The impact of selective genotyping on the response to selection using single-step genomic best linear unbiased prediction

Jeremy T. Howard, Tom A. Rathje, Caitlyn E. Bruns, Danielle F. Wilson-Wells, Stephen D. Kachman, Matthew L. Spangler

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Across the majority livestock species, routinely collected genomic and pedigree information has been incorporated into evaluations using single-step methods. As a result, strategies that reduce genotyping costs without reducing the response to selection are important as they could have substantial economic impacts on breeding programs. Therefore, the objective of the current study was to investigate the impact of selectively genotyping selection candidates on the selection response using simulation. Populations were simulated to mimic the genome and population structure of a swine and cattle population undergoing selection on an index comprised of the estimated breeding values (EBV) for 2 genetically correlated quantitative traits. Ten generations were generated and genotyping began generation 7. Two phenotyping scenarios were simulated that assumed the first trait was recorded early in life on all individuals and the second trait was recorded on all versus a random subset of the individuals. The EBV were generated from a bivariate animal model. Multiple genotyping scenarios were generated that ranged from not genotyping any selection candidates, a proportion of the selection candidates based on either their index value or chosen at random, and genotyping all selection candidates. An interim index value was utilized to decide who to genotype for the selective genotype strategy. The interim value assumed only the first trait was observed and the only genotypic information available was on animals in previous generations. Within each genotyping scenario 25 replicates were generated. Within each genotyping scenario the mean response per generation and the degree to which EBV were inflated/ deflated was calculated. Across both species and phenotyping strategies, the plateau of diminishing returns was observed when 60% of the selection candidates with the largest index values were genotyped. When randomly genotyping selection candidates, either 80 or 100% of the selection candidates needed to be genotyped for there not to be a reduction in the index response. Across both populations, no differences in the degree that EBV were inflated/deflated for either trait 1 or 2 were observed between nongenotyped and genotyped animals. The current study has shown that animals can be selectively genotyped in order to optimize the response to selection as a function of the cost to conduct a breeding program using single-step genomic best linear unbiased prediction.

Original languageEnglish (US)
Pages (from-to)4532-4542
Number of pages11
JournalJournal of animal science
Volume96
Issue number11
DOIs
StatePublished - Nov 21 2018

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genotyping
Breeding
genomics
prediction
breeding value
Population
Genotype
Costs and Cost Analysis
Livestock
Pedigree
phenotype
animals
selection response
Swine
Animal Models
genotype
breeding
Economics
Genome
economic impact

Keywords

  • Genomic selection
  • Genotype strategy
  • Simulation

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology
  • Genetics

Cite this

The impact of selective genotyping on the response to selection using single-step genomic best linear unbiased prediction. / Howard, Jeremy T.; Rathje, Tom A.; Bruns, Caitlyn E.; Wilson-Wells, Danielle F.; Kachman, Stephen D.; Spangler, Matthew L.

In: Journal of animal science, Vol. 96, No. 11, 21.11.2018, p. 4532-4542.

Research output: Contribution to journalArticle

Howard, Jeremy T. ; Rathje, Tom A. ; Bruns, Caitlyn E. ; Wilson-Wells, Danielle F. ; Kachman, Stephen D. ; Spangler, Matthew L. / The impact of selective genotyping on the response to selection using single-step genomic best linear unbiased prediction. In: Journal of animal science. 2018 ; Vol. 96, No. 11. pp. 4532-4542.
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