Whole-genome resequencing reveals signatures of selection in European pig breeds and wild boars

Abstract

Natural and artificial directional selection in cosmopolitan and autochthonous livestock and wild relative populations have shaped their genomes defining the level of variability and determining selective sweeps as final adaptation to different environmental conditions and production systems. In this study we analyzed the genetic variability and selection signatures in 19 European local pig breeds sampled from 7 countries (Croatia, France, Germany, Italy, Lithuania, Portugal, Serbia, Slovenia and Spain) (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian, Casertana, Cinta Senese, Gascon, Krskopolje, Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein, Swallow-Bellied Mangalitsa and Turopolje), 3 cosmopolitan Italian breeds (Large White, Landrace and Duroc) and Italian wild boars. For each population, we prepared DNA pools using equimolar DNA from 30 to 35 animals. Whole-genome 150-bp paired-end sequencing was carried out on an Illumina HiSeq machine. More than 18.4 billion of reads were obtained and mapped on the Sscrofa11.1 genome version with BWA, obtaining a mean depth of sequencing of 42X, respectively. CRISP, coupled to an ad hoc bioinformatic pipeline, was used to detect more than 30 million of high-quality variants (18% not included in dbSNP yet). Variant annotation, carried out with VEP, highlighted that the 0.34% of the autosomal SNPs impacted genes at the protein level. Selection signature analyses (Fst and the Pooled Heterozygosity) highlighted more than 400 sweep regions distributed along the 18 porcine autosomes and scaffolds. Some of these genome regions harboured major genes affecting body shape/size (e.g., NR6A1, PLAG1, LCORL and CASP10), coat color (e.g., KIT, MC1R) and growth/fatness (e.g., MC4R), providing a first global variability analysis of European Sus scrofa populations.