Selective sweep analysis reveals extensive parallel selection traits between Large white and Duroc Pigs and Their polygenic basis

Here, 28 whole genome sequencing data of Danish Large White pigs with an approximately 25 fold depth each were generated, resulting in about 12 million high quality SNPs for each individual. Combined with the sequencing data of 27 Duroc and 23 European wild boars, we investigated the parallel selection of Danish Large White and Duroc pigs using two complementary methods, Fst and iHS. In total, 67 candidate regions were identified as the signatures of parallel selection. The genes in candidate regions of parallel selection were mainly associated with sensory perception, growth rate, and body size. Further functional annotation suggested that the striking consistency of the terms may be caused by the polygenetic basis of quantitative traits, and revealing the complex genetic basis of parallel selection.