Full pedigree quantitative trait locus analysis in commercial pigs using variance components

D J de Koning, R Pong-Wong, L Varona, G J Evans, E Giuffra, A Sanchez, G Plastow, J L Noguera, L Andersson, C S Haley

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In commercial livestock populations, QTL detection methods often use existing half-sib family structures and ignore additional relationships within and between families. We reanalyzed the data from a large QTL confirmation experiment with 10 pig lines and 10 chromosome regions using identity-by-descent (IBD) scores and variance component analyses. The IBD scores were obtained using a Monte Carlo Markov Chain method,,as implemented in the LOKI software, and were used to model a putative QTL in a mixed animal model. The analyses revealed 61 QTL at a nominal 5% level (out of 650. tests). Twenty-seven QTL mapped to areas where QTL have been reported, and eight of these exceeded the threshold to claim confirmed linkage (P < 0.01). Forty-two of the putative QTL were detected previously using half-sib analyses, whereas 46 QTL previously identified by half-sib analyses could not be confirmed using the variance component approach. Some of the differences could be traced back to the underlying assumptions between the two methods. Using a deterministic approach to estimate IBD scores on a subset of the data gave very similar results to LOKI. We have demonstrated the feasibility of applying variance component QTL analysis to a large amount of data, equivalent to a genome scan. In many situations, the deterministic IBD approach offers a fast alternative to LOKI.

Original languageEnglish
Pages (from-to)2155-2163
Number of pages9
JournalJournal of Animal Science
Issue number9
Publication statusPublished - Sep 2003


  • Analysis of Variance
  • Animals
  • Data Interpretation, Statistical
  • Female
  • Genetic Linkage
  • Genotype
  • Male
  • Quantitative Trait Loci
  • Swine/genetics

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