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Accurate genotype imputation from low-coverage whole-genome sequencing data of rainbow trout.

G3 (Bethesda, Md.) - 4 Sept 2024

Liu Sixin, Martin Kyle E, Snelling Warren M, Long Roseanna, Leeds Timothy D, Vallejo Roger L, Wiens Gregory D, Palti Yniv

Abstract excerpt

With the rapid and significant cost reduction of next-generation sequencing, low-coverage whole-genome sequencing (lcWGS), followed by genotype imputation, is becoming a cost-effective alternative to single-nucleotide polymorphism (SNP)-array genotyping. The objectives of this study were 2-fold: (1) construct a haplotype reference panel for genotype imputation from lcWGS data in rainbow trout (Oncorhynchus...

Topics

Animals
Oncorhynchus mykiss
Polymorphism, Single Nucleotide
Whole Genome Sequencing
Genotype
Haplotypes
High-Throughput Nucleotide Sequencing
Genome
Breeding

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Identifiers

PMID: 39041837
DOI: 10.1093/g3journal/jkae168
PMCID: PMC11373650

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