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- Title
Application of Nanopore Sequencing for High Throughput Genotyping in Horses.
- Authors
Gurgul, Artur; Jasielczuk, Igor; Szmatoła, Tomasz; Sawicki, Sebastian; Semik-Gurgul, Ewelina; Długosz, Bogusława; Bugno-Poniewierska, Monika
- Abstract
Simple Summary: Detection and genotyping of genetic variants across genomes has several applications that include, e.g., identification of genetic background of phenotypic traits, detection of disease-related variation, and analysis of population genetic structure. In this study, we attempt to develop a Nanopore sequencing-based genotyping strategy (with MinION system from Oxford Nanopore) that allows simple and cost-efficient genome-wide analysis in horse species. With this method, we generated 28,426 polymorphisms that were genotyped with high accuracy, with a level of error not exceeding 3%. The method can be further improved to increase the number of detected variants and improve their reliability by increasing the sequencing depth. 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.
- Subjects
GENETIC variation; NUCLEIC acids; NUCLEOTIDE sequencing; GENOME size; HORSES; GENOMES
- Publication
Animals (2076-2615), 2023, Vol 13, Issue 13, p2227
- ISSN
2076-2615
- Publication type
Article
- DOI
10.3390/ani13132227