Genet. Sel. Evol. 36 (2004) 261-279
DOI: 10.1051/gse:2004001

Mapping multiple QTL using linkage disequilibrium and linkage analysis information and multitrait data

Theo H.E. Meuwissen^a and Mike E. Goddard<sup>b

a</sup>  Centre for Integrative Genetics (Cigene), Institute of Animal Science, Agricultural University of Norway, Box 5025, Ås, Norway
^b  Institute of Land and Food Resources, University of Melbourne, and Victorian Institute of Animal Science, Attwood, Australia

(Received 17 February 2003; accepted 10 November 2003)

Abstract
A multi-locus QTL mapping method is presented, which combines linkage and linkage disequilibrium (LD) information and uses multitrait data. The method assumed a putative QTL at the midpoint of each marker bracket. Whether the putative QTL had an effect or not was sampled using Markov chain Monte Carlo (MCMC) methods. The method was tested in dairy cattle data on chromosome 14 where the DGAT1 gene was known to be segregating. The DGAT1 gene was mapped to a region of 0.04 cM, and the effects of the gene were accurately estimated. The fitting of multiple QTL gave a much sharper indication of the QTL position than a single QTL model using multitrait data, probably because the multi-locus QTL mapping reduced the carry over effect of the large DGAT1 gene to adjacent putative QTL positions. This suggests that the method could detect secondary QTL that would, in single point analyses, remain hidden under the broad peak of the dominant QTL. However, no indications for a second QTL affecting dairy traits were found on chromosome 14.

Key words: QTL mapping / linkage analysis / linkage disequilibrium mapping / multitrait analysis / multi-locus mapping

Correspondence and reprints: theo.meuwissen@iha.nlh.no

© INRA, EDP Sciences 2004