Research

Detection of multiple quantitative trait loci and their pleiotropic effects in outbred pig populations

Yoshitaka Nagamine^1,2 , Ricardo Pong-Wong² , Peter M Visscher³ and Chris S Haley^2,4

¹  National Institute of Livestock and Grassland Science, Tsukuba, 305-0901, Japan

²  The Roslin Institute (The University of Edinburgh), Midlothian, EH25 9PS, UK

³  Queensland Institute of Medical Research, Brisbane, QLD, 4029, Australia

⁴  Human Genetics Unit, Medical Research Centre, Edinburgh, EH4 2XU, UK

author email corresponding author email

Genetics Selection Evolution 2009, 41:44doi:10.1186/1297-9686-41-44

Published:	6 October 2009

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.

Conclusion

Detection of the second QTL in a model reduced the polygenic heritability and should improve accuracy of estimated heritabilities for both QTLs.