Affordable sequencing method deciphers polyploid crops

For decades, scientists have struggled to untangle the genetic complexity of crops with multiple chromosome sets. Now, researchers have unveiled a cost-effective sequencing method, dpMIG-seq, that makes this task both faster and more accessible. Applied to tetraploid blueberries, the approach delivered accurate, reproducible genetic markers even from very small amounts of DNA. The team constructed a high-density genetic map and uncovered how chromosomes pair randomly—or sometimes preferentially—during reproduction. They also detected unique features of polyploid inheritance, such as quadrivalent formation and double reduction. This discovery offers a powerful new tool for exploring polyploid genomes and accelerating crop improvement.

Polyploid crops like potato, wheat, and blueberry are essential to agriculture, yet their genetics remain notoriously difficult to decode. Traditional sequencing approaches are often expensive, slow, and reliant on pristine DNA samples—barriers that limit their practical use in breeding programs. In blueberries, debates have long persisted over whether tetraploid cultivars inherit traits in a disomic or polysomic manner, leaving breeders with unanswered questions.

A research team from Kyoto University and Okayama University has introduced a game-changing approach for decoding polyploid genomes. In their study, published (DOI: 10.1093/hr/uhae248) on September 4, 2024 in Horticulture Research, they describe how the dpMIG-seq method provided an accurate genetic roadmap of tetraploid blueberry inheritance. Unlike conventional techniques, dpMIG-seq is inexpensive, fast, and effective even with low-quality DNA. The findings not only clarify the chromosome behavior of blueberries but also establish a foundation for tackling complex inheritance in other polyploid crops.

The study focused on two blueberry cultivars, ‘Spartan’ and ‘Blue Muffin’. Using dpMIG-seq, the researchers bypassed the need for restrictive DNA purification steps by employing degenerate primers in PCR, enabling the detection of genome-wide single nucleotide polymorphisms (SNPs) from minimal DNA inputs. Tests showed that the method was remarkably consistent, with correlation coefficients between replicates exceeding 0.91, even at extremely low DNA concentrations. After filtering, the team assembled an integrated linkage map spanning more than 1,380 centimorgans and containing 6,000 reliable SNP markers. This map revealed that most chromosomes paired randomly during meiosis, though chromosome 11 in one cultivar exhibited a clear preference for specific pairings. The team also documented widespread quadrivalent formations—unique to polyploids—and identified double reduction events, both of which affect how traits are inherited. Costing just about one dollar per sample, dpMIG-seq outperformed conventional sequencing methods in both efficiency and affordability. The findings highlight not only how blueberry genomes are structured but also how dpMIG-seq could transform the way scientists approach polyploid crops.

“Polyploid genetics has always been a frontier filled with complexity,” explained senior author Dr. Ryohei Nakano. “Our work shows that dpMIG-seq can make this frontier accessible. By applying the method to blueberries, we uncovered both the expected random pairing and surprising signs of preferential pairing in certain chromosomes. This new level of detail changes how we view inheritance in polyploids. More importantly, it demonstrates that affordable, high-throughput genotyping is possible, which could accelerate progress across many crop species.”

The success of dpMIG-seq in blueberries signals a turning point for crop science. For plant breeders, it provides a low-cost route to generate dense genetic maps that can guide selection for traits like disease resistance, flavor, and climate resilience. Its tolerance for low-quality DNA means researchers can work directly with diverse field samples, expanding its use to large-scale germplasm studies. Beyond blueberries, the method is expected to unlock inheritance mysteries in other polyploid crops, from potatoes to sweetpotatoes. By lowering technical and financial barriers, dpMIG-seq paves the way for more precise breeding strategies and sustainable agricultural innovation.

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References

DOI

10.1093/hr/uhae248

Original Source URL

https://doi.org/10.1093/hr/uhae248

Funding information

This work was supported by JSPS KAKENHI Grant Numbers 22K05630 and 22H04925 (PAGS).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2023. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.