Twenty Years of Artificial Directional Selection Have Shaped the Genome of the Italian Large White Pig Breed

In this study we investigated the effect on the pig genome of twenty years of artificial directional selection based on a genetic evaluation program of boars obtained with a classical BLUP animal model. All Italian Large White boars born from 1992 to 2012 with estimated breeding value reliability >0.85 (n. = 200) were genotyped with markers in five major genes (IGF2 intron3-g.3072G>A, MC4R p.D298N, VTNR PRE1 insertion, PRKAG3 p.I199V and FTO g.276T>G) and with the Illumina PorcineSNP60 BeadChip. Genotyping data were analysed grouping boars in several classes according to their year of birth. Then we evaluated the influence of the time on allele frequencies for all analysed markers using a multinomial logit regression model. Four out or five gene markers (IGF2, MC4R, VTNR and FTO) showed significant changes of allele frequencies during the 20 years window time, according to the directional selection program in the breed. In addition, other 464 single nucleotide polymorphisms changed significantly allele frequencies within the 20 years of selection (P<0.05, Bonferroni corrected). Most of them were very close or within annotated genes providing potential information on the functional effects of these allele shifts. These results indicated that selection carried out during the last two decades modified substantially the genome of the Italian Large White pig population