Free Access
Genet. Sel. Evol.
Volume 39, Number 3, May-June 2007
Page(s) 285 - 299
Published online 14 April 2007
Genet. Sel. Evol. 39 (2007) 285-299
DOI: 10.1051/gse:2007004

Fine mapping of multiple QTL using combined linkage and linkage disequilibrium mapping - A comparison of single QTL and multi QTL methods

Eivind Uleberg and Theo H. E. Meuwissen

Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences, 1432 Ås, Norway

(Received 26 May 2006; accepted 28 November 2006; published online 14 April 2007)

Abstract - Two previously described QTL mapping methods, which combine linkage analysis (LA) and linkage disequilibrium analysis (LD), were compared for their ability to detect and map multiple QTL. The methods were tested on five different simulated data sets in which the exact QTL positions were known. Every simulated data set contained two QTL, but the distances between these QTL were varied from 15 to 150 cM. The results show that the single QTL mapping method (LDLA) gave good results as long as the distance between the QTL was large (>90 cM). When the distance between the QTL was reduced, the single QTL method had problems positioning the two QTL and tended to position only one QTL, i.e. a "ghost" QTL, in between the two real QTL positions. The multi QTL mapping method (MP-LDLA) gave good results for all evaluated distances between the QTL. For the large distances between the QTL (>90 cM) the single QTL method more often positioned the QTL in the correct marker bracket, but considering the broader likelihood peaks of the single point method it could be argued that the multi QTL method was more precise. Since the distances were reduced the multi QTL method was clearly more accurate than the single QTL method. The two methods combine well, and together provide a good tool to position single or multiple QTL in practical situations, where the number of QTL and their positions are unknown.

Key words: fine mapping / multiple QTL / simulations

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© INRA, EDP Sciences 2007