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Anim Genet. 2015 Dec;46(6):697-701. doi: 10.1111/age.12349. Epub 2015 Sep 16.

Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data.

Wang Z1,2, Chen Q1,2, Yang Y1,2, Liao R1,2, Zhao J1,2, Zhang Z1,2, Chen Z1,2, Zhang X1,2, Xue M3, Yang H3, Zheng Y3, Wang Q1,2, Pan Y1,2.

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Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
Shanghai Key Laboratory of Veterinary Biotechnology, Shanghai, 200240, China.
National Station of Animal Husbandry, Beijing, 100125, China.


The Chinese indigenous pig breeds in the Taihu Lake region are the most prolific pig breeds in the world. In this study, we investigated the genetic diversity and population structure of six breeds, including Meishan, Erhualian, Mi, Fengjing, Shawutou and Jiaxing Black, in this region using whole-genome SNP data. A high SNP with proportions of polymorphic markers ranging from 0.925 to 0.995 was exhibited by the Chinese indigenous pigs in the Taihu Lake region. The allelic richness and expected heterozygosity also were calculated and indicated that the genetic diversity of the Meishan breed was the greatest, whereas that of the Fengjing breed was the lowest. The genetic differentiation, as indicated by the fixation index, exhibited an overall mean of 0.149. Both neighbor-joining tree and principal components analysis were able to distinguish the breeds from each other, but structure analysis indicated that the Mi and Erhualian breeds exhibited similar major signals of admixture. With this genome-wide comprehensive survey of the genetic diversity and population structure of the indigenous Chinese pigs in the Taihu Lake region, we confirmed the rationality of the current breed classification of the pigs in this region.


Next-generation sequencing; genetic distance; genetic variation; pig genome

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