Geoscience Reference
In-Depth Information
markers. Moreover, the relationship between genetic and phys-
ical distance varies along a chromosome. For example, there
are recombinations of 'hot spots' and 'cold spots', which are
chromosomal regions where recombination occurs more fre-
quently or less frequently, respectively (Faris et al. 2000; Ma
et al. 2001; Yao et al. 2002).
QtL analysis
Quantitative traits in crop plants are controlled and regulated
by polygenes, which make their study difficult by Mendelian
methods of genetic analysis. In recent years, the availability of
polymorphic molecular markers facilitated the genetic anal-
ysis of those quantitative attributes by treating polygenes as
QTLs, which also segregate in a Mendelian manner. A QTL
(a term first coined by Gelderman 1975) is defined as 'a region
of the genome that is associated with an effect on a quantita-
tive trait'. Conceptually, a QTL can be a single gene, or it may
be a cluster of linked genes that affect the trait. QTL map-
ping studies have been reported in most crop plants for diverse
traits, including yield, quality, disease and insect resistance,
abiotic stress tolerance and environmental adaptation (Singh
et al. 2012).
Principle of QTL analysis
Identification and mapping of
a good number of segregating markers (10-50) per chromo-
some are not difficult in the populations of most crop plants.
However, most of those markers would be in the noncoding
regions of the genome and might not affect the trait of inter-
est directly, but a few of these markers might be linked to
genomic regions (QTLs) that do influence the trait of inter-
est. Wherever such linkage occurs, the marker locus and also
the QTL will co-segregate. Therefore, the basic principle of
determining whether a QTL is linked to a marker is to par-
tition the mapping population into different genotype classes
based on genotypes at the marker locus, and apply correlative
statistics to determine whether the individuals of one genotype
differ significantly with the individuals of another genotype
with respect to the trait being measured. Circumstances where
genes fail to segregate independently are said to display 'link-
age disequilibrium (LD)'. QTL analysis, thus, depends on the
LD. With natural populations, consistent association between
QTL and marker genotype will not frequently exist, except in
a very rare condition wherever the marker is completely linked
to the QTL. Therefore, QTL analysis is undertaken in segre-
gating mapping populations, such as F
2
-derived populations,
RILs, near-isogenic lines, DHs and backcross populations
