title: Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication.
abstract: Domesticated organisms have experienced strong selective pressures directed at genes or genomic regions controlling traits of biological, agricultural or medical importance. The genome of native and domesticated pigs provide a unique opportunity for tracing the history of domestication and identifying signatures of artificial selection. Here we used whole-genome sequencing to explore the genetic relationships among the European native pig Berkshire and breeds that are distributed worldwide, and to identify genomic footprints left by selection during the domestication of Berkshire. Numerous nonsynonymous SNPs-containing genes fall into olfactory-related categories, which are part of a rapidly evolving superfamily in the mammalian genome. Phylogenetic analyses revealed a deep phylogenetic split between European and Asian pigs rather than between domestic and wild pigs. Admixture analysis exhibited higher portion of Chinese genetic material for the Berkshire pigs, which is consistent with the historical record regarding its origin. Selective sweep analyses revealed strong signatures of selection affecting genomic regions that harbor genes underlying economic traits such as disease resistance, pork yield, fertility, tameness and body length. These discoveries confirmed the history of origin of Berkshire pig by genome-wide analysis and illustrate how domestication has shaped the patterns of genetic variation.
authors.affiliation: 1] Biodynamic Optical Imaging Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, and School of Life Sciences, Peking University, Beijing 100871, People's Republic of China [2] Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China [3].
authors.forename: Mingzhou
authors.initials: M
authors.lastname: Li
authors.affiliation: 1] Novogene Bioinformatics Institute, Beijing 100083, People's Republic of China [2].
authors.forename: Shilin
authors.initials: S
authors.lastname: Tian
authors.affiliation: 1] Novogene Bioinformatics Institute, Beijing 100083, People's Republic of China [2].
authors.forename: Carol K L
authors.initials: CK
authors.lastname: Yeung
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100083, People's Republic of China.
authors.forename: Xuehong
authors.initials: X
authors.lastname: Meng
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Qianzi
authors.initials: Q
authors.lastname: Tang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Lili
authors.initials: L
authors.lastname: Niu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Xun
authors.initials: X
authors.lastname: Wang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Long
authors.initials: L
authors.lastname: Jin
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Jideng
authors.initials: J
authors.lastname: Ma
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Keren
authors.initials: K
authors.lastname: Long
authors.affiliation: 1] Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China [2] Department of Animal Science, Southwest University at Rongchang, Chongqing 402460, People's Republic of China.
authors.forename: Chaowei
authors.initials: C
authors.lastname: Zhou
authors.affiliation: Novogene Bioinformatics Institute, Beijing 100083, People's Republic of China.
authors.forename: Yinchuan
authors.initials: Y
authors.lastname: Cao
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Li
authors.initials: L
authors.lastname: Zhu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Lin
authors.initials: L
authors.lastname: Bai
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Guoqing
authors.initials: G
authors.lastname: Tang
authors.affiliation: Sichuan Animal Science Academy, Chengdu 610066, People's Republic of China.
authors.forename: Yiren
authors.initials: Y
authors.lastname: Gu
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: An'an
authors.initials: A
authors.lastname: Jiang
authors.affiliation: Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, People's Republic of China.
authors.forename: Xuewei
authors.initials: X
authors.lastname: Li
authors.affiliation: 1] Biodynamic Optical Imaging Center (BIOPIC), Peking-Tsinghua Center for Life Sciences, and School of Life Sciences, Peking University, Beijing 100871, People's Republic of China [2] Novogene Bioinformatics Institute, Beijing 100083, People's Republic of China.
authors.forename: Ruiqiang
authors.initials: R
authors.lastname: Li
mesh_terms: D000818:Animals; D000829:Animals, Domestic / Q000235:genetics; D049628:Body Size / Q000235:genetics; D002874:Chromosome Mapping; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing; D054643:INDEL Mutation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D012641:Selection, Genetic; D017422:Sequence Analysis, DNA; D013552:Swine / Q000145:classification / Q000235:genetics*
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