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PLANT BIOTECHNOLOGY & GENETIC
ENGINEERING
(3 CREDIT HOURS)
LECTURE 12
HAPLOTYPE
ALLELE FREQUENCY
POPULATION GENETICS
FITNESS
GENOTYPE FREQUENCY
LINKAGE
LINKAGE EQUILIBRIUM & DISEQUILIBRIUM
MORGAN
HAPLOTYPE
• A haplotype is a group of genes within an organism that is
inherited together from a single plant.
• The word “haplotype” is derived from the word “haploid”, which
describes cells with only one set of chromosomes, and from the
word “genotype”, which refers to the genetic makeup of an
organism.
• A haplotype can describe a pair of genes inherited together from
one parent on one chromosome, or it can describe all the genes
on a chromosome that were inherited together from a single
parent.
• This group of genes is inherited together because of genetic
linkage, or the phenomenon by which genes that are close to
each other on the same chromosome are often inherited
together.
HAPLOTYPE
• In addition, the term “haplotype” can also refer to the
inheritance of a cluster of single nucleotide polymorphisms
(SNPs), which are variations at single positions in the DNA
sequence among individuals.
• By examining haplotypes, scientists can identify patterns of
genetic variation that are associated with health and disease
states. For instance, if a haplotype is associated with a
certain disease, then scientists can examine stretches of
DNA near the SNP cluster to try to identify the gene or genes
responsible for causing the disease.
ALLELE FREQUENCY
• Allele frequency or gene frequency is the proportion of a
particular allele (variant of a gene) among all allele copies being
considered.
• It can be formally defined as the percentage of all alleles at a
given locus in a population gene pool represented by a
particular allele.
• In other words, it is the number of copies of a particular allele
divided by the number of copies of all alleles at the genetic
place (locus) in a population.
• It is usually expressed as a percentage.
• In population genetics, allele frequencies are used to depict the
amount of genetic diversity at the individual, population and
species level. It is also the relative proportion of all alleles of a
gene that are of a designated type.
ALLELE FREQUENCY
A particular locus on a chromosome and the gene occupying
that locus
A population of N individuals carrying n loci in each of their
somatic cells (e.g., two loci in the cells of diploid species, which
contain 2 sets of chromosomes)
Different alleles of the gene exist
One allele exists in copies
GENOTYPE FREQUENCY
• Genotype frequencies are the frequencies of the homozygous
dominant (AA), heterozygous (Aa) and the homozygous
recessive (aa). In population genetics, they are p2, 2pq and q2.
• Allele frequencies are the frequencies of each allele, dominant
(A) and recessive (a). In population genetics, these are p and q.
• Gamete frequencies refer to the proportion of gametes made
that have each allele. So, a heterozygous individual (Aa) makes
½ A and ½ a gametes. A homozygous individual makes only one
kind of gamete.
POPULATION GENETICS
Based on Darwin’s 4 principles:
1.Heritable differences among individuals in population
2.Heritable differences passed to offspring.
3.More offspring are born that survive.
4.Some offsprings are more “fit” than others in a given
environment.
POPULATION GENETICS
• Population genetics is the study of allele and genotype
frequencies in population
• Population: Group of individuals of one species that actually
or potentially interbreed
• Genotype Frequency: Fraction of population with given
genotype
• Allele Frequency: Fraction of gametes with given allele
• Gene Pool: All gametes made by breeding members in a
generation (i.e., all inherited genes)
FITNESS
• The quantifiable measure of an individual’s genetic
contribution to the future.
• High Fitness
Genotypes with high rate of survival and/or high level of
reproduction (genes are passed on)
• Low Fitness
Genotypes with low rate of survival and/or low level of
reproduction (genes are NOT passed on)
• Lethal genotype is WORST CASE SCENARIO – extremely low
fitness
LINKAGE
Two genes are said to be linked if they are located on the same
chromosome. We assume that different chromosomes segregate
independently during meiosis. Therefore, for two genes located at different
chromosomes, we may assume that their alleles also segregate
independently. The chance that an allele at one locus co-inherits with an
allele at another locus of the same parental origin is then 0.5 and such
genes are unlinked.
Parent 1
x
Parent 2
AABB
aabb
AbBb (100%)
F1 gametes
A & B are unlinked: frequency%
A & B linked:
A & B tightly linked:
AB
25
35
48
Ab
25
15
2
aB
25
15
2
ab
25
35
48
LINKAGE EQUILIBRIUM & LINKAGE
DISEQUILIBRIUM
• If two genes/traits/loci are in linkage equilibrium, it means that
they are inherited completely independently in each generation.
• An example would be loci that are on two different chromosomes
and encode unrelated, non-interacting proteins.
• If two genes are in linkage disequilibrium, it means that certain
alleles of each gene are inherited together more often that would
be expected by chance.
• This may be due to actual genetic linkage – that is the genes are
closely located on the same chromosome.
• Or it could be due to some form of functional interaction where
some combinations of alleles at the two loci affect the viability of
potential offspring.
LINKAGE DISEQUILIBRIUM
• Linkage equilibrium and its opposite; linkage disequilibrium, are
terms used for the chance of co-inheritance of alleles at
different loci.
• Alleles that are in random association are said to be in linkage
equilibrium.
• The chance of finding one allele at one locus is independent of
finding another allele at another locus.
• If the chance of finding either the B-allele or the b-allele is 50%,
the genes are in linkage equilibrium.
• Hence, if we look at the gamete frequencies, then we speak of
linkage equilibrium if the
Freq (AB) = Freq (Ab) = Freq (aB) = Freq (ab)
And the amount of disequilibrium is measured as:
D = Freq (AB). Freq (ab) – Freq (Ab). Freq (aB)
LINKAGE DISEQUILIBRIUM
• Linkage disequilibrium is the result of physical linkage of
genes.
• However, if the genes are even on the different
chromosomes, there can be linkage disequilibrium.
• This can be due to selection.
• If A and B both affect a characteristic positively, and the
characteristic is selected for, then in the selected offspring
there will be a negative association between A and B.
LINKAGE DISEQUILIBRIUM
Linkage disequilibrium can also be the result of crossing or
migration.
If a new individual with AB gametes come into a population with
ab gametes, then in the offsprings there will be more AB and ab
gametes if the genes are linked.
However, after a number of generations, the number of AB and
ab gametes will approach that of the recombinant aB and Ab
gametes, indicating linkage equilibrium.
If the linkage is closer, the process will take longer.
But ultimately, even if the distance between two genes is less
that 1cM, genes will become in linkage equilibrium (with no
selection).
LINKAGE DISEQUILIBRIUM
Hence, linkage disequilibrium is due to:
• Recent migration or crossing
• Selection
• Recent mutation
MORGAN
• The distance between two genes is determined by their
recombination fraction. The map units are Morgans. One
Morgan is the distance over which, on average, one
crossover occurs per meiosis.
• The distances on the genetic map are mapped using a
mapping function. A mapping function translates
recombination frequencies between two loci into a map
distance in cM.
• A mapping function gives the relationship between the
distance between two chromosomal locations on the genetic
map (in cM) and their recombination frequency.
MORGAN
Two properties of a good mapping function is that:
1. Distances are additive, i.e., the distance AC should be equal
to AB + BC if the order is ABC
1. A distance of more than 50cM should translate into a
recombination fraction of 50%.
RECOMBINATION FREQUENCY
• Genetic mapping is also known as gene mapping or
chromosome mapping
• 1% recombination = 1 map unit (m.u) = 1 cM
• Recombination Frequency between 2 genes = No. of
recombinant offspring/Total no. of offsprings
THE END