Geoscience Reference
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are rarely confirmed and validated. Validation is a very impor-
tant aspect that needs to be taken care by the molecular mark-
ers. Some notable exceptions are the confirmation of QTLs
associated with root-knot nematode resistance (Li et al. 2001)
and bud blight resistance in soybean (Fasoula et al. 2003).
QTLs can also be confirmed by using a specific type of popula-
tion called NILs. NILs are generated by crossing a donor par-
ent (e.g. wild parent possessing a specific trait of interest) to a
recurrent parent (e.g. an elite cultivar). The F
1
hybrids are then
backcrossed to the recurrent parents to produce first backcross
generation (BC
1
). The BC
1
s are then repeatedly backcrossed
to the recurrent parents for a number of generations (at least
6-7 generations). The final BC
7
will contain practically all of
the recurrent parent genome except for the small chromosomal
region containing a gene or QTL of interest. Homozygous F
2
lines can be obtained by self-pollinating the BC
7
plants. It
should be noted that in order to produce NILs containing tar-
get genes, the genes have to be selected for during each round
of backcrossing. By genotyping NILs with important markers,
and comparing mean trait values of particular NIL lines with
the recurrent parent, the effects of QTLs could be confirmed.
Short cuts for gene/QTL mapping
The construction of link-
age maps and QTL analysis require considerably more time
and effort, and may be cost-effective. Therefore, other methods
would be of use that can save time and money. The 'short-cut'
methods that tag QTLs to discover markers are bulked seg-
regant analysis (BSA) and selective genotyping. The require-
ment of both the methods is mapping populations. BSA detects
markers located in specific chromosomal regions (Michelmore
et al. 1991). In the BSA method, two pools or 'bulks' of DNA
samples are pooled from 10 to 20 individual plants from a
segregating population, but these two bulks should be differ-
ent for a trait of interest. DNA bulks are made to randomise
every loci, except for the region enclosing the gene of interest.
Across the two bulk markers are screened. The polymorphic
markers identified may represent markers that are linked to a
gene or QTL of interest. The identification of linked markers by
using BSA is given in Figure 17.6. These polymorphic markers
are then used for the genotyping of the entire population, and
a localised linkage map may be generated. This enables QTL
analysis to be performed and the location of a QTL to be deter-
mined (Ford et al. 1999). Generally, BSA is used to tag genes
controlling simple traits, but the method may also be used to
identify markers linked to major QTLs (Wang and Paterson
