Researchers Have Cracked the Sweet Potato’s Unusually Complex DNA

Sweet potato DNA decoded, revealing hybrid ancestry. Discovery aids future breeding and resilience.

The sweet potato is a staple food for millions of people worldwide, particularly in sub-Saharan Africa, where its ability to withstand climate extremes makes it essential for food security. Despite its importance, the crop’s genetic makeup has remained elusive for decades. Scientists have now succeeded in decoding its highly complex genome, uncovering a detailed evolutionary history and creating valuable resources to guide future crop improvement.

Unlike humans, who inherit two sets of chromosomes, sweetpotatoes carry six. This condition, known as hexaploidy, has made interpreting its genome especially difficult—similar to trying to organize six overlapping sets of encyclopedias that have been thoroughly mixed together.

A research team led by Professor Zhangjun Fei at the Boyce Thompson Institute has now overcome this challenge. As reported in Nature Plants, they used state-of-the-art DNA sequencing and other advanced methods to assemble the first fully resolved genome of ‘Tanzania,’ a sweet potato variety widely valued in Africa for its resistance to disease and its high dry matter content.

Solving the chromosome puzzle

The biggest obstacle was to sort through the plant’s 90 chromosomes and reconstruct them into their six original groups, known as haplotypes. The researchers accomplished a complete separation, or “phasing,” of this intricate genetic puzzle—an achievement never before reached.

“Having this complete, phased genome gives us an unprecedented level of clarity,” said Fei. “It allows us to read the sweet potato’s genetic story with incredible detail.”

What they uncovered was unexpectedly complex. The sweetpotato genome turned out to be a patchwork formed from several wild ancestors, some of which remain unknown. Roughly one-third of its genetic makeup derives from Ipomoea aequatoriensis, a wild species native to Ecuador that appears to be a direct descendant of an early sweetpotato ancestor. Another major portion closely resembles a Central American wild species known as Ipomoea batatas 4x, although the true contributor may still be unrecognized 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 sweetpotato, the ancestral sequences are intertwined on the same chromosomes, creating a unique genomic architecture.”

Evolutionary advantages of polyploidy

This intertwined genetic heritage means that sweetpotato 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 sweet potato its remarkable adaptability and disease resistance, traits crucial for subsistence farmers worldwide.

“The sweetpotato’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.”

Broader applications for agriculture

However, achieving a full understanding of sweetpotato’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 sweetpotato, 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.

Reference: “Phased chromosome-level assembly provides insight into the genome architecture of hexaploid sweetpotato” by Shan Wu, Honghe Sun, Xuebo Zhao, John P. Hamilton, Marcelo Mollinari, Gabriel De Siqueira Gesteira, Mercy Kitavi, Mengxiao Yan, Hongxia Wang, Jun Yang, G. Craig Yencho, C. Robin Buell and Zhangjun Fei, 8 August 2025, Nature Plants.
DOI: 10.1038/s41477-025-02079-6

Funding: Bill and Melinda Gates Foundation, National Institute of Food and Agriculture

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