An assessment of genetic diversity and population structures of fifteen Vietnamese indigenous pig breeds for supporting the decision making on conservation strategies

Abstract

The study aimed to characterize genetic diversity, genetic clusters, and phylogenetic relationships of 15 Vietnamese indigenous pig breeds across the country for supporting the decision making of the conservation strategies. For this purpose, 638 samples from the breeds together with two wild pig breeds and an exotic breed were genotyped with 19 microsatellite markers recommended from FAO/ISAG for diversity studies. The higher genetic diversity was observed for indigenous breeds (mean He\u2009=\u20090.67) and wild breeds (mean He\u2009=\u20090.74); the indigenous CoAluoi breed compared the out-breed Landrace (He\u2009=\u20090.59). Fifteen percent of the genetic variation came from differences among breeds. The unrooted neighbor-joining dendrogram obtained from Nei’s genetic distances showed three nodes with 100% supported bootstrap values. The first node included the three indigenous breeds ( Hung , LungPu , and MuongKhuong ), the second node included the indigenous BaXuyen and the exotic Landrace, and the third node included the two wild Thailand and Vietnam pig breeds. The discriminant analysis of principal component (DAPC) of 18 studied breeds resulted in 12 genetic clusters. Unlike the other indigenous breeds, the BaXuyen was in the same genetic cluster with the exotic Landrace—which agreed with the 100% bootstrap value of their node—so the BaXuyen should not be conserved. The five indigenous pig breeds— Huong , VanPa , Soc , ChuProng , and CoAluoi —were assigned to their own clusters, which agreed with the low supported bootstrap values of their nodes. These five breeds should be in the high conservation priority. Finally, the 9 indigenous pig breeds ( MuongKhuong , LungPu , Hung , TapNa , MongCai , HaLang , Lung , Meo , and Ban breeds) formed four genetic admixture structures. These results suggest the conservation strategies should be built based on from five to nine pig groups thus reducing the cost of conservation whereas still remaining the genetic diversity of the studied breeds.