Wild Potato + Tomato = Edible Potato?

French fries, tater tots, crispy chips… We humans derive a lot of value from the underground tuber of Solanum tuberosum. Yet, some of its closest relatives don’t have tubers for us to eat. So, how did the potato come about? Turns out, we owe this starchy goodness to tomatoes.

Potatoes are the underground tubers of the potato plant (Solanum tuberosum). The tubers are modified stems that store food for the plant, and is used to grow another potato plant asexually. Yet some of its closest relatives have no tubers. So how did the potato get its tuber?

A recent study by the Chinese Academy of Agricultural Sciences concluded that they got it from the tomato. Or more accurately, around 9 million years ago, a plant from the tomato and wild potato (etuberosum) lineage formed a hybrid. This hybrid survived and reproduced lots, becoming the Petota lineage (cute name), of which the great potato is a part of. All members of Petota have tubers.

Hybrids help drive evolution, by inducing changes in the gene pool. Around 25% of plants and 10% of animals show evidence of hybridisation.

Hybrids

A hybrid is an organism with parents that are different species. The species are typically closely related.

DNA is a physical structure in us and all living things. In multicellular organisms, it is located in the nucleus, a structure in the cell. When we say “passing on our genes”, we actually mean passing on our DNA in the nucleus of our egg/sperm (gamete). Gametes have half the number of chromosomes as our typical body cells. The nucleus in the gamete fuses with the nucleus of another person’s gamete, to create a new human.

Sometimes, the gamete of one species fuses with the gamete of another species, forming a hybrid. Hence, the hybrid has genes from 2 different species, leading to new combinations of genes. This can remove important functions or give rise to new functions. This could give a survival advantage or disadvantage. Both occurred in the potato.

The Potato Study

The scientists used a method to determine which genes became more important after hybridisation occurred (positively selected genes, PSG). They compared mutations in the same gene in the modern day potato and tomato/etuberosum.

• If there are more mutations that lead to amino acid changes than mutations that do not lead to amino acid changes, it is very important to the potato (and less important to the tomato/wild potato).

• Amino acids make up proteins, and protein shape determines what it can do. Changes in amino acids lead to changes in protein shape, which can make it better or worse at what it does. 

• If the protein is important, any beneficial changes in amino acid will help with potato survival and so spread really fast in potatoes.

• To clarify, this analyses the genes, as in protein coding regions. Non coding regions of DNA are not considered here. 

They found 229 PSGs from wild potato and 269 PSGs from tomato, some of which were already known to be involved in tuberisation. This suggests that after hybridisation, the genes involved in tuberisation became more important, so it is likely that hybridisation indeed led to tuberisation.

Since different genes are now involved in the potato’s function, it leads to different genes being expressed (producing protein) in different cells.

SP6A and IT1 lead to tuber formation

A gene encodes for a protein. Proteins which have a complementary size, shape, and charge can bind to each other, like 2 puzzle pieces. Oftentimes this binding forms a new shape, such that it becomes complementary and can bind to another protein or molecule.

The presence of genes from tomato and wild potato was what led to tuber formation (tuberisation). A perfect example of this is the interaction between SP6A protein originating from tomato and IT1 originating from wild potato.

In modern day potatoes, SP6A protein leads to tubers forming, while IT1 protein regulates where the tuber is. This occurs when SP6A binds to IT1. The wild potato SP6A is missing a section compared to tomato SP6A. So, only tomato SP6A can bind to IT1. IT1 is found in the wild potato lineage. 

Tomato SP6A + wild potato IT1 = bind

Upon hybridisation, the tomato SP6A and wild potato IT1 finally met and could bind. This protein interaction is an outcome of hybridisation that contributed to potato formation.

SP6A and IT1 are not the only proteins involved in tuberisation. Many others are key to this process, such as SP6A binding with other proteins to form the Tuberigen Activation Complex (TAC). 

SP6A in Petota lineage is more related to SP6A in tomato, and IT1 in potato is more related to IT1 in etuberosum.

It is the PEBP domain that is truncated in etuberosum (ETB) in SP6A, that causes it to be unable to bind to IT1.

Survival of the hybrid

Fitness refers to how well an organism can survive to reproductive age and pass on its genes. Genes that result in a survival advantage in a specific environment get passed on more often.

Hybrids do not always form when gametes from 2 different species fuse. Oftentimes the gametes are not compatible and cannot form an offspring (unviable). Other times, the hybrid offspring cannot form another offspring (sterile). If this occurs in later generations of the hybrid, it is called hybrid breakdown.

The Dobzhansky–Muller model posits that this is due to incompatible genes. In the image above, having one a allele and one b allele leads to a sterile or inviable hybrid. This does not occur in the parent species, but unfortunately the a and b allele meet in the hybrid. 

Another reason for hybrid sterility is seen in mules. Chromosomes are unable to pair up during meiosis, which forms the gametes (egg/sperm). The different number of chromosomes lead to sterility, with 31 from male donkey sperm and 32 from female horse egg. With 63 chromosomes, the chromosomes cannot pair up during meiosis to form eggs or sperm. In very different organisms, the chromosomes will be too different to pair up, or missing entirely. So only closely related species form hybrids.

2n - diploid, aka number of chromosomes in body cell

n - haploid, aka number of chromosomes in gamete

Hybrids being less fit could lead to resources needed to reproduce being wasted on forming unfit hybrids. It could mean less non-hybrid offspring are formed, threatening the survival of the parent lineage. This is called demographic swamping.

Fitness brotato

The Petota lineage had different traits making it less or more fit, which are commonly seen in hybrids.

Tomato, wild potato, and potato hybrids have mostly sterile hybrid seeds. The initial plants of the Petota lineage likely had trouble with many unviable seeds from sexual reproduction. The paper hypothesises that the potato tuber, allowing for asexual reproduction, helped the Petota lineage survive until they could sexually reproduce again. It is not known how potatoes regained the ability for sexual reproduction.

On the other hand, hybrids could have unique traits that help them better adapt to new environments. A typical example is the Helianthus (sunflower) hybrids. The parent plants formed the hybrid Helianthus deserticola, which, as the name suggests, thrive in the desert. Its new traits allow it to survive better, hence it is more fit (in the desert). 

Helianthus deserticola thrives in the dry desert, such as in Arizona. 

The tuber allows a new plant to grow from it. This helped the plant climb up mountainous regions. The formation of the Petota lineage and its subsequent diversification coincides with the “rapid uplift of the Andes”. Today, Petota is most diverse in “high-elevation, cold-adapted montane habitats in central Mexico and the central Andes”. This indicates that the tuber allowed the ancestral potato to adapt to new environments and subsequently form even more species, and the lineage also evolved to be more adapted to the cold. This is called adaptive radiation, where new species form at a fast rate to fill new environments that they can now survive in.

The very pretty graphical abstract found in the paper illustrates the tuber formation and subsequent adaptive radiation well.

A river of genes

Gene flow is the transfer of genetic material (DNA) from one population to another. A population refers to members of the same species living in one area. The two populations can be the same species or different species

Gene pool refers to all the genes in a particular species.

In the image above, species 1 and 2 form a hybrid. The hybrid, with genes from species 2, may then breed with species 1. Eventually, the genes from species 2 enter species 1 and remain in its gene pool.

This is called introgression, and it introduces new genes, increasing genetic variation. This allows natural selection to have more genes to “select” from, so species can become more adaptable to different circumstances.  

An example of gene flow helping parent lineage is the wing pattern in Heliconius butterflies. These butterflies taste bad so their predators avoid them. They also mimic each other, so that predators have to recognise less wing patterns, and can more easily avoid eating them (Mullerian mimicry). The gene* for wing pattern has been passed from species to species, so they can directly mimic each other.

Heliconius numata (top) and Melinaea mneme (bottom). Taken by Mathieu Chouteau.

*It’s actually a supergene, a group of tightly linked genes that does not undergo recombination. During meiosis, the chromosomes that pair up can cross over, literally exchanging bits of the chromosome. In the supergene, parts of the chromosome are inversed, and the inverted part cannot cross over because the DNA base sequence does not match. 

However, gene flow can cause the parent lineage to be replaced by the hybrid, called genetic swamping. This could affect one or both of the parent lineage.

An example of gene flow bringing harm to parental species is the Eucalyptus Tetrapleura, a rare species (it is not eaten by the Koala). After clearing out this tree to build a highway, populations have become smaller and fragmented. Since the population is small, there is a higher chance of hybrids forming with the more common ironbark trees. This could lead to genetic swamping or demographic swamping.

Conclusion

From above, we can see how hybridisation leads to new combinations of alleles, which can lead to new functions or loss of important functions. Hybrids forming also affects the parental lineage, through resources being wasted on unfit hybrids and gene flow which has both positive and negative impacts on the parent lineage. Hence, species become more or less fit, and new species can form, and different species could merge. This impacts the survival and thus evolutionary outcomes of the lineage.

With climate change and human intervention, the habitats of many species are changing. Some species may have more overlap in their habitats, and form more hybrids. This can be detrimental to some species, yet save others from extinction. Introgression and hybridisation has been put forth as a method to improve certain species’ adaptability to the changing climate, but there is concern that it could cause even more harm, which may not reveal itself immediately. Yet doing nothing will mean that many species will go extinct. A less risky approach could be assisted evolution of specific species. Already, corals are being bred to find more heat-resistant corals to grow (* cough * read my article cough *). Corals have already hit their tipping point, and if we cannot keep temperatures from rising, such methods may be the only way to save coral reefs and the many species and humans relying on them. 

Better understanding on the effects of hybridisation and gene flow could help humanity decide how it goes about conserving species.

Works Cited

Intro

Mallet, J. (2005). ‘Hybridization as an invasion of the genome’. Trends in Ecology & Evolution, [online] 20(5), pp.229–237. doi:https://doi.org/10.1016/j.tree.2005.02.010.

Potato

Zhang, Z., et al. (2025). ‘Ancient hybridization underlies tuberization and radiation of the potato lineage’. Cell. [online] doi:https://doi.org/10.1016/j.cell.2025.06.034.

Bao, X., Zhu, Y., Li, G. and Liu, L. (2025). ‘Regulation of storage organ formation by long-distance tuberigen signals in potato’. Horticulture Research. doi:https://doi.org/10.1093/hr/uhae360.

Tang, D., et al. (2022). ‘Fig. 3: Identification of a potato tuber identity gene,’, in ‘Genome evolution and diversity of wild and cultivated potatoes’. Nature, [online] 606(7914), pp.535–541. doi:https://doi.org/10.1038/s41586-022-04822-x.

Hybrid

Johnson, N.A. (2008). Evolutionary Genetics of Hybrid Incompatibility | Learn Science at Scitable. Available at: https://www.nature.com/scitable/topicpage/hybrid-incompatibility-and-speciation-820/ (Accessed: 24 November 2004).

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Presgraves, D.C. (2007). ‘Figure 1 The Dobzhansky–Muller model for loss of fitness in hybrids between recently diverged species.’, in ‘Speciation Genetics: Epistasis, Conflict and the Origin of Species’. Current Biology, 17(4), pp.R125–R127. doi:https://doi.org/10.1016/j.cub.2006.12.030.

Gross, B.L., et al. (2004). ‘Reconstructing the Origin of Helianthus deserticola: Survival and Selection on the Desert Floor’. The American Naturalist, 164(2), pp.145–156. doi:https://doi.org/10.1086/422223.

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Berger, M. (2023). Dune Sunflower [Photograph]. Available at: https://www.inaturalist.org/photos/323158618 (Accessed: 24 November 2025).

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Aguillon, S.M., Dodge, T.O., Preising, G.A. and Schumer, M. (2022). ‘Figure 2. The integration of segments of DNA through introgression’ in ‘Introgression’. Current Biology, 32(16), pp.R865–R868. doi:https://doi.org/10.1016/j.cub.2022.07.004.

Jay, P., et al. (2018). ‘Supergene Evolution Triggered by the Introgression of a Chromosomal Inversion’. Current Biology, 28(11), pp.1839-1845.e3. doi:https://doi.org/10.1016/j.cub.2018.04.072.

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Chouteau, M. (n. d.). Heliconius numata (top) and Melinaea mneme (bottom) [Photograph]. Available at:  https://mathieuchouteau.weebly.com/research.html  (Accessed: 24 November 2025)

NSW Government Environment, Energy and Science(2024). Koala habitat. Available at: https://www.environment.nsw.gov.au/topics/animals-and-plants/native-animals/native-animal-facts/koala/koala-habitat. (Accessed: 24 November 2025)

Rutherford, S., van der Merwe, M., Wilson, P.G., Kooyman, R.M. and Rossetto, M. (2019). ‘Managing the risk of genetic swamping of a rare and restricted tree’. Conservation Genetics, 20(5), pp.1113–1131. doi:https://doi.org/10.1007/s10592-019-01201-4.