Geoscience Reference
In-Depth Information
The genetic properties of QTLs controlling traits comprise the
magnitude of the effect of individual QTLs. Only QTLs with
sufficiently large phenotypic effects would be detected; QTLs
with small effects may fall below the significance threshold of
detection. Another genetic property is the distance between
linked QTLs. Closely linked QTLs (~20 cM or less) will usu-
ally be detected as a single QTL in typical population sizes
(<500). Environmental effects may have a profound influence
on the expression of quantitative traits. Experiments that are
replicated across sites and over time (e.g. different seasons
and years) may enable the researcher to investigate environ-
mental influences on QTLs affecting trait(s) of interest. RI or
DH populations are ideal for these purposes. The principal
experimental design factor is the size of the population used
in the mapping study. The larger the population size, the more
accurate the mapping study and the more likely it is to allow
detection of QTLs with smaller effects. An increase in pop-
ulation size provides gains in statistical power, estimates of
gene effects and confidence intervals of the locations of QTLs
(Darvasi et al. 1993; Beavis 1998). Error in phenotypic evalu-
ation and mistakes in marker genotyping are the main sources
of experimental errors during QTL analysis. Genotyping errors
and missing data may affect the order and distance between
markers within the linkage maps (Hackett 2002). The phe-
notyping of the mapping population is of paramount impor-
tance for the accuracy of QTL mapping studies. A reliable
QTL map can only be produced from reliable phenotypic data.
Replicated phenotypic measurements can be used to improve
the accuracy of QTL mapping by reducing background 'noise'
(Danesh et al. 1994; Haley and Anderson 1997).
Confirmation of QTL
Ideally, due to the factors described
above, QTL mapping studies should be independently con-
firmed or verified. Such confirmation studies referred to as
'replication studies' (by Lander and Kruglyak 1995) involve
independent populations constructed from the same parental
genotypes or closely related genotypes used in the primary
QTL mapping study. Sometimes, larger population sizes may
be used. Furthermore, some recent studies have suggested that
QTL positions and effects should be evaluated in independent
populations, because QTL mapping based on typical popula-
tion sizes result in a low power of QTL detection and a large
bias of QTL effects. Unfortunately, due to constraints such as
lack of research funding and time, and possibly a lack of under-
standing of the need to confirm results, QTL mapping studies
