Implementation of SNPs in pig genetics: LD and QTL analysis

B.J. Jungerius

Research output: Thesisinternal PhD, WU


The aim of this thesis was the implementation and application of SNP markers in animal breeding and genetics. The emphasis was on the analysis of fatness traits in pigs, in particular of the imprinted QTL region on SSC2p. Several aspects of the implemetation of SNP markers in genetic analysis oflivestock wereaddressed, including SNP discovery methods and tools for enhancing sequencing and genotyping data analysis. The QTL on SSC2p was reanalysed after the identification of a SNP in the IGF2 gene that had high impact on lean muscle growth and back fat thickness. This re-analysis showed that the QTL region is narrowed down to a single base pair: the quantitative trait nucleotide (QTN). For research in other genomic regions, the SNP marker density needed in association studies was an issue of discussion. To address this question, the extent of LD in the porcine genome was studied. It was estimated that the majority of marker pairs separated by less than 50 kb show levels of LD that might be useful in association studies. Further investigation of LD and the extent of LD,however, is crucial in order to develop a map of the patterns of sequence variation in the porcine genome.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • Wageningen University
  • Groenen, M.A.M., Promotor
  • van Oost, B.A., Promotor, External person
  • te Pas, Marinus, Co-promotor
Award date27 Oct 2004
Place of PublicationWageningen
Print ISBNs9789085040712
Publication statusPublished - 2004


  • pigs
  • genetic markers
  • obesity
  • quantitative traits
  • dna sequencing
  • nucleotides
  • polymorphism
  • genetic analysis
  • genetics
  • animal breeding


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