‘Tanzania’ variety of sweetpotato. Credit: Benard Yada at National Crops Resources Research Institute (NaCRRI), Uganda
The sweet potato feeds millions worldwide, especially in sub-Saharan Africa, where its natural resilience to climate extremes makes it crucial for food security. But this humble root vegetable has guarded its genetic secrets for decades. Now, scientists have finally decoded its complex genome, revealing an intricate origin story and providing powerful tools to help improve this vital crop.
Sweet potato DNA is extraordinarily complex. While humans have two sets of chromosomes, one from each parent, sweet potatoes have six. This condition, called hexaploidy, made deciphering their genetic code like trying to reconstruct six different, yet similar, sets of encyclopedias that have been shuffled together.
A team led by Professor Zhangjun Fei at the Boyce Thompson Institute achieved a significant breakthrough, as reported in Nature Plants. Using cutting-edge DNA sequencing, along with other advanced techniques, they created the first complete genetic makeup of “Tanzania”—a sweet potato variety prized in Africa for its disease resistance and high dry matter content.
The central challenge was to untangle the plant’s 90 chromosomes and organize them into their six original sets, called haplotypes. The team succeeded in fully separating (“phasing”) this complex genetic puzzle, something that had never been achieved before.
“Having this complete, phased genome gives us an unprecedented level of clarity,” explains Fei. “It allows us to read the sweet potato’s genetic story in incredible detail.”
The research revealed surprising complexity. The sweet potato genome is a mosaic assembled from multiple wild ancestors, some of which have yet to be identified. About one-third comes from Ipomoea aequatoriensis, a wild species found in Ecuador that appears to be a direct descendant of a sweet potato progenitor. Another significant portion resembles a wild Central American species called Ipomoea batatas 4x, though the actual donor may still remain undiscovered in the wild.
“Unlike what we see in wheat, where ancestral contributions can be found in distinct genome sections,” says Shan Wu, the study’s first author, “in sweet potato, the ancestral sequences are intertwined on the same chromosomes, creating a unique genomic architecture.”
This intertwined genetic heritage means that the sweet potato can be tentatively classified as a “segmental allopolyploid”—essentially a hybrid that arose from different species but behaves genetically as if it came from a single one. This genomic merging and recombination gives the sweet potato its remarkable adaptability and disease resistance, traits crucial for subsistence farmers worldwide.
“The sweet potato’s six sets of chromosomes also contribute to its enhanced resilience,” adds Fei. “With multiple versions of important genes, the plant can maintain backup copies that help it survive drought, resist pests, and adapt to different environments—a feature known as polyploid buffering.”
However, achieving a full understanding of the sweet potato’s genetic potential will require decoding multiple varieties from different regions, as each may carry unique genetic features that have been lost in others.
The work by Fei and his team represents more than just an academic milestone. Equipped with a clearer understanding of sweet potato’s complex genetics, breeders can now more efficiently identify genes responsible for key traits like yield, nutritional content, and resistance to drought and disease. This precision could accelerate the development of improved varieties.
Beyond sweet potato, this research demonstrates how modern genomic tools can help decode other complex genomes. Many important crops, including wheat, cotton, and banana, have multiple sets of chromosomes.
As climates shift and pest and disease pressures increase, understanding these genetic puzzles is critical for breeding resilient crops and addressing challenges in food security.
More information:
Nature Plants (2025). www.nature.com/articles/s41477-025-02079-6
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Boyce Thompson Institute
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Decoding sweet potato DNA: New research reveals surprising ancestry (2025, August 8)
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