A method to approximate parents' contribution to gene content at marker locus

Gene content is the number of copies of an allele in a genotype of an animal. It can be used to study additive gene action of a candidate gene. A new method to approximate paternal and maternal contributions to gene content for an untyped animal being a member of large complex pedigree with incomplete molecular data was proposed. The proposed method was derived from gametic model and mixed model equations. In the model the sire and dam contribution to gene content at single biallelic locus are treated as random additive effects. A genotype elimination algorithm was used before computation to construct (co)variance matrix of parental contribution based on pedigree and molecular data available for the considered locus and linked markers, and to extend the vector of observations by concluding the only possible gene content for as many gametes as possible. The proposed method was compared to MCMC approach on a large complex pedigree and simulated data for hypothetical SNP. An average absolute difference between the results obtained by the use of MCMC approach and the proposed method was 0.037. The potential of the method was further evaluated for the model under exact (co)variance matrix, which was obtained by the use of MCMC approach. It was concluded that it can provide good approximation to parental contribution of gene content at single marker locus when MCMC approach is impractical.