Runs of homozygosity islands in Italian cosmopolitan and autochthonous pig breeds identify selection signatures in the porcine genome

Abstract

Runs of homozygosity (ROH) in a diploid organism can be defined as continuous chromosome regions in which all loci have a homozygous genotype. Shared ROH within a livestock population identify chromosome regions in which a reduced haplotype variability produces ROH islands. ROH islands can provide information on hotspot of selection putatively derived from different selection history, genetic events and adaptation to several production systems. In this study we evaluated the distribution of ROH in the genome of a total of 2860 pigs belonging to seven Italian breeds, three commercial breeds (Italian Large White, Italian Duroc and Italian Landrace) and four autochthonous breeds (Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano). All animals were genotyped with the Illumina PorcineSNP60 BeadChip array. PLINK software was used to call ROH. The largest number of ROH per animal was observed in the Italian Duroc breed. The mean largest size of ROH was detected in Apulo-Calabrese pigs. Nero Siciliano pigs had the lowest mean number of ROH per animal. Italian Large White pigs had the lowest mean length of ROH. ROH islands were identified in all breeds except in Nero Siciliano. ROH islands spanned from a total of 25.5 (Cinta Senese) to 33.1 Mbp (Italian Landrace) of genomic regions distributed from four to ten autosomes and encompassing from a total of 126 to 262 annotated genes. These selection hotspot regions differed among breeds. Functional inference of the observed ROH islands provided some insights into the mechanisms of adaptation of these pig genetic resources.