TY - JOUR
T1 - Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds
AU - Cai, Zexi
AU - Sarup, Pernille
AU - Ostersen, Tage
AU - Nielsen, Bjarne
AU - Fredholm, Merete
AU - Karlskov-Mortensen, Peter
AU - Sørensen, Peter
AU - Jensen, Just
AU - Guldbrandtsen, Bernt
AU - Lund, Mogens Sandø
AU - Christensen, Ole Fredslund
AU - Sahana, Goutam
N1 - © The Author(s) 2020. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: [email protected].
PY - 2020/7
Y1 - 2020/7
N2 - Whole genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace, and Yorkshire) 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 like gain or lost of stop codon. Using the whole-genome sequence dataset as the reference, imputation accuracy for pigs genotyped with high-density SNP chips was examined. The overall average imputation accuracy for all bi-allelic 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 animals for further studies to fine map quantitative trait loci as well as improving prediction accuracy in genomic selection. Signatures of selection were identified both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during breed development or subsequent divergent selection. However, the fixation indices did not indicate a strong divergence among these three breeds. In Landrace and Yorkshire, the integrated haplotype score identified genomic regions under recent selection. These regions contained genes for olfactory receptors and oxidoreductases. Olfactory receptor genes that might have played a major role in the domestication were previously reported to have been under selection in several species including cattle and swine.
AB - Whole genome sequencing of 217 animals from three Danish commercial pig breeds (Duroc, Landrace, and Yorkshire) 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 like gain or lost of stop codon. Using the whole-genome sequence dataset as the reference, imputation accuracy for pigs genotyped with high-density SNP chips was examined. The overall average imputation accuracy for all bi-allelic 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 animals for further studies to fine map quantitative trait loci as well as improving prediction accuracy in genomic selection. Signatures of selection were identified both through analyses of fixation and differentiation to reveal selective sweeps that may have had prominent roles during breed development or subsequent divergent selection. However, the fixation indices did not indicate a strong divergence among these three breeds. In Landrace and Yorkshire, the integrated haplotype score identified genomic regions under recent selection. These regions contained genes for olfactory receptors and oxidoreductases. Olfactory receptor genes that might have played a major role in the domestication were previously reported to have been under selection in several species including cattle and swine.
KW - Commercial pig
KW - Imputation
KW - Population structure
KW - Whole-genome sequencing
UR - http://www.scopus.com/inward/record.url?scp=85089127499&partnerID=8YFLogxK
U2 - 10.1093/jas/skaa229
DO - 10.1093/jas/skaa229
M3 - Journal article
C2 - 32687196
SN - 0021-8812
VL - 98
JO - Journal of Animal Science
JF - Journal of Animal Science
IS - 7
M1 - 229
ER -