Deciphering the DNA of Sweet Potatoes: Unraveling the Hexaploid Labyrinth - What Sweet Potato DNA Reveals About Its "Mosaic Ancestors"

Deciphering the DNA of Sweet Potatoes: Unraveling the Hexaploid Labyrinth - What Sweet Potato DNA Reveals About Its "Mosaic Ancestors"

Despite the "gentle" taste of sweet potatoes, they are genetically quite formidable. While humans are diploid, receiving one set of chromosomes from each parent, sweet potatoes are hexaploid. This is akin to organizing a massive library catalog where six sets of the same book are mixed together and need to be sorted back onto their original shelves. Researchers have long struggled with this "untangling process" known as phasing.


In August 2025, this challenge was finally overcome. A team led by Professor Zhangjun Fei at BTI completed a chromosome-level "phased genome" of the popular African variety "Tanzania" and reported it in Nature Plants. The paper and press release not only reveal the full scope of the hexaploid genome but also trace its evolutionary history. NatureBoyce Thompson Institute


What was "untangled": The Mosaic Ancestry

The greatest achievement was precisely demonstrating that sweet potatoes have a genome like a "mosaic" that mixes sequences from different wild species. One of the main ancestors, Ipomoea aequatoriensis, native to the coast of Ecuador, has a significant contribution. Meanwhile, there are also traces of an unidentified donor closely related to I. batatas 4x distributed in Central America. Surprisingly, these are not neatly separated into different "subgenomes" but are intricately mixed on the same chromosome. The research team suggests that sweet potatoes behave as a **"segmental allopolyploid". Essentially, it has a clever structure that acts as a "hybrid past" while functioning as a "single genome." Nature


This intricate structure, combined with the hexaploid's **"extra gene copies,"** likely contributes to its resilience to drought and pests, i.e., adaptability. In other words, having **redundancy (buffer) in components** makes it easier to maintain performance as a crop even in harsh environments.


Technical Breakthrough: Sorting 90 Chromosomes into 6 Sets

Sweet potatoes have 90 chromosomes (15 chromosomes × 6 sets). The core achievement here is the complete phasing of these 90 chromosomes into the original 6 sets (haplotypes). By combining cutting-edge technologies such as long-read sequencing and Hi-C, a chromosome-level reference sequence for the sample variety "Tanzania" was constructed. The data is available on the Sweetpotato Genomics Resource, and the raw data is registered with NCBI's BioProject. Nature


This achievement is also a leap built on the reference genomes of **diploid relatives (I. trifida/I. triloba)** accumulated since the 2010s and the pre-released data from the SweetGAINS project. With the definitive "hexaploid main body" in place, genomic selection, QTL analysis, and eQTL analysis can quickly be put into practical use. Naturesweetpotato.uga.edu


What Changes in Breeding Sites?

Reverse Engineering from Desired Traits will accelerate. For example, there are many important targets in Africa and Asia, such as drought tolerance, disease resistance, starch quality, and carotenoid content (source of vitamin A). In hexaploids, it is known that "allele dosage" affects traits, making it easier to predict how many copies of what should be stacked to achieve the desired phenotype in the shortest distance. Research at the end of 2024 also showed that the unique **"tuning of copy number"** in hexaploids is key to breeding. The reference sequence from this study provides a high-resolution map for this.


Another aspect not to be overlooked is food security. Sweet potatoes are robust, resource-efficient, and nutritious, making them a crucial crop, especially in Sub-Saharan Africa. If resistance and yield can be designed from the genome to balance, it will directly contribute to stabilizing yields in drought-prone areas. Boyce Thompson Institute


Also Known as a "Natural GMO"

Sweet potatoes are famous as a **"naturally gene-modified crop"** because they contain T-DNA from Agrobacterium in their genome. Although this is not directly related to the current findings, as the genome becomes clearer, the history of such horizontal gene transfer and the footprints of trait evolution should be readable with greater precision. PNAS


Data and Reproducibility: Towards a "Common Infrastructure" Accessible to All

The Nature Plants paper page organizes the locations of raw data (PRJNA1138727) and assembly/annotation, with browser and BLAST provided by the Sweetpotato Genomics Resource. The pre-released SweetGAINS data is also expected to become widely accessible with the lifting of "competition avoidance" restrictions following this official announcement (see each site's policy for details). Naturesweetpotato.uga.edu+1


SNS Reactions (Initial Notes)

As of the time of writing this article (morning of August 9, 2025 Japan time), it is about a day since the release. Initial information is spreading mainly through BTI's official news post, EurekAlert!, and Phys.org's editorial article. In the professional community, there is a noticeable positive reception, with comments like "completion of fully phased reference was eagerly awaited" and "breeding implementation will advance rapidly." Official routes for dissemination are as follows:
・BTI's news post (with explanations and images) Boyce Thompson Institute
・EurekAlert! distribution (with DOI and funding information) EurekAlert!
・Phys.org's summary (with editorial review) Phys.org

※ Due to platform specifications, individual posts on X (Twitter) may be difficult to verify due to login restrictions. If necessary, we can also handle chronological collection and visualization of specific keywords/hashtags (reactions from the Japanese-speaking community can also be investigated separately).


Looking Ahead: Future Research Themes

  • Refining Origin Analysis: Tracking the unidentified Central American donor. Comprehensive genome of wild populations and preserved strains. Nature

  • Mapping Trait Development: Integrating protein function prediction, expression (eQTL), and allele dosage models. Phys.org

  • Disease Resistance and Microbiomes: Designing multilayer resistance to viral and pathogenic pressures (utilizing NLRome and metagenomic resources). BioRxiv

Important Links (Primary Information)

  • Paper: Nature Plants "Phased chromosome-level assembly … of hexaploid sweetpotato" (Published August 8, 2025) Nature

  • Explanation: Phys.org (Summary article provided by BTI) Phys.org

  • Press: BTI Official News (Including image credits) Boyce Thompson Institute

  • Data: Sweetpotato Genomics Resource (Browser/BLAST) sweetpotato.uga.edu


Reference Article

Decoding Sweet Potato DNA: New Research Reveals Surprising Ancestry
Source: https://phys.org/news/2025-08-decoding-sweet-potato-dna-reveals.html

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