Estimates of the actual relationship between half-sibs in a pig population.
Genomic relationships based on markers capture the actual instead of the expected (based on pedigree) proportion of genome shared identical by descent (IBD). Several methods exist to estimate genomic relationships. In this research, we compare four such methods that were tested looking at the empirical distribution of the estimated relationships across 6704 pairs of half-sibs from a cross-bred pig population. The first method based on multiple marker linkage analysis displayed a mean and standard deviation (SD) in close agreement with the expected ones and was robust to changes in the minor allele frequencies (MAF). A single marker method that accounts for linkage disequilibrium (LD) and inbreeding came second, showing more sensitivity to changes in the MAF. Another single marker method that considers neither inbreeding nor LD showed the smallest empirical SD and was the most sensible to changes in MAF. A higher mean and SD were displayed by VanRaden's method, which was not sensitive to changes in MAF. Therefore, the method based on multiple marker linkage analysis and the single marker method that considers LD and inbreeding performed closer to theoretical values and were consistent with the estimates reported in literature for human half-sibs.
Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.|Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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García-Baccino
Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.
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Munilla
INRA, GenPhySE (Génétique, Physiologie et Systèmes d'Elevage), Castanet-Tolosan, France.
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Legarra
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.
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Vitezica
Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.|Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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Forneris
Department of Animal Science, Michigan State University, East Lansing, MI, USA.
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Bates
Department of Animal Science, Michigan State University, East Lansing, MI, USA.
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Ernst
Department of Animal Science, Michigan State University, East Lansing, MI, USA.
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Raney
Department of Animal Science, Michigan State University, East Lansing, MI, USA.|Department of Fisheries and Wildlife, Michigan State University, East Lansing, MI, USA.
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Steibel
Departamento de Producción Animal, Facultad de Agronomía, Universidad de Buenos Aires, Buenos Aires, Argentina.|Instituto de Investigaciones en Producción Animal - Consejo Nacional de Investigaciones Científicas y Técnicas, Buenos Aires, Argentina.
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Cantet
D000818:Animals; D003433:Crosses, Genetic; D005260:Female; D005838:Genotype; D008297:Male; D010375:Pedigree; D020641:Polymorphism, Single Nucleotide; D035781:Siblings; D034421:Sus scrofa / Q000235:genetics*
Actual relationships; estimation methods; genomic selection; identity by descent