Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens

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dc.contributor.author Wolc, Anna
dc.contributor.author Lamont, Susan
dc.contributor.author Wang, Chong
dc.contributor.author Habier, D.
dc.contributor.author Peiris, B. L.
dc.contributor.author Wolc, Anna
dc.contributor.author Wang, Chong
dc.contributor.author Kranis, A.
dc.contributor.author Watson, K. A.
dc.contributor.author Avendano, S.
dc.contributor.author Garrick, D. J.
dc.contributor.author Fernando, Rohan
dc.contributor.author Lamont, Susan
dc.contributor.author Dekkers, Jack
dc.contributor.department Animal Science
dc.date 2021-01-07T16:02:18.000
dc.date.accessioned 2021-02-24T21:12:03Z
dc.date.available 2021-02-24T21:12:03Z
dc.date.copyright Tue Jan 01 00:00:00 UTC 2013
dc.date.issued 2013-07-01
dc.description.abstract <p>One approach for cost-effective implementation of genomic selection is to genotype training individuals with a high-density (HD) panel and selection candidates with an evenly spaced, low-density (ELD) panel. The purpose of this study was to evaluate the extent to which the ELD approach reduces the accuracy of genomic estimated breeding values (GEBV) in a broiler line, in which 1,091 breeders from 3 generations were used for training and 160 progeny of the third generation for validation. All birds were genotyped with an Illumina Infinium platform HD panel that included 20,541 segregating markers. Two subsets of HD markers, with 377 (ELD-1) or 766 (ELD-2) markers, were selected as ELD panels. The ELD-1 panel was genotyped using KBiosciences KASPar SNP genotyping chemistry, whereas the ELD-2 panel was simulated by adding markers from the HD panel to the ELD-1 panel. The training data set was used for 2 traits: BW at 35 d on both sexes and hen house production (HHP) between wk 28 and 54. Methods Bayes-A, -B, -C and genomic best linear unbiased prediction were used to estimate HD-marker effects. Two scenarios were used: (1) the 160 progeny were ELD-genotyped, and (2) the 160 progeny and their dams (117 birds) were ELD-genotyped. The missing HD genotypes in ELD-genotyped birds were imputed by a Gibbs sampler, capitalizing on linkage within families. In scenario (1), the correlation of GEBV for BW (HHP) of the 160 progeny based on observed HD versus imputed genotypes was greater than 0.94 (0.98) with the ELD-1 panel and greater than 0.97 (0.99) with the ELD-2 panel. In scenario (2), the correlation of GEBV for BW (HHP) was greater than 0.92 (0.96) with the ELD-1 panel and greater than 0.95 (0.98) with the ELD-2 panel. Hence, in a pedigreed population, genomic selection can be implemented by genotyping selection candidates with about 400 ELD markers with less than 6% loss in accuracy. This leads to substantial savings in genotyping costs, with little sacrifice in accuracy.</p>
dc.description.comments <p>This article is published as Wang, C., D. Habier, B. L. Peiris, A. Wolc, A. Kranis, K. A. Watson, S. Avendano, D.J. Garrick, R.L. Fernando, S.J. Lamont, and J.C.M. Dekkers. "Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens." <em>Poultry Science</em> 92, no. 7 (2013): 1712-1723. DOI: <a href="https://doi.org/10.3382/ps.2012-02941" target="_blank">10.3382/ps.2012-02941</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/ans_pubs/597/
dc.identifier.articleid 1599
dc.identifier.contextkey 20153356
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath ans_pubs/597
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/93352
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/ans_pubs/597/2013_LamontSusan_AccuracyGenomic.pdf|||Sat Jan 15 01:04:30 UTC 2022
dc.source.uri 10.3382/ps.2012-02941
dc.subject.disciplines Agriculture
dc.subject.disciplines Animal Sciences
dc.subject.disciplines Genomics
dc.subject.disciplines Poultry or Avian Science
dc.subject.keywords genomic selection
dc.subject.keywords broiler
dc.subject.keywords accuracy
dc.subject.keywords low-density panel
dc.title Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 7103f024-4508-422f-82ff-1d5e544596a2
relation.isAuthorOfPublication 5dee3d24-aa7a-4fe1-abf6-f0bb615bfe24
relation.isAuthorOfPublication b715071c-c3bd-419c-b021-0ac4702f346a
relation.isOrgUnitOfPublication 85ecce08-311a-441b-9c4d-ee2a3569506f
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