Abstract
BackgroundHigh-density single nucleotide polymorphism genotypes have recently been used to identify a number of novel recessive mutations that adversely affect fertility in dairy cattle, as well as to track other conditions such as red coat color and polled. Most current methods for mate allocation fail to consider this information, and it will become increasingly difficult to manage matings as the number of recessive mutations to be accounted for increases.MethodsA modified version of a mating strategy that constrains inbreeding based on genomics (the Pryce method) was developed that also accounts for the economic effects of Mendelian disorders on overall economic merit (modified Pryce method) and compared with random mating, truncation selection, and the Pryce scheme. Several scenarios were considered, including scenarios with six hypothetical recessive alleles and 12 recessive alleles that are currently segregating in the US Holstein population.ResultsThe Pryce method and the modified Pryce method showed similar ability to reduce frequencies of recessive alleles, particularly for loci with frequencies greater than 0.30. The modified Pryce method outperformed the Pryce method for low-frequency alleles with small economic value. Cumulative genetic gain for the selection objective was slightly greater when using the Pryce method, but rates of inbreeding were similar across methods.ConclusionsThe proposed method reduces allele frequencies faster than other methods, and also can be used to maintain or increase the frequency of desirable recessives. It can be easily implemented in software for mate allocation, and the code used in this study is freely available as a reference implementation.
Highlights
High-density single nucleotide polymorphism genotypes have recently been used to identify a number of novel recessive mutations that adversely affect fertility in dairy cattle, as well as to track other conditions such as red coat color and polled
Test matings were used to identify carriers of recessive disorders [2], but most recessive mutations were identified after the carrier bull had sired many daughters and had sons used for artificial insemination (AI)
Two different comparisons were made using the slopes from these regressions: actual allele frequencies were compared to expected allele frequencies within methods to determine if allele frequencies were changing faster than expectations, and actual allele frequencies were compared across methods to determine if allele frequencies were changing more quickly based on the method used
Summary
High-density single nucleotide polymorphism genotypes have recently been used to identify a number of novel recessive mutations that adversely affect fertility in dairy cattle, as well as to track other conditions such as red coat color and polled. Most current methods for mate allocation fail to consider this information, and it will become increasingly difficult to manage matings as the number of recessive mutations to be accounted for increases. Several authors have proposed methods for including information on quantitative trait loci (QTL) in breeding programs. Shepherd and Kinghorn [11] described how QTL information can be included in a look-ahead mate selection scheme, and they have suggested that this could be incorporated into a comprehensive mating service, such as Total Genetic Resource ManagementTM Li et al [13, 14] reported that the use of QTL genotypes
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