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Development of DNA melting peak profile-based high-resolution melting (MP-HRM) analysis for genotyping germplasms in onion breeding

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Abstract

Germplasm genotyping using molecular markers is important for the protection of crop varieties, crop breeding, and intellectual property rights. It is essential to for characterizing germplasm and identifying genetic characters using molecular markers for crops that take a long time to breed, such as bulb onions. In this study, we established a sensitive and inexpensive analytical method to characterize the germplasm of onion cultivars. Our method leverages existing high resolution melting (HRM) analysis techniques and combines melting peak profile-based HRM data collection, statistics, and database building. In terms of statistics, the Benjamini–Hochberg procedure was found to be more accurate than other statistical methods. Our method uses melting peak profiles, which are values unique to each germplasm based on various molecular markers. This method not only eliminates the need for comparative criteria, but also has the advantage of operating as a co-dominant marker that enables genotyping within populations. In addition, our method can be used regardless of the type of molecular marker, and it allows for easier construction of genotyping databases than previous methods. Importantly, our method will also be useful for molecular breeding of crops other than onion.

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Acknowledgements

This work was supported by the Korea Institute of Planning and Evaluation for Technology in Food, Agriculture, and Forestry (IPET) through the Golden Seed Project, funded by Ministry of Agriculture, Food and Rural Affairs (MAFRA) (213007-05-3-SBB20).

Author information

Gi-Ho Lee performed the majority of the experiment and data analysis. Hyun-Min Lee and So-Jeong Kim contributed to experimental implementation. Young-Doo Park designed the experiments and analyzed data. Gi-Ho Lee and Young-Doo Park wrote the manuscript. All authors reviewed and approved the manuscript.

Correspondence to Young-Doo Park.

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Communicated by Sung-Chur Sim.

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Lee, G., Lee, H., Kim, S. et al. Development of DNA melting peak profile-based high-resolution melting (MP-HRM) analysis for genotyping germplasms in onion breeding. Hortic. Environ. Biotechnol. 61, 139–152 (2020). https://doi.org/10.1007/s13580-019-00204-x

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Keywords

  • Breeding
  • Dendrogram
  • Molecular marker
  • Single nucleotide polymorphism
  • Simple sequence repeats