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Method to estimate genotype probabilities at individual loci in farm livestock

Summary

A Bayesian method to estimate genotype probabilities at a single locus using information on the individual and all its relatives and their mates has been developed. The method uses data over several generations, can deal with large numbers of individuals in large livestock families and allows for missing information. It can be extended to multiple alleles and can be used for autosomal or sex-linked loci. The allele frequencies and the form of expression (dominance, penetrance) must be specified. An algorithm using the method and involving an iterative procedure has been developed to calculate the genotype probabilities for practical use in livestock breeding. The method and algorithm were used to determine the accuracy of estimating genotype probabilities of sires for a female sex-limited trait, such as genetic variants of milk proteins. Data were similated and genotype probabilities estimated for 100 sires (20 replicates) with 3, 6 and 12 female offspring per sire, for different population frequencies, for additive and dominance gene action and for variable genotypic expression. Such simulation is useful in the design of testing systems for the use of information on specific genetic loci in selection.

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References

  1. Cannings C, Thompson EA, Skolnick MH (1978) Probability functions on complex pedigrees. Adv Appl Probab 10:26–81

  2. Carden AE, Hill WG, Webb AJ (1983) The inheritance of halothane susceptibility in pigs. Génét Sél Evol 15:65–82

  3. Elston RC (1987) Human quantitative genetics. In: Weir BS, Eisen EJ, Goodman MM, Namkoong G (eds) Proc 2nd Int Conf Quant Genet. Sinauer, Sunderland, pp 281–282

  4. Elston RC, Rao DC (1978) Statistical modeling and analysis in human genetics. Annu Rev Biophys Bioeng 7:253–286

  5. Elston RC, Stewart J (1971) A general model for the genetic analysis of pedigree data. Hum Hered 21:523–542

  6. Henderson CR (1984) Application of linear models in animal breeding. University of Guelph Press, Guelph

  7. Heuch I, Li FHF (1972) Pedig — A computer program for calculation of genotype probabilities using phenotype information. Clin Genet 3:501–504

  8. Kennedy BW, Schaeffer LR, Sorensen DA (1988) Genetic properties of animal models. J Dairy Sci 71(suppl 2):17–26

  9. Murphy EA, Mutalik GS (1969) The application of Bayesian methods to genetic counselling. Hum Hered 19:126–151

  10. Smith C, Bampton PR (1977) Inheritance of reaction to halothane anaesthesia in pigs. Genet Res 29:287–292

  11. Southwood OI, Simpson SP, Webb AJ (1988) Reaction of halothane anaesthesia among hetrozygotes at the halothane locus in British Landrace pigs. Génét Sél Evol 20:357–366

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Prepared during a leave at Centre for Genetic Improvement of Livestock, Guelph, Canada

Communicated by E.J. Eisen

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van Arendonk, J.A.M., Smith, C. & Kennedy, B.W. Method to estimate genotype probabilities at individual loci in farm livestock. Theoret. Appl. Genetics 78, 735–740 (1989). https://doi.org/10.1007/BF00262571

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Key words

  • Individual loci
  • Estimation
  • Genetic counseling
  • Genotype probabilities
  • Accuracy