title: Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology.
abstract: BACKGROUND
  The dissection of complex traits of economic importance to the pig industry requires the availability of a significant number of genetic markers, such as single nucleotide polymorphisms (SNPs). This study was conducted to discover several hundreds of thousands of porcine SNPs using next generation sequencing technologies and use these SNPs, as well as others from different public sources, to design a high-density SNP genotyping assay.
  
  
  RESULTS
  A total of 19 reduced representation libraries derived from four swine breeds (Duroc, Landrace, Large White, Pietrain) and a Wild Boar population and three restriction enzymes (AluI, HaeIII and MspI) were sequenced using Illumina's Genome Analyzer (GA). The SNP discovery effort resulted in the de novo identification of over 372K SNPs. More than 549K SNPs were used to design the Illumina Porcine 60K+SNP iSelect Beadchip, now commercially available as the PorcineSNP60. A total of 64,232 SNPs were included on the Beadchip. Results from genotyping the 158 individuals used for sequencing showed a high overall SNP call rate (97.5%). Of the 62,621 loci that could be reliably scored, 58,994 were polymorphic yielding a SNP conversion success rate of 94%. The average minor allele frequency (MAF) for all scorable SNPs was 0.274.
  
  
  CONCLUSIONS
  Overall, the results of this study indicate the utility of using next generation sequencing technologies to identify large numbers of reliable SNPs. In addition, the validation of the PorcineSNP60 Beadchip demonstrated that the assay is an excellent tool that will likely be used in a variety of future studies in pigs.
authors: Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands.
authors: Antonio M
authors: AM
authors: Ramos
authors: Richard P M A
authors: RP
authors: Crooijmans
authors: Nabeel A
authors: NA
authors: Affara
authors: Andreia J
authors: AJ
authors: Amaral
authors: Alan L
authors: AL
authors: Archibald
authors: Jonathan E
authors: JE
authors: Beever
authors: Christian
authors: C
authors: Bendixen
authors: Carol
authors: C
authors: Churcher
authors: Richard
authors: R
authors: Clark
authors: Patrick
authors: P
authors: Dehais
authors: Mark S
authors: MS
authors: Hansen
authors: Jakob
authors: J
authors: Hedegaard
authors: Zhi-Liang
authors: ZL
authors: Hu
authors: Hindrik H
authors: HH
authors: Kerstens
authors: Andy S
authors: AS
authors: Law
authors: Hendrik-Jan
authors: HJ
authors: Megens
authors: Denis
authors: D
authors: Milan
authors: Danny J
authors: DJ
authors: Nonneman
authors: Gary A
authors: GA
authors: Rohrer
authors: Max F
authors: MF
authors: Rothschild
authors: Tim P L
authors: TP
authors: Smith
authors: Robert D
authors: RD
authors: Schnabel
authors: Curt P
authors: CP
authors: Van Tassell
authors: Jeremy F
authors: JF
authors: Taylor
authors: Ralph T
authors: RT
authors: Wiedmann
authors: Lawrence B
authors: LB
authors: Schook
authors: Martien A M
authors: MA
authors: Groenen
mesh_terms: D000818:Animals; D005838:Genotype; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D013045:Species Specificity; D013552:Swine / Q000235:genetics*