title: Twenty years of artificial directional selection have shaped the genome of the Italian Large White pig breed.
abstract: In this study, we investigated at the genome-wide level if 20 years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n = 192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni  < 0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20 years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Schiavo
authors.affiliation: Department of Statistical Sciences 'Paolo Fortunati', University of Bologna, Via delle Belle Arti, 40126, Bologna, Italy.
authors.forename: G
authors.initials: G
authors.lastname: Galimberti
authors.affiliation: Department of Statistical Sciences 'Paolo Fortunati', University of Bologna, Via delle Belle Arti, 40126, Bologna, Italy.
authors.forename: D G
authors.initials: DG
authors.lastname: Calò
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
authors.forename: A B
authors.initials: AB
authors.lastname: Samorè
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
authors.forename: F
authors.initials: F
authors.lastname: Bertolini
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
authors.forename: V
authors.initials: V
authors.lastname: Russo
authors.affiliation: Associazione Nazionale Allevatori Suini, Via L. Spallanzani 4, 00161, Roma, Italy.
authors.forename: M
authors.initials: M
authors.lastname: Gallo
authors.affiliation: Centro di Ricerca per la Produzione delle Carni e il Miglioramento Genetico, Consiglio per la Ricerca in Agricoltura e l'Analisi dell'Economia Agraria (CREA), Monterotondo, Roma, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Buttazzoni
authors.affiliation: Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale Fanin 46, 40127, Bologna, Italy.
authors.forename: L
authors.initials: L
authors.lastname: Fontanesi
mesh_terms: D000818:Animals; D001947:Breeding; D005787:Gene Frequency; D016678:Genome; D005838:Genotype; D016015:Logistic Models; D008297:Male; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013552:Swine / Q000235:genetics*
keywords: Sus scrofa; genome-wide analysis; selection signature; selection sweep; single nucleotide polymorphism