ArticleScientific reports2019
A highly flexible and repeatable genotyping method for aquaculture studies based on target amplicon sequencing using next-generation sequencing technology.
Article in Scientific reports, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Approaches to Thoroughbred Horse Identification in Diverse Sample Types Using Multiplexed SNP-PCR Sequencing Panels.Animal genetics · 2026Article
- Removal of Transgenes and Evaluation of Yield Penalties in Genome Edited Bacterial Blight Resistant Rice Varieties.Plant biotechnology journal · 2026Article
- MKDESIGNER and TASEQ: a set of tools for plant genotyping by targeted amplicon sequencing.BMC bioinformatics · 2025Article
- A free lunch: microhaplotype discovery in an existing amplicon panel improves parentage assignment for the highly polymorphic Pacific oyster.G3 (Bethesda, Md.) · 2025Article
- Deep learning for genomic selection of aquatic animals.Marine life science & technology · 2024Review
- HASCH - A high-throughput amplicon-based SNP-platform for medicinal cannabis and industrial hemp genotyping applications.BMC genomics · 2024Article
- A multispecies amplicon sequencing approach for genetic diversity assessments in grassland plant species.Molecular ecology resources · 2022Article
- GWAS Reveal Novel Sex-Related Markers and Candidate Genes in Sea Urchin Mesocentrotus nudus.Marine biotechnology (New York, N.Y.) · 2022Article
- Genomic Prediction of Complex Traits in Perennial Plants: A Case for Forest Trees.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Genomic prediction for testes weight of the tiger pufferfish, Takifugu rubripes, using medium to low density SNPs.Scientific reports · 2021Article
- Handling of targeted amplicon sequencing data focusing on index hopping and demultiplexing using a nested metabarcoding approach in ecology.Scientific reports · 2021Article
- Genetic Dissection of a Precocious Phenotype in Male Tiger Pufferfish (Takifugu rubripes) using Genotyping by Random Amplicon Sequencing, Direct (GRAS-Di).Marine biotechnology (New York, N.Y.) · 2021Article
- Targeted amplicon sequencing + next-generation sequencing-based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum).BMC plant biology · 2021Article
- Population Genetic Analyses ofFrontiers in microbiology · 2021Article
- Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population.Evolution; international journal of organic evolution · 2021Article
- Genomic selection for heterobothriosis resistance concurrent with body size in the tiger pufferfish, Takifugu rubripes.Scientific reports · 2020Article
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7 authors.
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Abstract
Studies using genome-wide single nucleotide polymorphisms (SNPs) have become commonplace in genetics and genomics, due to advances in high-throughput sequencing technologies. Since the numbers of required SNPs and samples vary depending on each research goal, genotyping technologies with high flexibility in the number of SNPs/samples and high repeatability have been intensively investigated. For example, the ultrahigh-multiplexed amplicon sequencing, Ion AmpliSeq, has been used as a high-throughput genotyping method mainly for diagnostic purposes. Here, we designed a custom panel targeting 3,187 genome-wide SNPs of fugu, Takifugu rubripes, and applied it for genotyping farmed fugu to test its feasibility in aquaculture studies. We sequenced two libraries consisting of different pools of individuals (n = 326 each) on the Illumina MiSeq sequencer. Consequently, over 99% target regions (3,178 SNPs) were amplified and 2,655 SNPs were available after filtering steps. Strong correlation was observed in the mean depth of coverage of each SNP between duplicate runs (r = 0.993). Genetic analysis using these genotype data successfully detected the known population structure and the sex determining locus of fugu. These results show the method is superior in repeatability and flexibility, and suits genetic studies including molecular breeding, such as marker assisted and genomic selection.
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