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A simple strategy for managing many recessive disorders in a dairy cattle breeding program.

Cole JB - Genet. Sel. Evol. (2015)

Bottom Line: 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.Several scenarios were considered, including scenarios with six hypothetical recessive alleles and 12 recessive alleles that are currently segregating in the US Holstein population.It can be easily implemented in software for mate allocation, and the code used in this study is freely available as a reference implementation.

View Article: PubMed Central - PubMed

Affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA. john.cole@ars.usda.gov.

ABSTRACT

Background: 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.

Methods: A 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.

Results: The 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.

Conclusions: The 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.

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Embryonic deaths by birth year. Proportion of embryos in each birth year that died due to the effects of recessive genotypes
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Fig5: Embryonic deaths by birth year. Proportion of embryos in each birth year that died due to the effects of recessive genotypes

Mentions: More affected calves were observed in the Pryce and modified Pryce schemes than in the random mating and truncation selection schemes. Figure 5 shows the proportion of simulated calves that were culled due to having homozygous recessive genotypes averaged over replicates for the Holstein scenario; results were similar for the high value and high frequency scenario and for the low value and low frequency scenario (data not shown). This is as expected because a bull can have a greater genetic superiority over its contemporaries than the value of the recessive alleles it may carry. Selection for a smaller total number of recessive alleles carried by an animal, rather than a lower frequency of homozygous recessive genotypes, could result in fewer embryonic losses [15]. Thus, there is a conflict between the goal of eliminating recessive alleles from the population, which involves fixing associated haplotypes in a homozygous state, and the goal of minimizing inbreeding, which seeks to avoid such increases in homozygous individuals.Fig. 5


A simple strategy for managing many recessive disorders in a dairy cattle breeding program.

Cole JB - Genet. Sel. Evol. (2015)

Embryonic deaths by birth year. Proportion of embryos in each birth year that died due to the effects of recessive genotypes
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4666089&req=5

Fig5: Embryonic deaths by birth year. Proportion of embryos in each birth year that died due to the effects of recessive genotypes
Mentions: More affected calves were observed in the Pryce and modified Pryce schemes than in the random mating and truncation selection schemes. Figure 5 shows the proportion of simulated calves that were culled due to having homozygous recessive genotypes averaged over replicates for the Holstein scenario; results were similar for the high value and high frequency scenario and for the low value and low frequency scenario (data not shown). This is as expected because a bull can have a greater genetic superiority over its contemporaries than the value of the recessive alleles it may carry. Selection for a smaller total number of recessive alleles carried by an animal, rather than a lower frequency of homozygous recessive genotypes, could result in fewer embryonic losses [15]. Thus, there is a conflict between the goal of eliminating recessive alleles from the population, which involves fixing associated haplotypes in a homozygous state, and the goal of minimizing inbreeding, which seeks to avoid such increases in homozygous individuals.Fig. 5

Bottom Line: 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.Several scenarios were considered, including scenarios with six hypothetical recessive alleles and 12 recessive alleles that are currently segregating in the US Holstein population.It can be easily implemented in software for mate allocation, and the code used in this study is freely available as a reference implementation.

View Article: PubMed Central - PubMed

Affiliation: Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, USA. john.cole@ars.usda.gov.

ABSTRACT

Background: 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.

Methods: A 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.

Results: The 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.

Conclusions: The 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.

Show MeSH
Related in: MedlinePlus