title: Whole-genome resequencing analyses of five pig breeds, including Korean wild and native, and three European origin breeds.
abstract: Pigs have been one of the most important sources of meat for humans, and their productivity has been substantially improved by recent strong selection. Here, we present whole-genome resequencing analyses of 55 pigs of five breeds representing Korean native pigs, wild boar and three European origin breeds. 1,673.1 Gb of sequence reads were mapped to the Swine reference assembly, covering ∼99.2% of the reference genome, at an average of ∼11.7-fold coverage. We detected 20,123,573 single-nucleotide polymorphisms (SNPs), of which 25.5% were novel. We extracted 35,458 of non-synonymous SNPs in 9,904 genes, which may contribute to traits of interest. The whole SNP sets were further used to access the population structures of the breeds, using multiple methodologies, including phylogenetic, similarity matrix, and population structure analysis. They showed clear population clusters with respect to each breed. Furthermore, we scanned the whole genomes to identify signatures of selection throughout the genome. The result revealed several promising loci that might underlie economically important traits in pigs, such as the CLDN1 and TWIST1 genes. These discoveries provide useful genomic information for further study of the discrete genetic mechanisms associated with economically important traits in pigs.
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Jung-Woo
authors.initials: JW
authors.lastname: Choi
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea.
authors.forename: Won-Hyong
authors.initials: WH
authors.lastname: Chung
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Kyung-Tai
authors.initials: KT
authors.lastname: Lee
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Eun-Seok
authors.initials: ES
authors.lastname: Cho
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Si-Woo
authors.initials: SW
authors.lastname: Lee
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Bong-Hwan
authors.initials: BH
authors.lastname: Choi
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea Department of Bioinformatics, Korea University of Science and Technology, Daejeon 305-806, Republic of Korea.
authors.forename: Sang-Heon
authors.initials: SH
authors.lastname: Lee
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea Department of Bioinformatics, Korea University of Science and Technology, Daejeon 305-806, Republic of Korea.
authors.forename: Wonjun
authors.initials: W
authors.lastname: Lim
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Dajeong
authors.initials: D
authors.lastname: Lim
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea Department of Bioinformatics, Korea University of Science and Technology, Daejeon 305-806, Republic of Korea.
authors.forename: Yun-Gyeong
authors.initials: YG
authors.lastname: Lee
authors.affiliation: Swine Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Republic of Korea.
authors.forename: Joon-Ki
authors.initials: JK
authors.lastname: Hong
authors.affiliation: Swine Division, National Institute of Animal Science, Rural Development Administration, Suwon 441-706, Republic of Korea.
authors.forename: Doo-Wan
authors.initials: DW
authors.lastname: Kim
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea.
authors.forename: Hyeon-Jeong
authors.initials: HJ
authors.lastname: Jeon
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea.
authors.forename: Jiwoong
authors.initials: J
authors.lastname: Kim
authors.affiliation: Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Republic of Korea Department of Bioinformatics, Korea University of Science and Technology, Daejeon 305-806, Republic of Korea thkim63@korea.kr n@rna.kr.
authors.forename: Namshin
authors.initials: N
authors.lastname: Kim
authors.affiliation: Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Jeonju 565-851, Republic of Korea thkim63@korea.kr n@rna.kr.
authors.forename: Tae-Hun
authors.initials: TH
authors.lastname: Kim
mesh_terms: D000818:Animals; D001947:Breeding; D019295:Computational Biology / Q000379:methods; D016678:Genome; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D013552:Swine / Q000235:genetics*
keywords: Pig; SNP; signature of selection; whole-genome sequencing