Geoscience Reference
In-Depth Information
and (3) highly significant. Lander and Kruglyak (1995) sug-
gested this classification in order to 'avoid a flood of false
positive claims' and also certify that 'true hints of linkage'
were not missed (Lander and Kruglyak 1995). Significant and
highly significant QTLs were given significance levels of 5%
and 0.1%, respectively, whereas a suggestive QTL is one that
would be expected to occur once at random in a QTL map-
ping study (in other words, there is a warning relating to the
dependability of suggestive QTLs). The mapping program
MapManager QTX reports QTL mapping results with this
classification (Manly et al. 2001).
Confidence intervals for QTLs
Although the map posi-
tion is that the most feasible position of a QTL at which the
highest LOD or LRS score is detected, in fact QTLs occur
within the confidence intervals. There are numerous ways
by which confidence intervals can be calculated. 'One-LOD
support interval' is the simplest one, which is determined by
finding the region on both sides of a QTL peak that corre-
sponds to a decrease of 1 LOD score (Lander and Botstein
1989; Hackett 2002). 'Bootstrapping', a statistical method for
resampling, is another method to determine the confidence
interval of QTLs (Visscher et al. 1996), and can be effort-
lessly applied within some mapping software programs such
as MapManager QTX.
Number of markers and marker spacing
The number of
markers required for a genetic map varies with the number
and length of chromosomes within the organism. For the
detection of QTLs, a comparatively thin 'framework' (or
'skeletal' or 'scaffold') map with evenly spaced markers is
adequate, and preliminary genetic mapping studies generally
contain between 100 and 200 markers (Mohan et al. 1997).
However, this depends on the genome size of the species;
for mapping species with large genomes more markers are
desired. Darvasi et al. (1993) reported that the power of recog-
nising a QTL was effectively the same for a marker spacing of
10 cM as for an infinite number of markers, and only slightly
decreased for marker spacing of 20 or even 50 cM (Darvasi
et al. 1993).
Factors influencing the detection of QTLs
The key factors
influencing the detection of QTLs segregating in a population
are the genetic properties of QTLs that control traits, envi-
ronmental effects, population size and experimental error.
