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Home / Equine Research Bank / Animals (Basel) / Application of Nanopore Sequencing for High Throughput Genot...
Animals : an open access journal from MDPI2023; 13(13); doi: 10.3390/ani13132227

Application of Nanopore Sequencing for High Throughput Genotyping in Horses.

Abstract: Nanopore sequencing is a third-generation biopolymer sequencing technique that relies on monitoring the changes in an electrical current that occur as nucleic acids are passed through a protein nanopore. Increasing quality of reads generated by nanopore sequencing systems encourages their application in genome-wide polymorphism detection and genotyping. In this study, we employed nanopore sequencing to identify genome-wide polymorphisms in the horse genome. To reduce the size and complexity of genome fragments for sequencing in a simple and cost-efficient manner, we amplified random DNA fragments using a modified DOP-PCR and sequenced the resulting products using the MinION system. After initial filtering, this generated 28,426 polymorphisms, which were validated at a 3% error rate. Upon further filtering for polymorphism and reproducibility, we identified 9495 SNPs that reflected the horse population structure. To conclude, the use of nanopore sequencing, in conjunction with a genome enrichment step, is a promising tool that can be practical in a variety of applications, including genotyping, population genomics, association studies, linkage mapping, and potentially genomic selection.
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Publication Date: 2023-07-06 PubMed ID: 37444025PubMed Central: PMC10340048DOI: 10.3390/ani13132227Google Scholar: Lookup
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  • Journal Article

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research paper discusses the use of Nanopore sequencing for genotyping in horses, effectively identifying nearly 10,000 single nucleotide polymorphisms (SNPs) that reflect the horse population structure.

Introduction to Nanopore Sequencing

  • Nanopore sequencing is a novel biopolymer sequencing technique. It identifies nucleic acids by measuring changes in electrical current as these molecules pass through a protein nanopore.
  • Due to advances in the technique which have improved the quality of reads, nanopore sequencing is increasingly being used for detecting genome-wide polymorphisms and genotyping.

Methodology

  • For this study, nanopore sequencing was used to identify genome-wide polymorphisms in the horse genome.
  • The researchers reduced the size and complexity of genome fragments to be sequenced using a modified DOP-PCR technique. This resulted in random DNA fragments being amplified.
  • Following this, the amplified DNA fragments were then sequenced using the MinION system.

Results

  • The initial screening process led to the detection of 28,426 polymorphisms. These were validated with a 3% error rate.
  • Upon further filtering for polymorphism and reproducibility, 9495 single nucleotide polymorphisms (SNPs) were isolated. These SNPs reflect the horse population structure.

Conclusion

  • The study concluded that the use of nanopore sequencing, partnered with a genome enrichment step, presents a promising tool for genotyping horses.
  • Furthermore, the technique could have practical implications in various applications, such as population genomics, association studies, linkage mapping, and potentially genomic selection.

Cite This Article

APA
Gurgul A, Jasielczuk I, Szmatoła T, Sawicki S, Semik-Gurgul E, Długosz B, Bugno-Poniewierska M. (2023). Application of Nanopore Sequencing for High Throughput Genotyping in Horses. Animals (Basel), 13(13). https://doi.org/10.3390/ani13132227

Publication

Animals : an open access journal from MDPI
ISSN: 2076-2615
NlmUniqueID: 101635614
Country: Switzerland
Language: English
Volume: 13
Issue: 13

Researcher Affiliations

Gurgul, Artur
  • Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
Jasielczuk, Igor
  • Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
Szmatoła, Tomasz
  • Center of Experimental and Innovative Medicine, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
Sawicki, Sebastian
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
Semik-Gurgul, Ewelina
  • Department of Animal Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083 Balice, Poland.
Długosz, Bogusława
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.
Bugno-Poniewierska, Monika
  • Department of Animal Reproduction, Anatomy and Genomics, University of Agriculture in Krakow, al. Mickiewicza 24/28, 30-059 Krakow, Poland.

Grant Funding

  • POIR.01.03.01-00-0005/17 / National Center for Research and Development

Conflict of Interest Statement

The authors declare no conflict of interest.

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Citations

This article has been cited 2 times.
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  2. Liu X, Zheng J, Ding J, Wu J, Zuo F, Zhang G. When Livestock Genomes Meet Third-Generation Sequencing Technology: From Opportunities to Applications. Genes (Basel) 2024 Feb 15;15(2).
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