Genome-Wide Analysis of Genetic Introgression on Vietnamese Native Pigs

As the expanding demand of pork in Vietnam, highly productive western pig breeds have been introduced to improve the pork production. The introduction of exogenous genetic source has been facilitated by a crossbreeding of the western breeds with local Vietnamese pig breeds. In this study, we aimed to investigate a degree of the genetic introgression from the western breeds to the Vietnamese native breeds by evaluating introgression signature of western breeds. We collected pig genomic DNA samples from geographically separated fifteen areas in Vietnam (six in the north mountain areas, three in the suburbs of Hanoi, one in the west mountain area, and five in south areas). We also used eight western breeds (Berkshire, Hampshire, Large White, Yorkshire, Landrace, Chester White, Duroc and Pietrain), two eastern breeds (Meishan and Jinhua), and two Asian wild boars (Japan and Ryukyu). We applied genome-wide approach using PorcineSNP60 Beadchip. The admixture analysis revealed that the pigs from the three areas have been already crossed with several western breeds. The results of pairwise shared haplotypes from the Beagle fastIBD function showed that the pigs of the three areas would have the genomic signatures shared with Large-White, Landrace, Duroc and Pietrain. However, the pigs from the other four areas in Vietnam were hardy found the genomic signatures of the Western breeds. On the other hand, we found little genomic signatures from two eastern breeds or the wild boars in all examined Vietnamese pigs.