Abstract
This study investigated the potential loss expected from marker-assisted selection (MAS) when only a proportion of animals are genotyped using several selective genotyping strategies. A population resembling a commercial dairy cattle population over 25 yr was simulated, and the most informative individuals for genotyping were identified among the potential breeding candidates (young bulls and bull-dams). Two strategies were used to identify the most informative animals. The first genotyping strategy was based on selecting individuals for genotyping with predicted total genetic effect [sum of the predicted quantitative trait locus (QTL) and polygenic effects] close to the truncation point for selection. The second strategy used an index that extended the previous strategy to include the variance due to segregation of the QTL in the parents. The 2 strategies for selective genotyping were applied at the 2 different genotyping levels and compared with random selection of candidates for genotyping and complete genotyping of the potential candidates. All selective genotyping strategies at the same proportion of genotyping showed similar cumulative genetic level. The frequency of the favorable QTL allele increased faster with more animals genotyped. Extra response in total genetic effect (polygenic and QTL) was not significantly different between genotyping all candidates (100%), 20%, and 50% genotyping (except for yr 13), but all MAS strategies resulted in significantly higher response than BLUP until yr 18. With 50% (20%) genotyping of candidates for selection within a population, 95% (89%) of maximum cumulative QTL response was achieved in yr 13. All MAS schemes resulted in a 19% decrease in the rate of inbreeding compared with the BLUP scheme. Therefore, it is possible to use selective genotyping in practical dairy cattle breeding and decrease the genotyping costs with a minimal loss of response compared with complete genotyping of the potential candidates.
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