Decoding sweetpotato DNA: New research reveals surprising ancestry

The sweetpotato 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.

Sweetpotato DNA is extraordinarily complex. While humans have two sets of chromosomes, one from each parent, sweetpotatoes 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 sweetpotato 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, or '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 sweetpotato's genetic story with incredible detail."

The research revealed surprising complexity. The sweetpotato 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 sweetpotato 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 sweetpotato, the ancestral sequences are intertwined on the same chromosomes, creating a unique genomic architecture."

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 sweetpotato 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.”

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 sweetpotato’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.

About the Boyce Thompson Institute (BTI)
Founded in 1924 and located in Ithaca, New York, BTI is at the forefront of plant science research. Our mission is to advance, communicate, and leverage pioneering discoveries in plant sciences to develop sustainable and resilient agriculture, improve food security, protect the environment, and enhance human health. As an independent nonprofit research institute, we are committed to inspiring and training the next generation of scientific leaders. Learn more at BTIscience.org.