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Zexi Cai

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

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Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds. / Cai, Zexi; Sarup, Pernille; Ostersen, Tage et al.
In: Journal of Animal Science, Vol. 98, No. 7, 229, 07.2020.

Research output: Contribution to journal/Conference contribution in journal/Contribution to newspaperJournal articleResearchpeer-review

Harvard

APA

CBE

Cai Z, Sarup P, Ostersen T, Nielsen B, Fredholm M, Karlskov-Mortensen P, Sørensen P, Jensen J, Guldbrandtsen B, Lund MS, et al. 2020. Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds. Journal of Animal Science. 98(7):Article 229. https://doi.org/10.1093/jas/skaa229

MLA

Vancouver

Cai Z, Sarup P, Ostersen T, Nielsen B, Fredholm M, Karlskov-Mortensen P et al. Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds. Journal of Animal Science. 2020 Jul;98(7):229. doi: 10.1093/jas/skaa229

Author

Cai, Zexi ; Sarup, Pernille ; Ostersen, Tage et al. / Genomic diversity revealed by whole-genome sequencing in three Danish commercial pig breeds. In: Journal of Animal Science. 2020 ; Vol. 98, No. 7.

Bibtex

@article{3974c8a61c414580854792c566165f17,
title = "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, 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.",
keywords = "Commercial pig, Imputation, Population structure, Whole-genome sequencing",
author = "Zexi Cai and Pernille Sarup and Tage Ostersen and Bjarne Nielsen and Merete Fredholm and Peter Karlskov-Mortensen and Peter S{\o}rensen and Just Jensen and Bernt Guldbrandtsen and Lund, {Mogens Sand{\o}} and Christensen, {Ole Fredslund} and Goutam Sahana",
note = "{\textcopyright} 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: journals.permissions@oup.com.",
year = "2020",
month = jul,
doi = "10.1093/jas/skaa229",
language = "English",
volume = "98",
journal = "Journal of Animal Science",
issn = "0021-8812",
publisher = "AMER SOC ANIMAL SCIENCE",
number = "7",

}

RIS

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: journals.permissions@oup.com.

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

VL - 98

JO - Journal of Animal Science

JF - Journal of Animal Science

SN - 0021-8812

IS - 7

M1 - 229

ER -