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Genetics Selection Evolution

Open Access

Genetic variation and relationships of eighteen Chinese indigenous pig breeds

  • Shu-Lin Yang1, 2,
  • Zhi-Gang Wang2,
  • Bang Liu1,
  • Gui-Xiang Zhang2,
  • Shu-Hong Zhao1,
  • Mei Yu1,
  • Bin Fan1,
  • Meng-Hua Li1,
  • Tong-An Xiong1 and
  • Kui Li1Email author
Genetics Selection Evolution200335:657

Received: 14 June 2002

Accepted: 31 March 2003

Published: 15 November 2003


Chinese indigenous pig breeds are recognized as an invaluable component of the world's pig genetic resources and are divided traditionally into six types. Twenty-six microsatellite markers recommended by the FAO (Food and Agriculture Organization) and ISAG (International Society of Animal Genetics) were employed to analyze the genetic diversity of 18 Chinese indigenous pig breeds with 1001 individuals representing five types, and three commercial breeds with 184 individuals. The observed heterozygosity, unbiased expected heterozygosity and the observed and effective number of alleles were used to estimate the genetic variation of each indigenous breed. The unbiased expected heterozygosity ranged between 0.700 (Mashen) and 0.876 (Guanling), which implies that there is an abundant genetic variation stored in Chinese indigenous pig breeds. Breed differentiation was shown by fixation indices (F IT , F IS , and F ST ). The F ST per locus varied from 0.019 (S0090) to 0.170 (SW951), and the average F ST of all loci was 0.077, which means that most of the genetic variation was kept within breeds and only a little of the genetic variation exists between populations. The Neighbor-Joining tree was constructed based on the Nei D A (1978) distances and one large cluster with all local breeds but the Mashen breed, was obtained. Four smaller sub-clusters were also found, which included two to four breeds each. These results, however, did not completely agree with the traditional type of classification. A Neighbor-Joining dendrogram of individuals was established from the distance of – ln(proportions of shared alleles); 92.14% of the individuals were clustered with their own breeds, which implies that this method is useful for breed demarcation. This extensive research on pig genetic diversity in China indicates that these 18 Chinese indigenous breeds may have one common ancestor, helps us to better understand the relative distinctiveness of pig genetic resources, and will assist in developing a national plan for the conservation and utilization of Chinese indigenous pig breeds.


genetic variationpopulation structuremicrosatellitepigChinese indigenous breed

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Authors’ Affiliations

Laboratory of Molecular Biology and Animal Breeding, School of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan, PR China
Center of Preservation and Utilization of Germplasm Resource of Animal Husbandry and Forage Grass, National Animal Husbandry and Veterinary Service, Ministry of Agriculture, Beijing, PR China


© INRA, EDP Sciences 2003