Copy Number Variation and Signatures of Diversifying Selection Between Chinese and Western Pig Breeds

Under multiple independent domestications, local pig types were developed in Europe and Asia from the Wild boar, resulting in large changes in phenotypes and underlying genotypes. Copy number variation (CNV) is one of numerous genome variations, and may be altered by domestication and subsequent selective pressures. Here we detected porcine CNVs of Chinese and Western breeds and scanned for signatures of diversifying selection utilizing the Illumina Porcine SNP60 Beadchip. A total of 324 animals from six Chinese local breeds, three Western breeds and one related hybrid were tested in this study. A total of 348 CNV Regions (CNVRs) across the genome were identified. Chinese local breeds were segregated from Western breeds after clustering with those CNVRs, indicating some interesting relationships among those breeds. Signatures of diversifying selection between Chinese and Western breeds were found in genomic regions associated with traits such as coat color and ear morphology. Some of these regions overlapped with the identified CNVRs, showing that copy numbers of genes are also altered by domestication. Breed unique selection regions were found in these results, and their relationship with CNVRs needs to be further investigated.