The determination of empirical confidence intervals for the
location of quantitative trait loci
(QTLs) by interval mapping was investigated using simulation. Confidence
intervals were created
using a non-parametric (resampling method) and parametric (resimulation
method) bootstrap for a
backcross population derived from inbred lines. QTLs explaining 1%, 5%
and 10% of the
phenotypic variance were tested in populations of 200 or 500 individuals.
Results from the two
methods were compared at all locations along one half of the chromosome.
The non-parametric
bootstrap produced results close to expectation at all non-marker locations,
but confidence
intervals when the QTL was located at the marker were conservative. The
parametric method
performed poorly; results varied from conservative confidence intervals
at the location of the
marker, to anti-conservative intervals midway between markers. The results
were shown to be
influenced by a bias in the mapping procedure and by the accumulation of
type 1 errors at the
location of the markers. The parametric bootstrap is not a suitable method
for constructing
confidence intervals in QTL mapping. The confidence intervals from the
non-parametric bootstrap
are accurate and suitable for practical use.