title: Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost.
abstract: BACKGROUND
  Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Genomic information offers great potential to increase rates of genetic gain but it is expensive to generate. Low-cost genotyping strategies combined with genotype imputation offer dramatically reduced costs. However, both the costs and accuracy of imputation of these strategies are highly sensitive to several factors. The objective of this paper was to explore the cost and imputation accuracy of several alternative genotyping strategies in pedigreed populations.
  
  
  METHODS
  Pedigree and genotype data from a commercial pig population were used. Several alternative genotyping strategies were explored. The strategies differed in the density of genotypes used for the ancestors and the individuals to be imputed. Parents, grandparents, and other relatives that were not descendants, were genotyped at high-density, low-density, or extremely low-density, and associated costs and imputation accuracies were evaluated.
  
  
  RESULTS
  Imputation accuracy and cost were influenced by the alternative genotyping strategies. Given the mating ratios and the numbers of offspring produced by males and females, an optimized low-cost genotyping strategy for a commercial pig population could involve genotyping male parents at high-density, female parents at low-density (e.g. 3000 SNP), and selection candidates at very low-density (384 SNP).
  
  
  CONCLUSIONS
  Among the selection candidates, 95.5% and 93.5% of the genotype variation contained in the high-density SNP panels were recovered using a genotyping strategy that costs respectively, $24.74 and $20.58 per candidate.
authors: Animal Science Department, North Carolina State University, Campus, Box 7621, Raleigh, NC 27695, USA.
authors: Yijian
authors: Y
authors: Huang
authors: John M
authors: JM
authors: Hickey
authors: Matthew A
authors: MA
authors: Cleveland
authors: Christian
authors: C
authors: Maltecca
mesh_terms: D000818:Animals; D001947:Breeding / Q000191:economics*; D005260:Female; D005821:Genetic Techniques / Q000191:economics*; D005838:Genotype; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D013552:Swine / Q000235:genetics* / Q000502:physiology