Issue |
Genet. Sel. Evol.
Volume 36, Number 2, March-April 2004
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Page(s) | 145 - 161 | |
DOI | https://doi.org/10.1051/gse:2003056 |
DOI: 10.1051/gse:2003056
The efficiency of designs for fine-mapping of quantitative trait loci using combined linkage disequilibrium and linkage
Sang Hong Lee and Julius H.J. van der WerfSchool of Rural Science and Agriculture, University of New England, Armidale, NSW 2351, Australia
(Received 19 March 2003; accepted 1 October 2003)
Abstract
In a simulation study, different designs were compared for efficiency of
fine-mapping of QTL. The variance component method for fine-mapping of QTL
was used to estimate QTL position and variance components. The design of
many families with small size gave a higher mapping resolution than a design
with few families of large size. However, the difference is small in half
sib designs. The proportion of replicates with the QTL positioned within 3
cM of the true position is 0.71 in the best design, and 0.68 in the worst
design applied to 128 animals with a phenotypic record and a QTL explaining
25% of the phenotypic variance.
The design of two half sib families each of size 64 was further investigated
for a hypothetical population with effective size of 1000 simulated for 6000
generations with a marker density of 0.25 cM and with marker mutation rate
per generation. In mapping using bi-allelic markers,
of replicated simulations could position QTL within 0.75 cM of the
true position whereas this was higher for multi allelic markers (
). The accuracy was lowest (48%) when mutation age was 100
generations and increased to 68% and 76% for mutation ages of 200 and
500 generations, respectively, after which it was about 70% for mutation
ages of 1000 generations and older. When effective size was linearly
decreasing in the last 50 generations, the accuracy was decreased (56 to 70%).
We show that half sib designs that have often been used for linkage mapping
can have sufficient information for fine-mapping of QTL. It is suggested
that the same design with the same animals for linkage mapping should be
used for fine-mapping so gene mapping can be cost effective in livestock
populations.
Key words: quantitative trait loci / fine-mapping / restricted maximum likelihood / simulation / designs
Correspondence and reprints: Sang Hong slee7@metz.une.edu.au
© INRA, EDP Sciences 2004