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A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations

By Natalia Soledad Forneris, J. P. Steibel, Andres Legarra, Zulma G. Vitezica, R. O. Bates, C. W. Ernst, Alicia Leonor Rufina Basso Abraham and Rodolfo Juan Carlos Cantet

Abstract

Accurate prediction of breeding values depends on capturing the variability in genome sharing of relatives with the same pedigree relationship. Here, we compare two approaches to set up genomic relationship matrices for precision of genomic relationships (GR) and accuracy of estimated breeding values (GEBV). Real and simulated data (pigs, 60k SNP) were analysed, and GR were estimated using two approaches: (i) identity by state, corrected with either the observed (GVR -O) or the base population (GVR -B) allele frequencies and (ii) identity by descent using linkage analysis (GIBD -L). Estimators were evaluated for precision and empirical bias with respect to true pedigree IBD GR. All three estimators had very low bias. GIBD -L displayed the lowest sampling error and the highest correlation with true genome-shared values. GVR -B approximated GIBD -L's correlation and had lower error than GVR -O. Accuracy of GEBV for selection candidates was significantly higher when GIBD -L was used and identical between GVR -O and GVR -B. In real data, GIBD -L's sampling standard deviation was the closest to the theoretical value for each pedigree relationship. Use of pedigree to calculate GR improved the precision of estimates and the accuracy of GEBV.Fil: Forneris, Natalia Soledad. 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; ArgentinaFil: Steibel, J. P.. Michigan State University; Estados UnidosFil: Legarra, Andres. Institut National de la Recherche Agronomique; FranciaFil: Vitezica, Zulma G.. Institut National de la Recherche Agronomique; Francia. Instituto Polytechnique de Toulouse; FranciaFil: Bates, R. O.. Michigan State University; Estados UnidosFil: Ernst, C. W.. Michigan State University; Estados UnidosFil: Basso Abraham, Alicia Leonor Rufina. Universidad de Buenos Aires. Facultad de Agronomia. Departamento de Biología Aplicada y Alimentos; ArgentinaFil: 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; Argentin

Topics: Accuracy, Genomic prediction, Genome sharing, Identity by descent, SNP, Otras Producción Animal y Lechería, Producción Animal y Lechería, CIENCIAS AGRÍCOLAS
Publisher: 'Wiley'
Year: 2016
DOI identifier: 10.1111/jbg.12217
OAI identifier: oai:ri.conicet.gov.ar:11336/51073
Provided by: CONICET Digital
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