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

TitleEstimates of the actual relationship between half-sibs in a pig population.
Publication TypeJournal Article
Year of Publication2017
AuthorsGarcía-Baccino, CA, Munilla, S, Legarra, A, Vitezica, ZG, Forneris, NS, Bates, RO, Ernst, CW, Raney, NE, Steibel, JP, Cantet, RJC
JournalJ Anim Breed Genet
Volume134
Issue2
Pagination109-118
Date Published2017 Apr
ISSN1439-0388
KeywordsAnimals, Crosses, Genetic, Female, Genotype, Male, Pedigree, Polymorphism, Single Nucleotide, Siblings, Sus scrofa
Abstract

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.

DOI10.1111/jbg.12236
Alternate JournalJ. Anim. Breed. Genet.
PubMed ID27670252