Genetic Diversity Of 17 South China Indigenous Pigs Reveled By SNP Array

Livestock and poultry resources are important component of biodiversity and valuable resource that was shaped through long-term evolution and was the guarantee for the sustainable development of animal husbandry.Thus,a comprehensive and clearly understanding of the evolution,genetic background and genetic relationship of pig germplasm resources is an important prerequisite for the protection and utilization of indigenous pig breeds.In this study,the genetic diversity,population genetic structure,linkage disequilibrium and effective population size of 17 indigenous pig breeds(groups)that distribute in South China region were analyzed using high-density SNP chip.The results were as follows:1)Genetic diversity analysis showed that the dahuabai,Luchuan,Minbeihua and Guanzhuanghua pig were low in genetic diversity,these pigs need strengthen protection and the other indigenous pig breeds had higher genetic diversity.2)Based on the genetic distance between individuals and between species,the evolutionary analysis showed that the genetic distance between Southern China indigenous pig breeds was relatively close,and the clustering results were roughly consistent with the geographical distribution of the pig breeds.Southern China indigenous pig breeds had genetic distance with Western pig breeds,but the Baoshan,Longlin,Meihua,Yuedonghei and Putianhei pig had close genetic distance with Western pig breeds.3)Principal component analysis and STRUCTURE analysis showed the different genetic backgrounds between Southern China indigenous pigs and Western pigs.There existed common blood resourse between Southern China indigenous pigs and Western pigs.The Baoshan,Longlin,Meihua,Yuedonghei and Putianhei pig contains a higher proportion of blood that existed in Western commercial pigs.These five breeds may have crossed with western commercial pigs.The Meihua pig has long genetic distance with the Dahuabai pig and has different genetic backgrounds,the Meihua pig should be treated as a breed.The Gaoligongshan and Baoshan pig has close genetic distance and has the same blood source,these two breeds should be combined as a breed.4)Compared with the western commercial pig breeds,the linkage disequilibrium extend between SNPs with short distance is generally lower in south china indigenous pigs,while high in long distance,the linkage disequilibrium can be extended to long distance in south china indigenous pigs,reflects the small population of south china indigenous pigs.The effective population size analysis showed that the effective population size of Chinese indigenous pig decreased rapidly,the south china indigenous pigs need to be protected.