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Foundation Animal Effects: Difference between revisions
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A founder animal can be assigned to more than one genetic group. The genetic group assignment is determined by the animals parents' breed or the animal's age group of origin. Additionally, if one parent is know (often the dam) then the animal is partially assigned to the breed of sire or year genetic group. | A founder animal can be assigned to more than one genetic group. The genetic group assignment is determined by the animals parents' breed or the animal's age group of origin. Additionally, if one parent is know (often the dam) then the animal is partially assigned to the breed of sire or year genetic group. | ||
Additive genetic groups are included as fixed effects in | Additive genetic groups are included as fixed effects in most North American national cattle evaluations. While computationally easy to set up, including additive genetic groups may cause instability during iteration for the solution of the mixed model equations. More sophisticated preconditioners can be useful to improve performance to convergence during iteration. | ||
=Metafounders= | =Metafounders= | ||
The use of genomic data allows for the inclusion of an alternative to additive genetic groups. Unlike additive genetic groups, metafounder effects can account for relationships between foundation groups even though they may be distinct breeds.<ref>Legarra A, Christensen OF, Vitezica ZG, Aguilar I, Misztal I. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships. Genetics. 2015 Jun;200(2):455-68. doi: 10.1534/genetics.115.177014. Epub 2015 Apr 14. PMID: 25873631; PMCID: PMC4492372.</ref> Because all breeds ultimately come from the same origins they have many of the same alleles. The genomic data can be used to | The use of genomic data allows for the inclusion of an alternative to additive genetic groups. Unlike additive genetic groups, metafounder effects can account for relationships between foundation groups even though they may be distinct breeds.<ref>Legarra A, Christensen OF, Vitezica ZG, Aguilar I, Misztal I. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships. Genetics. 2015 Jun;200(2):455-68. doi: 10.1534/genetics.115.177014. Epub 2015 Apr 14. PMID: 25873631; PMCID: PMC4492372.</ref> Because all breeds ultimately come from the same origins they have many of the same alleles. The genomic data can be used to estimate the alleles common by decent from an original ancestral population. | ||
The metafounder approach uses a "pseudo-individual" to represent an animal of ancestral origin analogous to additive genetic groups. These pseudo individuals are designated using pedigree and genomic data to estimate degree of relationship (i.e., homozygosity) across populations. | The metafounder approach uses a "pseudo-individual" to represent an animal of ancestral origin analogous to additive genetic groups. These pseudo individuals are designated using pedigree and genomic data to estimate degree of relationship (i.e., homozygosity) across populations. | ||
=References= | =References= | ||
Revision as of 19:09, 22 June 2024
UNDER CONSTRUCTION...
Implementing BLUP animal models without accounting for differences in foundation animals' genetic merit can result in biased EPDs. Differences in additive genetic merit between foundation animals can be a result of different breeds of origin, or founders of the same breed entering the data used for genetic evaluation at different periods of time. The latter differences are due to genetic trend resulting from within breed selection.
Additive genetic groups
All foundation animals are modeled as coming from a population with the same average genetic merit when additive genetic group effects are not included. [1][2] Including additive genetic groups permit the model to predict genetic differences that occur between the groups. These differences impact the EPDs of the descendants of the foundation animals.
When designating genetic groups by periods of time there is a balance between size of group and amount of time to cluster groups on. Too short a period results in groups prediction with high prediction errors. Too long a time period decreases the precision of the prediction. This problem is compounded in multi-breed evaluations where groups are designated with both breed of founder and generation.
A founder animal can be assigned to more than one genetic group. The genetic group assignment is determined by the animals parents' breed or the animal's age group of origin. Additionally, if one parent is know (often the dam) then the animal is partially assigned to the breed of sire or year genetic group.
Additive genetic groups are included as fixed effects in most North American national cattle evaluations. While computationally easy to set up, including additive genetic groups may cause instability during iteration for the solution of the mixed model equations. More sophisticated preconditioners can be useful to improve performance to convergence during iteration.
Metafounders
The use of genomic data allows for the inclusion of an alternative to additive genetic groups. Unlike additive genetic groups, metafounder effects can account for relationships between foundation groups even though they may be distinct breeds.[3] Because all breeds ultimately come from the same origins they have many of the same alleles. The genomic data can be used to estimate the alleles common by decent from an original ancestral population.
The metafounder approach uses a "pseudo-individual" to represent an animal of ancestral origin analogous to additive genetic groups. These pseudo individuals are designated using pedigree and genomic data to estimate degree of relationship (i.e., homozygosity) across populations.
References
- ↑ Westell, R. A., R. L. Quaas, and L. D. Van Vleck. 1988. Genetic groups in an animal model. J. Dairy Sci. 71:1310.
- ↑ Quaas, R. L. 1988. Additive genetic model with groups and relationships. J. Dairy Sci. 71:1338.
- ↑ Legarra A, Christensen OF, Vitezica ZG, Aguilar I, Misztal I. Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships. Genetics. 2015 Jun;200(2):455-68. doi: 10.1534/genetics.115.177014. Epub 2015 Apr 14. PMID: 25873631; PMCID: PMC4492372.
