title: A comparison of methods to estimate genomic relationships using pedigree and markers in livestock populations.
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-Ldisplayed the lowest sampling error and the highest correlation with true genome-shared values. GVR-Bapproximated GIBD-L's correlation and had lower error than GVR-O. Accuracy of GEBV for selection candidates was significantly higher when GIBD-Lwas used and identical between GVR-Oand 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.
authors.affiliation: Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: N S
authors.initials: NS
authors.lastname: Forneris
authors.affiliation: Department of Animal Science, Michigan State University, East Lansing, MI, USA.
authors.forename: J P
authors.initials: JP
authors.lastname: Steibel
authors.affiliation: INRA, GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Castanet-Tolosan, France.
authors.forename: A
authors.initials: A
authors.lastname: Legarra
authors.affiliation: INRA, GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Castanet-Tolosan, France.|INP, ENSAT, GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Université de Toulouse, Castanet-Tolosan, France.
authors.forename: Z G
authors.initials: ZG
authors.lastname: Vitezica
authors.affiliation: Department of Animal Science, Michigan State University, East Lansing, MI, USA.
authors.forename: R O
authors.initials: RO
authors.lastname: Bates
authors.affiliation: Department of Animal Science, Michigan State University, East Lansing, MI, USA.
authors.forename: C W
authors.initials: CW
authors.lastname: Ernst
authors.affiliation: Departamento de Biología Aplicada y Alimentos, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
authors.forename: A L
authors.initials: AL
authors.lastname: Basso
authors.affiliation: Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.|INPA-CONICET (Consejo Nacional de Investigaciones Científicas y Técnicas), Buenos Aires, Argentina.
authors.forename: R J C
authors.initials: RJ
authors.lastname: Cantet
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000032:analysis; D003198:Computer Simulation; D005260:Female; D005838:Genotype; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D015415:Biomarkers
keywords: Accuracy; SNP; genome sharing; genomic prediction; identity by descent