dpMIG-seq: a game-changer in genetic mapping of tetraploid crops

Understanding inheritance patterns in polyploid crops has long posed technical and financial challenges, particularly in species like tetraploid blueberry. This study introduces a cost-effective, PCR-based sequencing method—dpMIG-seq—that simplifies and accelerates genotyping even from low-concentration DNA. By applying dpMIG-seq to a tetraploid blueberry F1 population, researchers constructed a high-resolution linkage map and uncovered chromosome-level details about meiotic pairing, preferential pairing, and quadrivalent formation. The method demonstrated high reproducibility and accuracy, proving its suitability for allele dosage genotyping. This innovation holds promise for advancing polyploid research and accelerating breeding efforts in complex crop genomes.

Polyploid crops, such as blueberries, often exhibit complex inheritance patterns that complicate genetic analysis and hinder breeding efforts. Traditional genotyping techniques typically require high-quality DNA and enzymatic digestion, which makes them time-consuming, labor-intensive, and less suitable for large populations or degraded samples. Although next-generation sequencing (NGS) technologies have enabled high-throughput genotyping, they still pose challenges in terms of cost and the accurate estimation of allele dosage, especially in polyploids with polysomic inheritance. Existing approaches like RAD-seq and ddRAD-seq are limited by their dependency on restriction enzymes, and MIG-seq lacks sensitivity for smaller genomes. Due to these limitations, there is an urgent need to develop a more efficient, affordable, and robust genotyping method for polyploid crops.

Researchers from Kyoto University and Okayama University have developed and validated a low-cost PCR-based sequencing method, dpMIG-seq, in a study (DOI: 10.1093/hr/uhae248) published on September 4, 2024, in Horticulture Research. The team applied this technique to analyze inheritance patterns in tetraploid blueberry and successfully constructed an integrated linkage map. Their work sheds light on genome-wide chromosomal behavior during meiosis and demonstrates the method’s utility in allele dosage genotyping from low-concentration DNA—a breakthrough for polyploid crop genetics.

The study evaluated dpMIG-seq using both technical and biological replicates of tetraploid blueberry DNA, revealing high reproducibility with Pearson's correlation coefficients ranging from 0.91 to 0.98—even at low DNA concentrations. The method outperformed traditional restriction enzyme-based sequencing techniques in terms of cost and flexibility. When applied to a tetraploid F1 population derived from ‘Spartan’ and ‘Blue Muffin’, dpMIG-seq enabled the construction of a comprehensive 6000-marker linkage map across 12 linkage groups.

Beyond technical validation, the study revealed key genetic behaviors. Most chromosomes displayed random meiotic pairing, consistent with polysomic inheritance. However, chromosome 11 of ‘Spartan’ showed signs of preferential pairing—suggesting non-random chromosomal behavior in certain cultivars. The team also confirmed the presence of quadrivalent formations and double reduction events across the genome, which varied by chromosome and cultivar. These findings provide deeper insights into chromosomal pairing configurations and recombination rates in blueberry and serve as a model for studying other polyploid crops.

“Our results demonstrate that dpMIG-seq is not only cost-efficient but also highly accurate for polyploid genotyping,” said Dr. Ryohei Nakano, corresponding author of the study. “By removing the need for DNA purification and concentration adjustments, this method streamlines sample preparation while still delivering high-resolution genetic data. This opens new possibilities for studying complex genomes and accelerating marker-assisted breeding in crops with polysomic inheritance.”

The successful application of dpMIG-seq in tetraploid blueberry sets the stage for broader adoption of this method in polyploid crops such as sweetpotato, potato, and alfalfa. Its low cost—estimated at just one US dollar per sample—and tolerance for low-quality DNA make it especially valuable in breeding programs with limited resources. Moreover, the method's ability to detect chromosomal pairing preferences and quadrivalent formations provides powerful tools for unraveling genetic complexities. As dpMIG-seq becomes more widely used, it is expected to accelerate genomic research, inform breeding strategies, and enhance yield, resilience, and quality traits in agriculturally important polyploid crops.

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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.