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1000 Titel
  • Genomic selection using low density marker panels with application to a sire line in pigs
1000 Autor/in
  1. Wellmann, Robin |
  2. Preuß, Siegfried |
  3. Tholen, Ernst |
  4. Heinkel, Jörg |
  5. Bennewitz, Jörn |
  6. Wimmers, Klaus |
1000 Erscheinungsjahr 2013
1000 Art der Datei
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2013-07-29
1000 Erschienen in
1000 Quellenangabe
  • 45: 28
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2013
1000 Lizenz
1000 Verlagsversion
  • https://doi.org/10.1186/1297-9686-45-28 |
  • https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3750593/ |
1000 Ergänzendes Material
  • https://gsejournal.biomedcentral.com/articles/10.1186/1297-9686-45-28#Declarations |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • BACKGROUND: Genomic selection has become a standard tool in dairy cattle breeding. However, for other animal species, implementation of this technology is hindered by the high cost of genotyping. One way to reduce the routine costs is to genotype selection candidates with an SNP (single nucleotide polymorphism) panel of reduced density. This strategy is investigated in the present paper. Methods are proposed for the approximation of SNP positions, for selection of SNPs to be included in the low-density panel, for genotype imputation, and for the estimation of the accuracy of genomic breeding values. The imputation method was developed for a situation in which selection candidates are genotyped with an SNP panel of reduced density but have high-density genotyped sires. The dams of selection candidates are not genotyped. The methods were applied to a sire line pig population with 895 German Piétrain boars genotyped with the PorcineSNP60 BeadChip. RESULTS: Genotype imputation error rates were 0.133 for a 384 marker panel, 0.079 for a 768 marker panel, and 0.022 for a 3000 marker panel. Error rates for markers with approximated positions were slightly larger. Availability of high-density genotypes for close relatives of the selection candidates reduced the imputation error rate. The estimated decrease in the accuracy of genomic breeding values due to imputation errors was 3% for the 384 marker panel and negligible for larger panels, provided that at least one parent of the selection candidates was genotyped at high-density. Genomic breeding values predicted from deregressed breeding values with low reliabilities were more strongly correlated with the estimated BLUP breeding values than with the true breeding values. This was not the case when a shortened pedigree was used to predict BLUP breeding values, in which the parents of the individuals genotyped at high-density were considered unknown. CONCLUSIONS: Genomic selection with imputation from very low- to high-density marker panels is a promising strategy for the implementation of genomic selection at acceptable costs. A panel size of 384 markers can be recommended for selection candidates of a pig breeding program if at least one parent is genotyped at high-density, but this appears to be the lower bound.
1000 Fachgruppe
  1. Biologie |
  2. Agrarwissenschaften |
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://frl.publisso.de/adhoc/creator/V2VsbG1hbm4sIFJvYmlu|https://frl.publisso.de/adhoc/creator/UHJldcOfLCBTaWVnZnJpZWQ=|https://frl.publisso.de/adhoc/creator/VGhvbGVuLCBFcm5zdA==|https://frl.publisso.de/adhoc/creator/SGVpbmtlbCwgSsO2cmc=|https://frl.publisso.de/adhoc/creator/QmVubmV3aXR6LCBKw7Zybg==|http://orcid.org/0000-0002-9523-6790
1000 Label
1000 Förderer
  1. Ministerium für Ländlichen Raum und Verbraucherschutz Baden-Württemberg, Germany |
  2. Schweinezuchtverband Baden-Württemberg, Germany |
  3. Schweinezuchtverband Schleswig-Holstein, Germany |
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1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer Ministerium für Ländlichen Raum und Verbraucherschutz Baden-Württemberg, Germany |
    1000 Förderprogramm -
    1000 Fördernummer -
  2. 1000 joinedFunding-child
    1000 Förderer Schweinezuchtverband Baden-Württemberg, Germany |
    1000 Förderprogramm -
    1000 Fördernummer -
  3. 1000 joinedFunding-child
    1000 Förderer Schweinezuchtverband Schleswig-Holstein, Germany |
    1000 Förderprogramm -
    1000 Fördernummer -
1000 Objektart article
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1000 @id frl:6404555.rdf
1000 Erstellt am 2017-09-21T15:04:45.313+0200
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1000 Zuletzt bearbeitet Thu Jan 30 18:14:08 CET 2020
1000 Objekt bearb. Wed May 16 12:56:21 CEST 2018
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1000 Oai Id
  1. oai:frl.publisso.de:frl:6404555 |
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