Genomic analysis and selection signatures in local European pig breeds

European local pig breeds are a major genetic resource and share relevant phenotypic characteristics, such as high adipogenic potential, rusticity and high meat quality. One key factor for the conservation, promotion and sustainable use of these breeds is their genetic characterization. In this study, we assessed genome-wide diversity and selection signatures employing SNP genotyping data from twenty European autochthonous pig breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian, Casertana, Cinta Senese, Gascon, Iberian, Krškopolje, Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein, Swallow-Bellied Mangalitsa and Turopolje) from nine countries (Croatia, France, Germany, Italy, Lithuania, Portugal, Serbia, Slovenia, Spain), as well as from wild pigs sampled in the Iberian Peninsula, and from commercial pigs (Duroc, Large White and Landrace) of Spanish and Italian origins. A total of 1150 DNA samples were genotyped with the GGP Porcine HD Genomic Profiler v1 chip, including 68,528 SNPs. Results pointed out some breeds with very low diversity for which conservation strategies should be applied. We searched across the genome for loci under diversifying selection based on FST outlier tests. Putative signals of selection were detected for regions containing genes involved in growth, muscle development, reproduction, metabolism, behavior and sensory perception, which may be considered candidate genes that may underlie differences in adaptation to specific environments and productive systems, and phenotypic traits. The findings provide relevant information for the implementation of further conservation and selection strategies.