Redefining and interpreting genomic relationships of metafounders
Abstract Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice...
Saved in:
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | deu |
| Published: |
BMC
2024-05-01
|
| Series: | Genetics Selection Evolution |
| Online Access: | https://doi.org/10.1186/s12711-024-00891-w |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1850196444818964480 |
|---|---|
| author | Andres Legarra Matias Bermann Quanshun Mei Ole F. Christensen |
| author_facet | Andres Legarra Matias Bermann Quanshun Mei Ole F. Christensen |
| author_sort | Andres Legarra |
| collection | DOAJ |
| description | Abstract Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics—namely, heterozygosities, F ST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy–Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form $${\Gamma }_{\left(b,{b}^{\prime}\right)}=\left(\frac{2}{n}\right)\left(2{\mathbf{p}}_{b}-\mathbf{1}\right)\left(2{\mathbf{p}}_{{b}^{\prime}}-\mathbf{1}\right)^{\prime}$$ Γ b , b ′ = 2 n 2 p b - 1 2 p b ′ - 1 ′ with $$\mathbf{p}$$ p being vectors of allele frequencies at $$n$$ n markers in populations $$b$$ b and $$b^{\prime}$$ b ′ . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; F ST differentiation coefficients; segregation variance; and Nei’s genetic distance) can be obtained from elements of matrix $${\varvec{\Gamma}}$$ Γ . |
| format | Article |
| id | doaj-art-70659fe334ce4d1aad79e5e05221a320 |
| institution | OA Journals |
| issn | 1297-9686 |
| language | deu |
| publishDate | 2024-05-01 |
| publisher | BMC |
| record_format | Article |
| series | Genetics Selection Evolution |
| spelling | doaj-art-70659fe334ce4d1aad79e5e05221a3202025-08-20T02:13:27ZdeuBMCGenetics Selection Evolution1297-96862024-05-015611710.1186/s12711-024-00891-wRedefining and interpreting genomic relationships of metafoundersAndres Legarra0Matias Bermann1Quanshun Mei2Ole F. Christensen3CDCBAnimal and Dairy Science, University of GeorgiaDepartment of Biostatistics, Boston University School of Public HealthCenter for Quantitative Genetics and Genomics, Aarhus UniversityAbstract Metafounders are a useful concept to characterize relationships within and across populations, and to help genetic evaluations because they help modelling the means and variances of unknown base population animals. Current definitions of metafounder relationships are sensitive to the choice of reference alleles and have not been compared to their counterparts in population genetics—namely, heterozygosities, F ST coefficients, and genetic distances. We redefine the relationships across populations with an arbitrary base of a maximum heterozygosity population in Hardy–Weinberg equilibrium. Then, the relationship between or within populations is a cross-product of the form $${\Gamma }_{\left(b,{b}^{\prime}\right)}=\left(\frac{2}{n}\right)\left(2{\mathbf{p}}_{b}-\mathbf{1}\right)\left(2{\mathbf{p}}_{{b}^{\prime}}-\mathbf{1}\right)^{\prime}$$ Γ b , b ′ = 2 n 2 p b - 1 2 p b ′ - 1 ′ with $$\mathbf{p}$$ p being vectors of allele frequencies at $$n$$ n markers in populations $$b$$ b and $$b^{\prime}$$ b ′ . This is simply the genomic relationship of two pseudo-individuals whose genotypes are equal to twice the allele frequencies. We also show that this coding is invariant to the choice of reference alleles. In addition, standard population genetics metrics (inbreeding coefficients of various forms; F ST differentiation coefficients; segregation variance; and Nei’s genetic distance) can be obtained from elements of matrix $${\varvec{\Gamma}}$$ Γ .https://doi.org/10.1186/s12711-024-00891-w |
| spellingShingle | Andres Legarra Matias Bermann Quanshun Mei Ole F. Christensen Redefining and interpreting genomic relationships of metafounders Genetics Selection Evolution |
| title | Redefining and interpreting genomic relationships of metafounders |
| title_full | Redefining and interpreting genomic relationships of metafounders |
| title_fullStr | Redefining and interpreting genomic relationships of metafounders |
| title_full_unstemmed | Redefining and interpreting genomic relationships of metafounders |
| title_short | Redefining and interpreting genomic relationships of metafounders |
| title_sort | redefining and interpreting genomic relationships of metafounders |
| url | https://doi.org/10.1186/s12711-024-00891-w |
| work_keys_str_mv | AT andreslegarra redefiningandinterpretinggenomicrelationshipsofmetafounders AT matiasbermann redefiningandinterpretinggenomicrelationshipsofmetafounders AT quanshunmei redefiningandinterpretinggenomicrelationshipsofmetafounders AT olefchristensen redefiningandinterpretinggenomicrelationshipsofmetafounders |