomato breeding to this day at the UC Davis C.M. Rick Tomato Genetics Resource Center.
The tomato contains 12 chromosomes, and thanks to the pioneering work of Charles Rick and so many others, the location of many genes are well-documented (some locations have been refined since; from TGC Report No. 37, 1987)
One of the main things Charles Rick and others did with the wild relative genetics was to improve processing tomatoes. They diverged into their own type that is distinctly different from fresh-market tomatoes (which includes heirlooms and modern hybrids)
In 1940 San Joaquin county became the number one county in the US in canning tomato production, due to climate and soil. Through advances in incorporating wild relative genes for disease resistance and productivity and harvestability and more recently through advances in irrigation with subsurface drip, the yield per acre has quintupled. Yields: 1940: 10 tons/acre 1960: 17 tons/acre 1980: 24 tons/acre 2024: 50 tons/acre
Tomatoes are more adaptable to climate change than many crops, and with the availability of the wild relative genes and breeding programs, likely to continue being an important crop. Some of these genes are relevant to all tomato breeders, like disease resistance and shapes, and drought tolerance, others are desirable only for processing tomatoes. Besides vastly improving processing tomatoes, he contributed to the understanding of tomato genetics in general, which we will get to later, but first back to heirlooms.
As well as modern hybrids, fresh-market tomatoes include the heirlooms that were passed down through generations, like the famous Cherokee Purple. The flavor is so good, and vigor, that it has been used as a parent for many many other varieties, such as Berkeley Tie-Dye, Orange Caprese, Elgin Pink
These don’t have modern disease resistance (happened in the 1970s), but were round and could be in the parentage of some modern varieties. Around this time many heirlooms were being saved, Mortgage Lifter, Cherokee Purple, Amish Paste, that would later be widely shared especially in the 1980s onward by folks like William Woys Weaver, Carloyn Male, Craig LeHoullier. Many varieties were lost, but many are still available. Kind of like heirloom selection (saving seeds from the best, most vigor, most flavorful) but also looking for especially round and smooth and other new and unusual traits. “I can repeat the process at will, securing new varieties which will again produce after their kind; and, at least, under my cultivation, will never deteriorate, or ‘run out.’ For they are original, distinct varieties, and will bring forth their like, as will anything else; and they are as capable of being cultivated into ‘strains’ as are those of cattle, hogs, chickens, or other plants and fruits of distinct kinds. (p 22) Just imagine if he realized that he could crossbreed them with their wild relatives, all the varieties he could have made.
Thorburn’s Terra-Cotta 1893 Another old heirloom recently made available, seems to be many subtle variations- which is the real one? More important which grows best and tastes best?
These already have pretty good vigor, crossing with modern disease res would make them even more desireable. As long as you’re growing your favorite varieties anyway, you might as well try crossing them. But keep in mind the genes, so you can know what to expect.
Which one is the real “Cuban Salami”?
Besides adapting varieties to your taste and climate, saving your own seeds also ensures that you keep growing the exact variety you want, as long as you keep careful records yourself.