Estimates of the actual relationship between half‐sibs in a pig population

Summary 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 th...

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Bibliographic Details
Published in:Journal of animal breeding and genetics (1986) 2017-04, Vol.134 (2), p.109-118
Main Authors: García‐Baccino, C.A., Munilla, S., Legarra, A., Vitezica, Z.G., Forneris, N.S., Bates, R.O., Ernst, C.W., Raney, N.E., Steibel, J.P., Cantet, R.J.C.
Format: Article
Language:English
Subjects:
Actual relationships
Animal reproduction
Animals
Breeding of animals
Crosses, Genetic
Estimates
estimation methods
Female
Gene loci
genomic selection
Genotype
Hogs
identity by descent
Life Sciences
Male
Pedigree
Polymorphism, Single Nucleotide
Siblings
Sus scrofa - genetics
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Summary:Summary 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.
ISSN:0931-2668
1439-0388
DOI:10.1111/jbg.12236