title: Genetic diversity and population structure of six Chinese indigenous pig breeds in the Taihu Lake region revealed by sequencing data.
abstract: 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.
authors.affiliation: 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.
authors.forename: Z
authors.initials: Z
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Q
authors.initials: Q
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: Y
authors.initials: Y
authors.lastname: Yang
authors.affiliation: 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.
authors.forename: R
authors.initials: R
authors.lastname: Liao
authors.affiliation: 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.
authors.forename: J
authors.initials: J
authors.lastname: Zhao
authors.affiliation: 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.
authors.forename: Z
authors.initials: Z
authors.lastname: Zhang
authors.affiliation: 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.
authors.forename: Z
authors.initials: Z
authors.lastname: Chen
authors.affiliation: 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.
authors.forename: X
authors.initials: X
authors.lastname: Zhang
authors.affiliation: National Station of Animal Husbandry, Beijing, 100125, China.
authors.forename: M
authors.initials: M
authors.lastname: Xue
authors.affiliation: National Station of Animal Husbandry, Beijing, 100125, China.
authors.forename: H
authors.initials: H
authors.lastname: Yang
authors.affiliation: National Station of Animal Husbandry, Beijing, 100125, China.
authors.forename: Y
authors.initials: Y
authors.lastname: Zheng
authors.affiliation: 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.
authors.forename: Q
authors.initials: Q
authors.lastname: Wang
authors.affiliation: 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.
authors.forename: Y
authors.initials: Y
authors.lastname: Pan
mesh_terms: D000483:Alleles; D000818:Animals; D001947:Breeding; D002681:China; D014644:Genetic Variation; D005828:Genetics, Population; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000145:classification / Q000235:genetics*
keywords: Next-generation sequencing; genetic distance; genetic variation; pig genome