Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds.

ABSTRACT: Whole-genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace [LL], and Yorkshire [YY]) was performed. Twenty-six million single-nucleotide polymorphisms (SNPs) and 8 million insertions or deletions (indels) were uncovered. Among the SNPs, 493,099 variants were located in coding sequences, and 29,430 were predicted to have a high functional impact such as gain or loss of stop codon. Using the whole-genome sequence dataset as the reference, the imputation accuracy for pigs genotyped with high-density SNP chips was examined. The overall average imputation accuracy for all biallelic variants (SNP and indel) was 0.69, while it was 0.83 for variants with minor allele frequency > 0.1. This study provides whole-genome reference data to impute SNP chip-genotyped a

SUBMITTER: Cai Z 

PROVIDER: S-EPMC7394143 | biostudies-literature | 2020 Jul

REPOSITORIES: biostudies-literature