NZ 577870 Disclosed is a method of estimating a breeding value of a non-human individual for use in breeding of a non-human population having a genetic diversity equivalent to an effective population size (Ne) of less than 1000, said method comprising: genotyping a non-human individual in a current population for the presence or absence of informative markers in one or more chromosome segments, wherein at least one chromosome segment comprises a gene or locus of interest, and wherein said genotyping comprises determining genotypes at a subset of the informative markers at the gene or locus of interest and wherein genotype information for one or more other informative markers is missing from said determined genotypes； comparing the determined genotypes of the individual in the current population to the genotypes of informative markers in an ancestor and/or founder contributing at least 0.1% of the total genetic variance to the current population to thereby determine lineage of the chromosome segment of the non-human individual from an ancestor and/or founder of the current population from which the chromosome segment is derived, wherein the genotype of the ancestor and/or founder is known for the subset of the informative markers and for at least one informative marker for which genotype information is missing from the determined genotype of the individual in the current non-human population； inferring at least one informative genotype missing from the genotypes determined at (i) for the individual to be the same as for the ancestor and/or founder based on the lineage of the chromosome segments determined at (ii) to thereby produce at least one inferred genotype； estimating the breeding value of the individual by a process comprising estimating the effect of each determined genotype and the at least one inferred genotype on a trait for which the individual is to be bred to produce a genetic gain and summing the effects of each determined genotype and the at least one
