Inbreeding by pedigree and genomic markers in selection lines of pigs

Abstract Text: Dense SNP data of 2,358 pigs were analyzed to quantify inbreeding across nine generations in two Yorkshire selection lines that were divergently selected for residual feed intake. Alternative genomic inbreeding estimates were compared with pedigree-based inbreeding. In general, genomic markers traced the same trends in inbreeding as pedigree, although the observed rate of inbreeding was lower when based on genetic markers. Higher within-generation variation was observed for the marker-based estimates of inbreeding, implicating that the markers can capture Mendelian sampling variance and reveal the ‘realized’ homozygosity in the genome. The marker-based estimates of inbreeding were highly or moderately correlated with each other (0.74-0.98), but less correlated with pedigree-based estimates of inbreeding (0.57-0.69).

Keywords: genomic inbreeding; residual feed intake; runs of homozygosity