Genet. Sel. Evol. 35 (2003) 657-671
DOI: 10.1051/gse:2003045

Genetic variation and relationships of eighteen Chinese indigenous pig breeds

Shu-Lin Yang^{a, b}, Zhi-Gang Wang^b, Bang Liu^a, Gui-Xiang Zhang^b, Shu-Hong Zhao^a, Mei Yu^a, Bin Fan^a, Meng-Hua Li^a, Tong-An Xiong^a and Kui Li<sup>a

a</sup>  Laboratory of Molecular Biology and Animal Breeding, School of Animal Science and Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, P.R. China
^b  Center of Preservation and Utilization of Germplasm Resource of Animal Husbandry and Forage Grass, National Animal Husbandry and Veterinary Service, Ministry of Agriculture, Beijing 100094, P.R. China

(Received 14 June 2002; accepted 31 March 2003)

Abstract
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 (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.

Key words: genetic variation / population structure / microsatellite / pig / Chinese indigenous breed

Correspondence and reprints: Kui Li lkxblghi@public.wh.hb.cn

© INRA, EDP Sciences 2003