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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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Related in: MedlinePlus

Observed frequencies for a hypothetical recessive allele with a high frequency and a low economic value. Observed changes in minor allele frequency for a hypothetical recessive allele with a starting frequency of 0.90 and an economic value of $20 over 20 years under random selection, truncation selection, the Pryce method for controlling genomic inbreeding, and the modified Pryce method that accounts for recessives
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Fig4: Observed frequencies for a hypothetical recessive allele with a high frequency and a low economic value. Observed changes in minor allele frequency for a hypothetical recessive allele with a starting frequency of 0.90 and an economic value of $20 over 20 years under random selection, truncation selection, the Pryce method for controlling genomic inbreeding, and the modified Pryce method that accounts for recessives

Mentions: The rate of change in allele frequencies was similar for both the low ($20; Fig. 4) and high ($200; data not shown) value scenarios. This suggests that at high minor allele frequency the change from generation to generation is driven principally by genotype frequencies, not by the economic value. The fit of the observed to expected allele frequency changes was very good for both scenarios (data not shown).Fig. 4


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

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

Observed frequencies for a hypothetical recessive allele with a high frequency and a low economic value. Observed changes in minor allele frequency for a hypothetical recessive allele with a starting frequency of 0.90 and an economic value of $20 over 20 years under random selection, truncation selection, the Pryce method for controlling genomic inbreeding, and the modified Pryce method that accounts for recessives
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig4: Observed frequencies for a hypothetical recessive allele with a high frequency and a low economic value. Observed changes in minor allele frequency for a hypothetical recessive allele with a starting frequency of 0.90 and an economic value of $20 over 20 years under random selection, truncation selection, the Pryce method for controlling genomic inbreeding, and the modified Pryce method that accounts for recessives
Mentions: The rate of change in allele frequencies was similar for both the low ($20; Fig. 4) and high ($200; data not shown) value scenarios. This suggests that at high minor allele frequency the change from generation to generation is driven principally by genotype frequencies, not by the economic value. The fit of the observed to expected allele frequency changes was very good for both scenarios (data not shown).Fig. 4

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