Geoscience Reference
In-Depth Information
Linkage analysis
of markers
Coding of data for each DNA marker on each individual of a
population and conducting linkage analysis using computer
programs is the final step in the construction of a linkage map.
Missing marker data can also be acknowledged by mapping
programs. Computer programs are required to analyse link-
ages between large numbers of markers, which are not possible
manually. Linkage among markers is usually calculated using
odds ratios. Markers are assigned to linkage groups using the
odd ratios, which refers to the ratio of the probability that two
loci are linked with a given recombination value over a prob-
ability that the two are not linked. This ratio is more conve-
niently expressed as the logarithm of the ratio, and is called a
logarithm of odds (LOD) value or LOD score (Risch 1992). The
LOD values of >3 are typically used to construct linkage maps.
A LOD value of 3 between two markers indicates that the link-
age is 1000 times more likely (i.e., 1000:1) than no linkage
(null hypothesis). The LOD values may be lowered in order to
detect a greater level of linkage or to place additional markers
within maps constructed at higher LOD values. The commonly
used software programs include Mapmaker/EXP (Lander et al.
1987; Lincoln et al. 1992) and MapManager QTX (Manly et al.
2001), which are freely available from the Internet. JoinMap is
another commonly used program for constructing the linkage
maps (Stam 1993).
A typical output of a linkage map is shown in Figure 17.3.
Referring to the road map analogy, linkage groups symbolise
roads and markers represent signs or landmarks. A difficulty
linked with obtaining an equal number of linkage groups and
chromosomes is that the polymorphic markers detected are
not necessarily uniformly distributed over the chromosome,
but clustered in some regions and absent in others. Along with
this, the frequency of recombination is not equal along chro-
mosomes. The accuracy of measuring the genetic distance and
determining marker order is directly related to the number of
individuals examined in the mapping population. Ideally, the
mapping population should consist of a minimum of 50 indi-
viduals for constructing the linkage maps (Phillips et al. 2001).
Generally, frequency of recombination between genetic markers
is used to measure the distance along a linkage map. Mapping
functions are essential to convert recombination fractions into
centimorgans (cM) because recombination frequencies and
the frequencies of crossing-over are not related linearly. When
the map distance is small (<10 cM), the map distance equals the
recombination frequency. However, this relationship does not
Genetic
distance and
mapping
functions
