Using genome-wide data for detecting inbreeding depression in reproductive traits in Iberian pigs

Abstract Text: Genome-wide information was used for detecting inbreeding depression in total number of piglets born and number of piglets born alive in an ancient strain of Iberian pigs. A total of 109 sows with phenotypic records were genotyped with the PorcineSNP60 BeadChip. Inbreeding depression was estimated using a bivariate animal model. We used two different measures of genomic inbreeding: inbreeding estimated on a SNP-by-SNP basis and inbreeding estimated from runs of homozygosity. We also performed the analyses using pedigree-based inbreeding. Significant inbreeding depression for both traits was detected using all inbreeding measures. Genome-wide information allowed to narrow down one region significantly associated to inbreeding depression that was located on chromosome 13 and spanned from 27 to 54 Mb. This region overlaps with a previously detected QTL region comprising the inter-alpha-trypsin inhibitor genes that play an important role in embryo implantation.

Keywords:

Genomic inbreeding

Inbreeding depression

Iberian pig