title: Porcine single nucleotide polymorphism (SNP) development and population structure of pigs assessed by validated SNPs.
abstract: In this study, we identified porcine single nucleotide polymorphisms (SNPs) by aligning eight sequences generated with two approaches: amplification of 665 intronic regions using one sample from each of eight breeds, including three East Asian pigs, and amplification of 289 3'-UTR regions using two samples from each of four major commercial breeds. The 1,760 and 599 SNPs were validated using two 384-sample DNA panels by matrix-assisted laser desorption ionization time-of-flight mass spectrometry. The phylogenetic tree and Structure analyses classified the pigs into two large clusters: Euro-American and East Asian populations. The membership proportions, however, differed between inferred clusters for K = 2 generated by the two approaches. With intronic SNPs, Euro-American breeds constituted about 100% of the Euro-American cluster, but with 3'-UTR SNPs, about 17% of the East Asian cluster comprised five Euro-American breeds. The differences in the SNP discovery panels may affect population structure found in study panels of large samples.
authors.affiliation: Second Research Division, STAFF Institute, Tsukuba, Ibaraki, 305-0854, Japan.
authors.forename: Toshimi
authors.initials: T
authors.lastname: Matsumoto
authors.forename: Naohiko
authors.initials: N
authors.lastname: Okumura
authors.forename: Hirohide
authors.initials: H
authors.lastname: Uenishi
authors.forename: Takeshi
authors.initials: T
authors.lastname: Hayashi
authors.forename: Noriyuki
authors.initials: N
authors.lastname: Hamasima
authors.forename: Takashi
authors.initials: T
authors.lastname: Awata
mesh_terms: D020413:3' Untranslated Regions / Q000235:genetics; D000818:Animals; D014644:Genetic Variation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D034421:Sus scrofa / Q000235:genetics*
chemical_list: D020413:3' Untranslated Regions