Agriculture Reference
In-Depth Information
and makes conclusions on the basis of past recombination events that
form the haplotypic structure of the species under study (Oraguzie et al.
2006). LD exploits genotypic variation because when we work with
collections of tightly related species, we can use the number of
recombination events (through meiosis) that occurred between the acces-
sions since divergence from the common ancestor. This amount of
recombination events increases the resolution of LDmapping but requires
genotypic analysis with more markers. In order to understand how AM
works it is imperative to describe what LD is, how it is measured, and
which factors affect it.
B. Principles of Linkage Disequilibrium
LD is the nonrandom association of alleles at different loci. Sometimes it
is dif
cult to understand the concept of LD because when we talk about
linkage we refer to a physical linkage between two loci, but LD does not
refer to the physical linkage between loci, but rather the phenomenon of
allele associations. These associations can happen between two loci on
different chromosomes due to population structure but close physical
linkage on the same chromosome results in high levels of LD (Flint-
Garcia et al. 2003). LD is measured in different ways, but in general LD
measures the co-occurrence of alleles at different loci, taking into
account the expected frequency of that co-occurrence. LD could be
produced by the mixture of two populations with different gamete
frequencies, by a random association in small populations, or by selec-
tion pressure.
LD value is expressed using gamete frequencies. If the genotypes have
two loci with the alleles A
1
,A
2
and B
1
,B
2
, then there will be four types of
gametes (A
1
B
1
,A
1
B
2
,A
2
B
1
, and A
2
B
2
) and the population will be in
equilibrium if the gametes have random combinations of these alleles.
The
first commonly used measure of LD is the
D
value (Lewontin and
Kojima 1960). This value quanti
es disequilibrium as the difference
between the observed frequency of co-occurrence of an allele at locus A
with the alleles at locus B, and the expected frequency of co-occurrence
under linkage equilibrium (Table 2.1).
The value of
D
should be the same without the sign values, and
disequilibrium could be expressed in terms of the frequencies of
gametes in repulsion and in coupling. So A
1
B
1
/A
2
B
2
genotypes are
heterozygous individuals with alleles in coupling with a frequency of
2
ru
and A
1
B
2
/A
2
B
1
genotypes are heterozygous individuals with
alleles in repulsion with a frequency of 2
st
. If the population is in
