Linkage

Objectives
• Understand that linkage and linkage disequilibrium are properties of
populations, not individuals.

• Estimate recombination and disequilibrium statistics

 Introduction
• Plant breeding populations, by definition, employ methods
that force populations into states of disequilibrium.
• Plant breeders do not mate infinite (or even large) numbers of
parents, thus drift has a major impact on population disequilibrium.
• They select the parents that will be used in matings, thus selection,
linkage and pleiotropy affect the population structure.
• New lines from external breeding projects are often introduced to
the breeding nurseries, thus migration affects the structure of plant
breeding populations.
Disequilibrium Definitions
• Gametic and linkage disequilibrium used as measures of deviation
(disequilibrium) from Hardy-Weinberg Equilibrium.
• In other words the estimation of these population parameters are
based on a reference population and the reference population must be
defined or else the calculated values have no meaning.
• The motivation is to ‘map’ genetic loci based on how they are most
likely to be inherited relative to each other.
• Mechanisms that result in Disequilibrium are
• Linkage: among alleles at more than a single locus on the same chromosome.
• Other than linkage, e.g., selection and drift: among alleles at more than a
single locus.
Linkage
• Suppose:
 
• Parent 1 has the genotype
• Parnet 2 has the gentoype
• Loci A, B and C are on one homologous pair
of chromosomes, whereas locus D is on a
separate chromosome.
• The F1 progeny of parent 1 and parent 2 will
all have the genotype.
Figure 1. Crossing over between linked loci
• The frequency of each allele at each locus is
0.5
• At each locus, the expected genotype
frequencies in the F2 are: 1/4 1/4
• 25% homozygous dominat (i.e., )
• 50% heterozygous (i.e., 1/4 1/4
• 25% homozygous recessive (i.e.,
Linkage
• Each
  locus, considered individually, is
therefore in Hardy-Weinberg equilibrium
• Because the genotype frequencies with are
• If two or more loci behave independently
during meiosis, the proportion of genotypes
across loci is equal to the product of
genotype frequiencies at each locus.
• Eg. Frequency of A1A1 inds =0.25; D1D2=0.5,
then A1A1D1D2 inds = 0.25x0.50=0.1245
• Loci, however, do not always assort
independently.
• Linkage occurs when two or more loci are
close to each other on the same chromosome
such that certain genes at these loci tend to
be inherited together.
Linkage
• Unliked loci are:
• On differnet chromosomes eg loci D
• Far apart on the same chromosome
• Consequence: Frequent recombination and
and cause independent assortment.
• Locus D in our example is unlinked to A, B and C
by virtue of its location on a different chromosome.
• In figure 1 crossing over has occured between
loci A and B.
• Gametes recovered:
• Recombinant gametes (A1B2 and A2B1)
• Parental gametes (A1B1 and A2B2).
• The A and B loci are considered unliked if
crossing over between them produces 50%
recombinant and 50% parental gametes.
Linkage
• Suppose a large number of B1B2C1C2 plants are
testcrossed to parent 2 (table 1)
Table 1. Parental and recombinant gametes in a testcross.
Gamete from B1B2C1C2: Testcross (to B2B2C2C2)
Type Frequency genotype Number
B1C1 B1B2C1C2 270

B1C2
B1C2 B1B2C2C2
B1B2C2C2 30
30
B2C1 B2B2C1C2 30
B2C1 B2B2C1C2 30
B2C2 B2B2C2C2 270
B2C2 B2B2C2C2 270
Total = 600
Total = 600
Linkage
• When only the B and C loci are considered, the B1B2C1C2
and B2B2C2C2 progeny represent the union of a parental
gamete (i.e., B1C1 or B2C2) and a B2C2 gamete from parent Gamete from Testcross (to
B1B2C1C2: B2B2C2C2)
2.
Type
Type Frequency
Frequency genotype
genotype Number
Number
• The B1B2C2C2 and B2B2C1C2 progeny result from the B1C1 B1B2C1C2 270
union of a recombinant gamete (i.e., B1C2 or B2C1) and a B1C1 B1B2C1C2 270
B2C2 gamete from parent 2. B1C2 B1B2C2C2 30
B1C2 B1B2C2C2 30
• The frequency of recombinants in our example is B2C1 B2B2C1C2 30
r=(30+30)/600=0.10
B2C1 B2B2C1C2 30
• This recombination frequency is less than the 50% B2C2 B2B2C2C2 270
recombination frequency that is expected between B2C2 B2B2C2C2 Total
270= 600
unlinked loci. The B and C loci are therefore considered
linked. Total = 600
• Crossing over is more likely to occur between loci that are
far apart than between loci that are close to each other. The
recombination frequency is consequently indicative of the
relative distance between loci.
Coupling vs repulsion phases of linkage
• Loci are linked either in coupling or in repulsion phase.

• Coupling linkage:
• Dominat alleles are on one chromosome (i.e., from parent 1) whereas the recessive alleles
are on its homologous pair (i.e., from parent 2)

• Repulsion linkage:
• Both dominat and rececesive alleles are on both homologous chromosomes

• If one parent has the A1A1B1B1C2C2D1D1 genotype whereas the other parent has the
A2A2B2B2C1C1D1D1 genotype, then loci B and C would be linked in repulsion phase.

• With repulsion linkage the B1C2 and B2C1 gametes are the parental types,
whereas the B1C1 and B2C2 gametes are the recombinant types.
Effect of linkage on gametic output
• Likage affects the gametic output only of individulas that are
heterozygous at two or more linked loci.
• Consider the B and C loci in our example
• Linkage affects the gametic output of the B1B2C1C2 double heterozygoes.
• Inds. with the B1B1C1C1 genotype always produce B1C1 gametes regardless of
whether the loci are linked or not.
• Likewise, and individual with the B1B2C1C1 genotype will produce gametes
that are 50% B1C1 and 50% B2C1 regardless of whether the loci are linked or
not.
• Linkage between two loci therefore doesnot affect the gametic output
of homozygotes or single heterozygoes.
Linkage Disequilibrium and Lack of Random
Mating
• Linkage
  disequilibrium (or gametic disequilibrium), denoted by D, is
measured as the observed frequency of a gamete in a population minus the
product of the frequencies of the corresponding alleles:

• Where is the observed frequency of the gamete; is the frequency of ; and is the
frequency of .
• In our example in Table 1,
• for the B1C1 and B2C2 gametes,
• for the B1C2 and B2C1 gametes.
• For Breeding:
• Linkage disequilibrium may be advantageos or disadvantageous to a breeder,
depending on whether the alleles are associated in a favorable or unfavourable
manner.
 Linkage Disequilibrium and Lack of Random
Mating…
• Suppose an inbred that has the A1A1B2B2
genotype is crossed with an inbred that has the
A2A2B1B1.
• If the loci are unlinked (r=0.5), the expected
frequency of A1A1B1B1 individuals is
• 0.0625 in the F2 and
• 0.25 among recombinant inbreds derived from the F2
(Fig. 2).
• These frequiencies decrease as the linkage
between the loci becomes tighter.
Figure 2. Effect of linkage on the frequency of A1A1B1B1

• If the recombination frequency between the loci is r=0.10, the expected frequency of
A1A1B1B1 individuals is reduced to 0.0025 in the F2 and 0.0833 among inbreds
derived from the F2.
 Linkage Disequilibrium and Lack of Random
Mating …

  A1B2 A1B2     A1B1 A1B2 A2B1 A2B2

A2B1 A1A2B2B1 A2A1B1B2   A1B1 A1A1B1B1 A1A1B1B2 A1A2B1B1 A1A2B1B2

A2B1 A2A1B1B2 A2A1B1B2   A1B2 A1A1B1B2 A1A1B2B2 A2A2B1B1 A1A2B2B2

        A2B1 A1A2B1B1 A1A2B1B2 A2A2B1B1 A2A2B1B2

        A2B2 A1A2B1B2 A2A2B2B2 A2A2B1B2 A2A2B2B2

  F1         F2    

• Repulsion linkage therefore works to the breeder’s disadvantage if the

A1A1B1B1 genotype is considered favorable.
• But repulsion linkage will work to the breeder’s advantage if the A1A1B1B1
genotype is considered unfavorable.
Advantage of linkage
• In other words linkage helps preserve favorable allele combinations
that already exist in the parents.
• One might speculate that elite cultivars have accumulated linkage
combinations that are favorable.
• If so, then procedures that circumvent repeated meiosis during inbred
development are desirable eg., double haploids.
• Meiosis during each generation of selfing offers repeated opportunities
for crossing over.
• The frequency of recombinations (e.g., A1A1B1B1 in Fig. 2) is
consequently higher among inbres than among individuals in the
initial population.
Methods to Disrupt linkage
• Two methods for disrupting linkage
• Selfing during inbred development.
• Random mating.
• After many generations of random mating, the frequency of each of the
four types of gametes may all be equal to 0.25, which is the expected
frequency in the absence of linkage for allele frequencies of 0.50.
• At this point the population is in linkage equilibrium, yet the loci
remain linked by virtue of their being closer together on the same
chromosome.
• Linkage is often described as the lack of free recombination between
two loci, i.e., r<0.50.
Linkage Disequilibrium and Lack of Random
Mating
• Furhtermore, a nonzero D may be caused by population structure,
which occurs when the individuals in a group do not all belong to the
same conceptual or actual random-mating population.
• Plan breeders generally do not random mate F2 or backcross
populations prior to selfing. Random mating is difficult in self-
pollinated crops.
• Random mating adds at least one generation to the breeding process,
and most breeders of cross-pollinated crops probably prefer using any
additional generation for selection rather than for random mating.
• Besides, the approach to linkage equilibrium is slow for closely linked
loci and a few generations of random mating will have little effect.
Advantage of Random Mating in Plant Breeding
• Emperical data do not support the usefulness of random mating prior to selfing in
inbred development.
• In an eight-parent tobacco population, yield and leaf width decreased only slightly through five
generations of random mating (Humphrey et al., 1969). Three other tobacco traits were
unaffected.
• In three spring wheat populations, the best inbred in each of three generations of random mating
was not superior to the best inbred in the initial F2 population (Altman and BUSCH, 1984).
• In two maize F2 populations, estimates of genetic variances before and after five generations of
random mating were similar (Covarrubias-Prieto, 1987).

• Overall, empirical results suggest that random mating prior to selfing in F2 or BC1
populations has little practical use.
References
• Beavis, W. 2016. Linkage. In Quantitative Genetics, interactive e-
learning courseware. Plant Breeding E-Learning in Africa.