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

PY - 2020

Y1 - 2020

N2 - 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 animals for further studies to fine map quantitative trait loci as well as improving the 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 LL and YY, 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 [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 animals for further studies to fine map quantitative trait loci as well as improving the 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 LL and YY, 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

U2 - 10.1093/jas/skaa229

DO - 10.1093/jas/skaa229

M3 - Journal article

C2 - 32687196

AN - SCOPUS:85089127499

VL - 98

JO - Journal of Animal Science

JF - Journal of Animal Science

SN - 0021-8812

IS - 7

M1 - skaa229

ER -