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Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens
Poultry Science
  • Chong Wang, Iowa State University
  • D. Habier, Iowa State University
  • B. L. Peiris, Iowa State University
  • Anna Wolc, Iowa State University
  • A. Kranis, Aviagen Ltd.
  • K. A. Watson, Aviagen Ltd.
  • S. Avendano, Aviagen Ltd.
  • D. J. Garrick, Iowa State University
  • Rohan L. Fernando, Iowa State University
  • Susan J. Lamont, Iowa State University
  • Jack C. M. Dekkers, Iowa State University
Document Type
Article
Publication Version
Published Version
Publication Date
7-1-2013
DOI
10.3382/ps.2012-02941
Abstract

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.

Comments

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." Poultry Science 92, no. 7 (2013): 1712-1723. DOI: 10.3382/ps.2012-02941. Posted with permission.

Creative Commons License
Creative Commons Attribution-NonCommercial-No Derivative Works 4.0 International
Copyright Owner
Poultry Science Association Inc.
Language
en
File Format
application/pdf
Citation Information
Chong Wang, D. Habier, B. L. Peiris, Anna Wolc, et al.. "Accuracy of genomic prediction using an evenly spaced, low-density single nucleotide polymorphism panel in broiler chickens" Poultry Science Vol. 92 Iss. 7 (2013) p. 1712 - 1723
Available at: http://works.bepress.com/chong-wang/121/