Metafounders are related to Fst fixation indices and reduce bias in single - step genomic evaluations

Autor: Carolina A Garcia-Baccino, Ignacy Misztal, Zulma G. Vitezica, Ole F. Christensen, Andres Legarra, R.J.C. Cantet, Ivan Pocrnic
Jazyk: angličtina
Rok vydání: 2017
Předmět:
Male
0301 basic medicine
GENETIC MERIT
BASE POPULATION
[SDV]Life Sciences [q-bio]
METAFOUNDERS
breeding value
Single step
Breeding
genetic evaluation
Gene Frequency
GENOMIC RELATIONSHIP
Statistics
Genetics(clinical)
GENERALIZE LITTLE SQUARE
education.field_of_study
04 agricultural and veterinary sciences
General Medicine
Pedigree
Fixation (population genetics)
purl.org/becyt/ford/4.2 [https]
structured population
BIAS
genotyped animal
GENOMIC PREDICTION
Algorithms
Otras Producción Animal y Lechería
inbreeding coefficient
Research Article
Heterozygote
Population
Generalized least squares
Best linear unbiased prediction
Biology
linear unbiased predictor
relationship matrice
us holstein
large number
new zealand
03 medical and health sciences
Bias
Genetics
Journal Article
Animals
Selection
Genetic
Allele
education
Allele frequency
Ecology
Evolution
Behavior and Systematics
ssGBLUP
Models
Genetic
0402 animal and dairy science
Producción Animal y Lechería
Heritability
040201 dairy & animal science
030104 developmental biology
CIENCIAS AGRÍCOLAS
Evolutionary biology
Animal Science and Zoology
ESTIMATE BREEDING VALUE
purl.org/becyt/ford/4 [https]
Genome-Wide Association Study
Zdroj: Genetics Selection Evolution (49), Non paginé. (2017)
Garcia-Baccino, CA, Legarra, A, Christensen, OF, Misztal, I, Pocrnic, I, Vitezica, ZG & Cantet, RJ 2017, ' Metafounders are related to F st fixation indices and reduce bias in single-step genomic evaluations. ', Genetics Selection Evolution . https://doi.org/10.1186/s12711-017-0309-2
Garcia-Baccino, C A, Legarra, A, Christensen, O F, Misztal, I, Pocrnic, I, Vitezica, Z G & Cantet, R J C 2017, ' Metafounders are related to F st fixation indices and reduce bias in single-step genomic evaluations ', Genetics Selection Evolution, vol. 49, no. 1, 34, pp. 1-14 . https://doi.org/10.1186/s12711-017-0309-2
CONICET Digital (CONICET)
Consejo Nacional de Investigaciones Científicas y Técnicas
instacron:CONICET
Genetics selection evolution
Vol.49, no.1
FAUBA Digital (UBA-FAUBA)
Universidad de Buenos Aires. Facultad de Agronomía
instacron:UBA-FAUBA
Genetics Selection Evolution
Genetics Selection Evolution, BioMed Central, 2017, 49 (1), pp.34. ⟨10.1186/s12711-017-0309-2⟩
Genetics, Selection, Evolution : GSE
ISSN: 0999-193X
1297-9686
DOI: 10.1186/s12711-017-0309-2
Popis: Background: Metafounders are pseudo-individuals that encapsulate genetic heterozygosity and relationships within and across base pedigree populations, i.e. ancestral populations. This work addresses the estimation and usefulness of metafounder relationships in single-step genomic best linear unbiased prediction (ssGBLUP). Results: We show that ancestral relationship parameters are proportional to standardized covariances of base allelic frequencies across populations, such as Fst fixation indexes. These covariances of base allelic frequencies can be estimated from marker genotypes of related recent individuals and pedigree. Simple methods for their estimation include naïve computation of allele frequencies from marker genotypes or a method of moments that equates average pedigree-based and marker-based relationships. Complex methods include generalized least squares (best linear unbiased estimator (BLUE)) or maximum likelihood based on pedigree relationships. To our knowledge, methods to infer Fst coefficients from marker data have not been developed for related individuals. We derived a genomic relationship matrix, compatible with pedigree relationships, that is constructed as a cross-product of {-1,0,1} codes and that is equivalent (apart from scale factors) to an identity-by-state relationship matrix at genome-wide markers. Using a simulation with a single population under selection in which only males and youngest animals are genotyped, we observed that generalized least squares or maximum likelihood gave accurate and unbiased estimates of the ancestral relationship parameter (true value: 0.40) whereas the naïve method and the method of moments were biased (average estimates of 0.43 and 0.35). We also observed that genomic evaluation by ssGBLUP using metafounders was less biased in terms of estimates of genetic trend (bias of 0.01 instead of 0.12), resulted in less overdispersed (0.94 instead of 0.99) and as accurate (0.74) estimates of breeding values than ssGBLUP without metafounders and provided consistent estimates of heritability. Conclusions: Estimation of metafounder relationships can be achieved using BLUP-like methods with pedigree and markers. Inclusion of metafounder relationships reduces bias of genomic predictions with no loss in accuracy. Fil: García Baccino, Carolina Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina Fil: Legarra, Andres. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; Francia Fil: Christensen, Ole F.. University Aarhus; Dinamarca Fil: Misztal, Ignacy. University of Georgia; Estados Unidos Fil: Pocrnic, Ivan. University of Georgia; Estados Unidos Fil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; Francia. École Nationale Vétérinaire de Toulouse; Francia Fil: Cantet, Rodolfo Juan Carlos. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Unidad Ejecutora de Investigaciones en Producción Animal. Universidad de Buenos Aires. Facultad de Ciencias Veterinarias. Unidad Ejecutora de Investigaciones en Producción Animal; Argentina. Universidad de Buenos Aires. Facultad de Agronomía. Departamento de Producción Animal; Argentina
Databáze: OpenAIRE
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