BIO 370 Lecture Notes - Lecture 22: Linkage Disequilibrium, Genotype Frequency, Haplotype
Hardy-Weinberg Proportions for Two Loci
The frequencies of the gametes (haplotypes) will be directly associated with the frequencies of
the different arrangements of alleles in the heterozygous/heterozygous parents.
Let’s sa that the feueies of the AB, Ab, aB, ab haplotypes are s, t, u, and v, respectively.
we need to distinguish
between two different kinds of double heterozygote (Aa Bb) parents if we are to
correctly predict the genotypes of the offspring. In the absence of recombination,
AB|ab parents will produce only AB and ab gametes, whereas Ab|aB parents will
produce only Ab and aB gametes.
Dimensions
of rectangle
are proportional
to frequencies.
s > t,u > v
This is why the genotype frequencies shown here are simply equal to the products of the
haplotype frequencies.
The 4 haplotypes behave as a one locus, 4 allele model.
Or, 1 = s2 + 2st +2su + 2sv + t2 + 2tu + 2tv + u2 + 2uv + v2
the Hardy–Weinberg frequencies of each
s
s
t
t
u
u
v
v
find more resources at oneclass.com
find more resources at oneclass.com
genotype are equal to the chance that two gametes that are drawn randomly from
the population compose that genotype. The chance is simply the product of the
allele frequencies of the two alleles that make up that genotype
Quantifying Linkage Disequilibrium
Linkage Disequilibrium - associations between gene copies at two different loci.
Under HW EQ, with all assumptions met, genotype frequencies are equal to the products of
allele frequencies. This would be the same under 2 loci HW model, but each locus gene copies
is considered separately so genotype frequencies = haplotype frequencies.
If alleles and loci are segregating and assorting independently, then we expect frequency of
gametes to be equal to product of alleles.
Locus 1
f [A] = 0.6
f [a] = 0.4
Locus 2
f [B] = 0.8
f [b] = 0.2
f [AB gametes] = 0.6 x 0.8 = 0.48
f [Ab gametes] = 0.6 x 0.2 = 0.12
f [aB gametes] = 0.4 x 0.8 = 0.32
f [ab gametes] = 0.4 x 0.2 = 0.08
1.00
When the two frequencies are at the same level, then the population is in linkage equilibrium.
“as ull odel is’t ight, ad thee is idepedet assotet.
To measure the associations between allele frequencies at two loci A and B, we look at the
haplotype frequencies at these loci. Let fA, fa, fB, and fb be the frequencies of the A, a, B, and b
alleles, respectively, and let hAB, hAb, haB, and hab be the frequencies of the AB, Ab, aB, and ab
haplotypes, respectively.
If the allele at the A locus occurs independently of the allele at the B locus, the haplotype
frequencies will be given by:
hAB = fAfB
hAb = fAfb
haB = fafB
hab = fafb
find more resources at oneclass.com
find more resources at oneclass.com
Document Summary
The frequencies of the gametes (haplotypes) will be directly associated with the frequencies of the different arrangements of alleles in the heterozygous/heterozygous parents. Ab|ab parents will produce only ab and ab gametes, whereas ab|ab parents will produce only ab and ab gametes. Dimensions of rectangle are proportional to frequencies. s > t,u > v. This is why the genotype frequencies shown here are simply equal to the products of the haplotype frequencies. The 4 haplotypes behave as a one locus, 4 allele model. The chance is simply the product of the allele frequencies of the two alleles that make up that genotype. Linkage disequilibrium - associations between gene copies at two different loci. Under hw eq, with all assumptions met, genotype frequencies are equal to the products of allele frequencies. This would be the same under 2 loci hw model, but each locus gene copies is considered separately so genotype frequencies = haplotype frequencies.
