Genotype imputation from low-coverage whole-genome sequencing data of rainbow trout

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 SNP (single nucleotide polymorphism) array genotyping. The objectives of this study were 1) to construct a haplotype reference panel for genotype imputation from lcWGS data in rainbow trout (Oncorhynchus mykiss); and 2) to evaluate the concordance between imputed genotypes and SNP-array genotypes.