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Amplicon Sequencing using the Long-Read Sequencing Technologies
Published on: August 29, 2025
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A highly flexible and repeatable genotyping method for aquaculture studies based on target amplicon sequencing using
Mana Sato1, Sho Hosoya2, Sota Yoshikawa1,3
1Fisheries Laboratory, University of Tokyo, Hamamatsu, 431-0214, Japan.
Scientific Reports
|May 8, 2019
Summary
This study developed a flexible and repeatable genotyping method using custom SNP panels for farmed fugu (Takifugu rubripes). The method is suitable for aquaculture genetic studies, including molecular breeding and genomic selection.
Area of Science:
- Genetics and Genomics
- Aquaculture
- Molecular Breeding
Background:
- Genome-wide single nucleotide polymorphism (SNP) studies are crucial in genetics and genomics.
- High-throughput genotyping methods with flexibility in SNP and sample numbers are needed for diverse research goals.
- Existing methods like Ion AmpliSeq are often optimized for diagnostics, necessitating adaptable solutions for aquaculture.
Purpose of the Study:
- To design and validate a custom SNP genotyping panel for farmed fugu (Takifugu rubripes).
- To assess the feasibility of this method for aquaculture genetic studies, including molecular breeding.
- To evaluate the repeatability and flexibility of the custom panel for large-scale genotyping.
Main Methods:
- Designed a custom panel targeting 3,187 genome-wide SNPs for Takifugu rubripes.
- Applied amplicon sequencing on an Illumina MiSeq platform for genotyping farmed fugu (n=326 per library).
- Performed genetic analysis on genotype data to assess population structure and sex determination.
Main Results:
- Successfully amplified over 99% of target regions (3,178 SNPs), with 2,655 SNPs available after filtering.
- Demonstrated high repeatability with a strong correlation (r=0.993) in SNP coverage depth between duplicate runs.
- Genetic analysis accurately identified known fugu population structure and the sex-determining locus.
Conclusions:
- The custom SNP panel genotyping method offers superior repeatability and flexibility for aquaculture studies.
- This approach is well-suited for genetic research in fugu, including marker-assisted selection and genomic selection for molecular breeding.
- The developed method provides a valuable tool for advancing selective breeding programs in farmed fish.
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