How Did the Potato Get its Tubers?

The Wire

2 days ago

DNA studies have provided an answer.
Samosa, paratha, tikki, poori-bhaji and masala dosa are among the myriad ways the Indian palate liaises with the humble potato. And then there are chips, fries, wedges and mashed potatoes. Potatoes are a major chunk of our caloric intake.
The potato has a close evolutionary relationship to another popular favourite, the tomato. Both crops were domesticated about 7,000 to 10,000 years ago by the indigenous people of the Andean regions of South America. Then, in the late 15th and early 16th centuries, Portuguese and Spanish colonisers introduced them to the rest of the world.
The potatoes we buy in the market are the tubers of the potato plant. Tubers are swollen portions of the plant's underground stem. That is where the plant stores its nutrient reserves. Tubers bear buds from which new plants can arise. Potato plants are most often propagated from the buds on the tubers. This is called vegetative propagation.
In contrast, the tomatoes we buy in the market are the tomato plant's fruits (berries). Tomato plants do not develop tubers. The berries develop after the flower is pollinated, and contain the seeds. Their equivalents in the potato are called 'true potato seeds' (TPS) which develop inside the berries produced by the potato plant. Potato berries look a lot like small, green tomatoes. They are not consumed because of their mild toxicity. Also, many cultivated potatoes either do not flower, or their flowers are infertile, and do not produce berries. Varieties that make fertile flowers can be sexually propagated using the TPS.
Why do potatoes, but not tomatoes, develop tubers? The answer has now been found by a research team led by scientists from the Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China. They reported this on July 31, in the journal Cell. The potato tuber's origin story they unravelled had an element of surprise.
DNA and speciation
When any species splits to give rise to two new species, the genomes of the new species begin diverging from each other, and continue doing so with time. If we know the rate of DNA sequence divergence, we can estimate approximately how long ago the split occurred.
Why do the genomes diverge? One view of this process goes like this: Imagine we begin with a single species spread over a land mass which has two hills. A rise in the sea level then leads to geographical isolation of the hills from each other on two newly formed islands. Now the two hill populations are unable to interbreed. Mutations arising in one are unable to spread to the other. Over time the two populations accumulate distinct mutations in their genomes. It is as though one genome changes its 'colour' to red, while the other changes it to green. After say tens to hundreds of thousand years, pollen borne on a wind-blown insect fortuitously wafts over the waters from one island to other and fertilises the flowers there. It is quite likely that the fertilisation results in sterile seeds, or that the emergent hybrid plant is unable to efficiently produce pollen or ova. This is because the accumulated DNA differences make a few genes in one genome incompatible with their counterparts in the other. Now the two populations can be said to have become distinct species. Thereafter, both geographic isolation and suboptimal fertility leads the two species to continue the genome divergence.
The researchers sequenced the genome of multiple species of wild potatoes, wild tomatoes and etuberosum. Etuberosum is a group of three plant species that is closely related to potato and tomato but none of these species have been domesticated. By comparing the sequences, they inferred that the tomato and etuberosum genomes diverged at the earliest about 13-14 million years ago.
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A riddle
The sequences also told them the potato and tomato genomes diverged nine million years ago, while potato and etuberosum diverged 8.5 million years ago. These findings presented a conundrum. Since the tomato and etuberosum split was the earliest, how could the potato have split from both these species so much later? In conventional thinking, the subsequent splitting off of potato should either be from tomato or etuberosum, not both.
To solve the riddle, the researchers postulated that about 8-9 million years ago, the potato ancestor had descended from a tomato-etuberosum hybrid. Support for this came from the fact that the tomato- and etuberosum-related genome segments were distributed and evenly interdigitated on all the chromosomes of the potatoes. This unusual relationship is most easily explained by hypothesising that the ancestral genome of all potato species is descended from that of an ancient tomato-etuberosum hybrid.
Their hypothesis found support when they examined the genome sequences at a higher resolution. The potato genome was subdivided into smaller segments and they found that 51% of the segments were most closely related to corresponding segments in the tomato genome, while 37% were most closely related to the corresponding segments in the etuberosum genome. The remaining 12% were equally related to segments of both tomato and etuberosum. The tomato- and etuberosum-related segments were distributed evenly throughout the genome and were interdigitated on all the chromosomes of the potato. This unusual pattern was consistent with the idea that the potato genome has descended from the genome of a tomato-etuberosum hybrid.
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Tubers and seeds
The tomato-etuberosum hybrid likely had infertile flowers or produced non-germinating seeds, as is the case in most inter-species hybrid plants. However, if the ancient tomato-etuberosum hybrid was fortuitously able to store its nutrient reserves in portions of its underground stems, thus swelling them to make incipient tubers, then the buds in these portions would be better able to vegetatively propagate the hybrid plant. Since the tubers impart a better ability to persist via vegetative propagation, there would be a selection for genes that improved tubers formation.
By conferring the ability to persist via vegetative propagation, the tubers also bought some offspring of the hybrid plants the time to undergo additional mutations that restored their ability to make fertile flowers, and seeds (the TPS). These tuber-making plants thus regained the ability to sexually propagate.
Interestingly, among the genes with a role in tuber formation, some turned out to be from tomato-related segments of the potato genome, while others were from the etuberosum-related segments. This suggested that novel juxtaposition of unrelated related genes might also have contributed to triggering incipient tuber development in the hybrid.
The findings provide much food for thought. As scrumptious as a batata vada.
Durgadas P. Kasbekar is a retired scientist.
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