title: Genome-wide genetic variation discovery in Chinese Taihu pig breeds using next generation sequencing.
abstract: The Chinese Taihu pig breeds are an invaluable component of the world's pig genetic resources, and they are the most prolific breeds of swine in the world. In this study, the genomes of 252 pigs of the six indigenous breeds in the Taihu Lake region were sequenced using the genotyping by genome reducing and sequencing approach. A total of 950 million good reads were obtained using an Illumina Hiseq2000 at an average depth of 13× (for SNP calling) and an average coverage of 2.3%. In total, 122 632 indels, 31 444 insertions, 44 056 deletions and 455 CNVs (copy number variants) were identified in the genomes of the pigs. Approximately 2.3% of these genetic markers were mapped to gene exon regions, and 25% were in QTL regions related to economically important traits. The KEGG pathway or GO enrichment analyses revealed that genetic variants assumed to be large-effect mutations were significantly overrepresented in 22 SNP, 56 indel, 26 insertion, 28 deletion and three CNV gene sets. A total of 343 breed-specific SNPs were also identified in the six Chinese indigenous pigs. The findings from this study can contribute to future investigations of the genetic diversity, population structure, positive selection signals and molecular evolutionary history of these pigs at the genome level and can serve as a valuable reference for improving the breeding and cultivation of these pigs.
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: 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: 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: X
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Jiangshu Station of Animal Husbandry, Nanjing, 210036, China.
authors.forename: X
authors.initials: X
authors.lastname: Liu
authors.affiliation: Jiangshu Station of Animal Husbandry, Nanjing, 210036, China.
authors.forename: M
authors.initials: M
authors.lastname: Zhu
authors.affiliation: Jiangshu Station of Animal Husbandry, Nanjing, 210036, China.
authors.forename: W
authors.initials: W
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: D000818:Animals; D001947:Breeding; D002681:China; D002874:Chromosome Mapping; D056915:DNA Copy Number Variations; D005787:Gene Frequency; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA; D034421:Sus scrofa / Q000235:genetics*
keywords: 
  GGRS
  ; Chinese indigenous pigs; breed-specific SNPs; genome sequencing