Identification of Runs of Homozygosity in Large White and Landrace Sows Associated with Decreased Number of Piglets Born

Utilizing dense genotypes in swine genetic evaluations has become a routine practice. A supplemental use of the genotype information can be to identify regions of the genome that give rise to inbreeding depression. The objective of the study is to identify regions when in a run of homozygosity (ROH) impact the number of piglets born alive in a Landrace (LR) and Large White (LW) pig population. Genotyped dams (n = 5000 LR; n = 5000 LW) with number born alive (NBA) phenotypes were utilized to construct yield deviations. A ROH statistic (ROH5Mb), which is whether a SNP was in a ROH of 5 Mb, was calculated across the genome. Utilizing a Bayesian Ridge Regression approach yield deviations weighted by the information content were regressed on the additive and ROH5Mb effect of a SNP along with the polygenic effect of the dam. Regions that had a large variance based on 1-Mb sliding window genomic estimated breeding values were investigated further in order to determine the phenotypic effect. For each ROH investigated, the actual phenotype was used as phenotypes in an analysis along with fixed effects of contemporary group, parity, SNP contained within the ROH, ROH and random effects of dam and the permanent environmental effect of the dam. Regions on SSC1, SSC6 and SSC13 for LR and SSC4, SSC13 and SSC 17 for LW caused a significant reduction (ranged from -0.64 to -0.34) in the NBA. These regions can be utilized in mating programs to reduce the impact of inbreeding depression.