title: Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations.
abstract: BACKGROUND
  Simultaneous detection of multiple QTLs (quantitative trait loci) may allow more accurate estimation of genetic effects. We have analyzed outbred commercial pig populations with different single and multiple models to clarify their genetic properties and in addition, we have investigated pleiotropy among growth and obesity traits based on allelic correlation within a gamete.
  
  
  METHODS
  Three closed populations, (A) 427 individuals from a Yorkshire and Large White synthetic breed, (B) 547 Large White individuals and (C) 531 Large White individuals, were analyzed using a variance component method with one-QTL and two-QTL models. Six markers on chromosome 4 and five to seven markers on chromosome 7 were used.
  
  
  RESULTS
  Population A displayed a high test statistic for the fat trait when applying the two-QTL model with two positions on two chromosomes. The estimated heritabilities for polygenic effects and for the first and second QTL were 19%, 17% and 21%, respectively. The high correlation of the estimated allelic effect on the same gamete and QTL test statistics suggested that the two separate QTL which were detected on different chromosomes both have pleiotropic effects on the two fat traits. Analysis of population B using the one-QTL model for three fat traits found a similar peak position on chromosome 7. Allelic effects of three fat traits from the same gamete were highly correlated suggesting the presence of a pleiotropic QTL. In population C, three growth traits also displayed similar peak positions on chromosome 7 and allelic effects from the same gamete were correlated.
  
  
  CONCLUSIONS
  Detection of the second QTL in a model reduced the polygenic heritability and should improve accuracy of estimated heritabilities for both QTLs.
authors.affiliation: National Institute of Livestock and Grassland Science, Tsukuba 305-0901, Japan. yoshi.nagamine@roslin.ed.ac.uk
authors.forename: Yoshitaka
authors.initials: Y
authors.lastname: Nagamine
authors.forename: Ricardo
authors.initials: R
authors.lastname: Pong-Wong
authors.forename: Peter M
authors.initials: PM
authors.lastname: Visscher
authors.forename: Chris S
authors.initials: CS
authors.lastname: Haley
mesh_terms: D000818:Animals; D021461:Animals, Outbred Strains; D033481:Chromosomes, Mammalian / Q000235:genetics; D005260:Female; D006824:Hybridization, Genetic; D008297:Male; D008957:Models, Genetic; D040641:Quantitative Trait Loci; D013552:Swine / Q000235:genetics*