Genetic linkage map construction

Genetic Maps
A genetic map is a schematic representation of
various genetic markers in the specific order, in
which they are located in a chromosome along with
the distances between them.

Genetic maps have been constructed by using three

diverse strategies to generate three different types
of maps, viz.,
(1) linkage maps,
(2) cytogenetic or cytological maps, and
(3) physical maps.
Linkage Maps
A linkage map is a schematic representation of the
relative locations of various genetic markers present in
the chromosomes of an organism as determined from
the frequency of recombination between pairs of
markers.
The recombination frequencies between marker pairs
are estimated from suitable mapping populations and
are converted to map or genetic distances, which are
represented in centi morgan (cM).
 Based on the genetic distance, the markers are
grouped into linkage groups, and their order in the
linkage group is depicted as the linkage map.
Cytogenetic Maps
A cytogenetic map depicts the locations of various genes in the
chromosomes of a species relative to specific microscopically observable
landmarks in the chromosomes.
Even morphological landmarks like centromeres, nucleolus organizing
regions, knobs, etc., and heritable heterochromatic regions of identifiable
shape have been used for mapping.
Cytogenetic mapping is generally used in eukaryotes, which have relatively
large microscopically observable chromosomes.
Cytogenetic mapping may use one or more of the following approaches:
1. Fluorescence in situ hybridization (FISH), including multicolor FISH
(McFISH), using gene sequences as probes;
2. Human–mouse somatic cell hybridization, followed by genetic and
cytogenetic analyses of the hybrid clones; and
3. Analysis of small changes in polytene chromosomes and the genetic
alterations associated with them.
In addition, chromosome deletion, translocation, trisomic, monosomic,
and nullisomic lines serve as valuable tools for cytogenetic mapping.
Physical Maps
In a physical map, the genes/molecular markers are
depicted in the same order as they occur in the
chromosomes, but the distances between adjacent
genes/markers are depicted in terms of base pairs (bp),
kilobase pairs (kb), Mb (megabase pairs), or Gb
(gigabase pairs).
Physical mapping usually involves
1.cloning of many pieces of chromosomal DNA,
2. characterization of these fragments for size, and
3.determination of their relative locations along the
chromosomes using a suitable technique like McFISH.
 The molecular markers used for linkage mapping can
also be used for physical Mapping.
 Construction of linkage maps
Linkage maps indicate the position and relative
genetic distances between markers along
chromosomes, which is analogous to signs or
landmarks along a highway.

Genes or markers that are close together or

tightly-linked will be transmitted together from
parent to progeny more frequently than genes or
markers that are located further apart.
a
 Mapping functions
Correspondence between recombination frequency and
genetic distance progressively declines with the increasing
distance between the linked genes.
When map distances are small (<10 cM), the map distance
equals the recombination frequency. However, this relationship
does not apply for map distances that are greater than 10 cM.
As a consequence, recombination frequencies have to be
corrected for the occurrence of multiple crossovers to obtain the
estimates of genetic distance from them.
There are several methods for converting recombination
frequency into genetic distance-called mapping functions, but
the two most commonly used methods are
1. Kosambi mapping function – Allows interference
2. Haldane mapping function - No interference
The three main steps of linkage map construction are:
(1)production of a mapping population;
(2) Identification of polymorphism and
(3) linkage analysis of markers.

Mapping populations

The construction of a linkage map requires a segregating plant

population (i.e. a population derived from sexual reproduction).
The parents selected for the mapping population will differ for one or
more traits of interest.
Population sizes used in preliminary genetic mapping studies generally
range from 50 to 250 individuals however larger populations are
required for high-resolution mapping.
 If the map will be used for QTL studies (which is usually the case), that
the mapping population must be phenotypically evaluated (i.e. trait data
must be collected) before subsequent QTL mapping.
Diagram of main types of mapping populations for self-pollinating
species.
 Identification of polymorphism

It is critical that sufficient polymorphism exists between

parents in order to construct a linkage map.

Parents that provide adequate polymorphism are selected

on the basis of the level of genetic diversity between
parents.

Once polymorphic markers have been identified, they

must be screened across the entire mapping population,
including the parents and F1 hybrid.

 Deviation of the marker segregation from Mendelian

ratio is called segregation distortion
Linkage analysis of markers
Hypothetical gel photos representing segregating codominant
markers (left-hand side) and dominant markers (right-hand side) for
typical mapping populations.
Note that dominant markers cannot discriminate between
heterozygotes and one homozygote genotype in F2 populations.
Chi square test to be conducted
What is the genetic distance between M1 and M2
markers based on the following marker scoring data
obtained from a segregating population?
In the event of two genes segregating together, it
is important to decide whether they are
segregating independently or they are linked.
This decision can be based on either a chi-square
test or a logarithm of odds (LOD) score estimate.
 The chisquare test is simpler and far easier to
carry out than estimating LOD scores, but it
merely detects the presence of linkage and
generates no more information.
In contrast, LOD score detects linkage as well as
provides an estimate of the most likely frequency
of recombination between the two genes.
Linkage between markers is usually calculated using odds
ratios (i.e. the ratio of linkage versus no linkage). This ratio is
more conveniently expressed as the logarithm of the ratio,
and is called a logarithm of odds (LOD) value or LOD score.
LOD values of >3 are typically used to construct linkage
maps.
A LOD value of 3 between two markers indicates that
linkage is 1000 times more likely (i.e. 1000:1) than no
linkage (null hypothesis).
Commonly used software programs include
Mapmaker/EXP, MapDisto, MapManager QTX and
JoinMap

•Identify the marker interval where QTL is located?

Marker A B C D E F G H
LOD -6.3 -3.5 0.9 4.5 5.6 2.9 1.3 -2.1
LOD (Logarithm
of Odds) score analysis
Hypothetical ‘framework’ linkage map of five chromosomes
(represented by linkage groups).

Linked markers are grouped together into ‘linkage groups,’ which

represent chromosomal segments or entire chromosomes.