Missing genotypes were imputed by the no double crossovers method, in which missing genotypes are filled in unless a recombination event is predicted to occur (R/qtl package manual; Broman et al. 2010).
This test fills in missing genotypes when they can be inferred from other family members, correcting for the biases that occur as a result.
Simulated proportions of missing genotypes for the two scenarios of incomplete genotyping are given in Table 3. Scenario 1 could be regarded as a situation that occurs at the start of MA-BLUP in realistic breeding programs.
The performance of the genotyping assay for each method was assessed using three criteria: missing genotypes (assay fail rates), incomplete genotypes (loci departing from HWE) and inaccurate genotypes (inconsistent genotypes across replicate samples).
This has resulted in high rates of missing genotypes (assay fail rates of 21%), incomplete genotypes (64% of loci departing from HWE) and inaccurate genotypes (1% of genotypes inconsistent across replicates).
SNPs with ≥2 missing genotypes were excluded.
The overall rate of missing genotypes was 9%.
Based on estimated parameters, missing genotypes are inferred.
Samples were screened for the proportion of missing genotypes, and animals with greater than 10% missing genotypes were removed.
Regarding missing genotypes, PGMDR discards families entirely when data on one SNP are missing.
