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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 versus expected allele frequencies of Holstein recessive alleles under the Pryce scenario. Observed versus expected changes in minor allele frequencies for BLAD, brachyspina, CVM, DUMPS, HH1–HH5, horned, mulefoot, and red coat color over 20 years using the Pryce method for controlling genomic inbreeding. Note that the horned subplot is scaled differently on the y axis than the other subplots because of the horned allele frequency
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Fig2: Observed versus expected allele frequencies of Holstein recessive alleles under the Pryce scenario. Observed versus expected changes in minor allele frequencies for BLAD, brachyspina, CVM, DUMPS, HH1–HH5, horned, mulefoot, and red coat color over 20 years using the Pryce method for controlling genomic inbreeding. Note that the horned subplot is scaled differently on the y axis than the other subplots because of the horned allele frequency

Mentions: Changes in allele frequencies for 11 of the 12 recessive loci resulting from the four mating schemes are in Fig. 1. Frequencies are not shown for horned locus because the allele frequency remained above 99 % for all four schemes. The frequency of the 10 lethal alleles generally decreased over time in all scenarios. The frequencies of the HH1 and HH3 alleles decreased significantly faster (P < 0.05 after a Bonferroni correction) with the Pryce scheme than with the modified Pryce scheme. The rate of change in allele frequencies was similar for the Pryce (Fig. 2) and modified Pryce (data not shown) schemes. An advantage of the modified Pryce scheme is that it maintains the frequency of desirable recessive alleles, such as red coat color, in the population. With the Pryce scheme, the frequency of the red coat color allele decreased over time because with that scheme, there is no mechanism to balance undesirable economic effects of inbreeding against the desirable economic value of some recessive individuals. In the modified Pryce scheme, the positive economic value of red coat color offset the inbreeding penalty and it maintained a relatively constant gene frequency over time. Avoidance of genomic inbreeding limits homozygosity, but eventually the population should become homozygous for the favorable allele.Fig. 1


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

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

Observed versus expected allele frequencies of Holstein recessive alleles under the Pryce scenario. Observed versus expected changes in minor allele frequencies for BLAD, brachyspina, CVM, DUMPS, HH1–HH5, horned, mulefoot, and red coat color over 20 years using the Pryce method for controlling genomic inbreeding. Note that the horned subplot is scaled differently on the y axis than the other subplots because of the horned allele frequency
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

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

Fig2: Observed versus expected allele frequencies of Holstein recessive alleles under the Pryce scenario. Observed versus expected changes in minor allele frequencies for BLAD, brachyspina, CVM, DUMPS, HH1–HH5, horned, mulefoot, and red coat color over 20 years using the Pryce method for controlling genomic inbreeding. Note that the horned subplot is scaled differently on the y axis than the other subplots because of the horned allele frequency
Mentions: Changes in allele frequencies for 11 of the 12 recessive loci resulting from the four mating schemes are in Fig. 1. Frequencies are not shown for horned locus because the allele frequency remained above 99 % for all four schemes. The frequency of the 10 lethal alleles generally decreased over time in all scenarios. The frequencies of the HH1 and HH3 alleles decreased significantly faster (P < 0.05 after a Bonferroni correction) with the Pryce scheme than with the modified Pryce scheme. The rate of change in allele frequencies was similar for the Pryce (Fig. 2) and modified Pryce (data not shown) schemes. An advantage of the modified Pryce scheme is that it maintains the frequency of desirable recessive alleles, such as red coat color, in the population. With the Pryce scheme, the frequency of the red coat color allele decreased over time because with that scheme, there is no mechanism to balance undesirable economic effects of inbreeding against the desirable economic value of some recessive individuals. In the modified Pryce scheme, the positive economic value of red coat color offset the inbreeding penalty and it maintained a relatively constant gene frequency over time. Avoidance of genomic inbreeding limits homozygosity, but eventually the population should become homozygous for the favorable allele.Fig. 1

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