SNP genotypes reveal breed substructure, selection signatures and highly inbred regions in Pietrain pigs

The Pietrain pig originates from the Belgian village Pietrain some time between 1920 and 1950. Owing to its superior conformation, the Pietrain has spread worldwide since the 1960s. As initial population sizes were limited and close inbreeding was commonplace, the breed's genetic diversity has been questioned. Therefore, this study examines Pietrain breed substructure, diversity and selection signatures using SNP data in comparison with Duroc, Landrace and Large White populations. Principal component analysis indicated three subpopulations, and F-ST analysis showed that US Pietrains differ most from European Pietrains. Average inbreeding based on runs of homozygosity (ROH) segments larger than 4 Mb ranged between 16.7 and 20.9%. The highest chromosomal inbreeding levels were found on SSC8 (42.7%). ROH islands were found on SSC8, SSC15 and SSC18 in all Pietrain populations, but numerous population-specific ROH islands were also detected. Moreover, a large ROH island on SSC8 (34-126 Mb) appears nearly fixed in all Pietrain populations, with a unique genotype. Chromosomal ROH patterns were similar between Pietrain populations. This study shows that Pietrain populations are genetically diverging, with at least three genetically distinct populations worldwide. Increasing genetic diversity in local Pietrain populations by introgression from other Pietrain populations seems to be only limited. Moreover, a unique 90 Mb region on SSC8 appeared largely fixed in the Pietrain breed, indicating that fixation was already present before the 1960s. We believe that strong selection and inbreeding during breed formation fixed these genomic regions in Pietrains. Finally, we hypothesize that independent coat color selection may have led to large ROH pattern similarities on SSC8 between unrelated pig breeds.