Genetic Diversity and Population Structure of the Synthetic Pig Strain Tokyo X

<p>Tokyo X is a synthetic pig strain that was developed at the Tokyo Metropolitan Livestock Experiment Station by crossing Duroc, Berkshire, and Beijing Black breeds. The Tokyo X breeding program has been run for maintaining the strain while avoiding inbreeding since 1997, when Tokyo X was registered as a distinct strain by the Pig Breeders’ Association of Japan. However, Tokyo X has been maintained for 20 years, resulting in concerns regarding changes in the genetic diversity and structure. In addition, since the Beijing Black breed, one of the founder breeds of Tokyo X, itself is a synthetic pig strain and the genetic compositions of Beijing Black is not well studied, the phylogenetic property of Tokyo X is little known. Therefore, in this study, we aimed to characterize the phylogenetic position as well as the genetic diversity and structure of Tokyo X by analyzing microsatellite DNA in comparison with other domestic pig breeds. Genomic DNA was extracted from 72 Tokyo X pigs in 2014. In addition, genomic DNA of five Western breeds (Landrace, Large White, Middle White, Duroc, and Berkshire) and two Chinese breeds (Jinhua and Meishan) was used to represent other domestic pig breeds. Thirty microsatellite (MS) loci recommended by FAO/ISAG were used as DNA markers. Principal coordinate analysis (PCoA), phylogenetic analysis, as well as population structural analysis using the STRUCTURE program consistently supported the formations of two major clusters representing Western breeds and Chinese breeds, and Tokyo X was nested within Western breeds. In addition, these results also indicate that Tokyo X genetically resembles Duroc and Berkshire while still exhibiting a unique genetic structure. This unique structure seems to result from the original crossing with Beijing Black and the subsequent genetic drift occurring during the maintenance of the strain. Genetic diversity indices of Tokyo X were generally equal to those of Western breeds and higher than those of Chinese breeds, indicating that even though Tokyo X has been raised as a closed herd for 20 years, genetic diversity has been maintained in the population. Moreover, the results of PCoA and F_IS value revealed that Tokyo X was not subdivided into subpopulations. Genetic contributions of founder breeds based on pedigree information were almost equal in every individual. These suggest the pedigree control program of Tokyo X has effectively suppressed inbreeding. However, as far as the closed herds with the small population size are maintained, it is inevitable that the inbreeding coefficients will gradually increase no matter how the pedigree will be controlled. Therefore, it is important to use the genotype information obtained in this study for the pedigree control program to enhance the heterozygosity for suppressing the inbreeding degenerations.</p>