Detecting Strong Selective Signatures On Large White and Tongcheng Pigs

Due to the direction, intensity, duration and consistency of selection, especially the recent artificial directional selection, the performances of pigs have been significantly improved, such as external characteristics, growth and reproduction. Therefore, there must leave much footprints or selection signatures during the evolution and they are should be detected. Here, based on 60K BeadChip genotyping data of both commercial Large White (n=408) and local Tongcheng (n=45) pigs, extended haplotype homozygosity (EHH) values were estimated by long-range haplotype (LRH) method to detect selection signatures. The results indicated that 34 candidate regions including 62 known genes were detected in Large White pigs, while 25 regions involving 57 known genes in Tongcheng pigs. They were mostly distributed on SSC1, SSC4, SSC7 and SSC14. According to QTL and network pathway analysis, most of the regions and genes were related to growth, reproduction and immune responses. For example, ER can promote embryonic development and influence pig litter size; IL-2, secreted in an autocrine fashion by antigen-stimulated T cells, is a key cytokine for T cell activation and proliferation. In addition, the genetic differentiation coefficient F_ST was 0.254 and it demonstrated the analyzed populations had significant differentiation. The findings from this study will contribute to better understanding of pig evolution and differentiation mechanisms, and also provide valuables reference for breeding improvement.