Download BL414 Genetics Spring 2006 Linkage and Genetic Maps Outline February 22, 2006

BL414 Genetics Spring 2006
Linkage and Genetic Maps Outline
February 22, 2006
In the principle of independent assortment, we saw that the two parental alleles
have a 50/50 chance of being transmitted to offspring. For example, the cross of
Dd x dd gives offspring with a 50/50 chance of getting the D or d allele from one
parent, and a 100% of getting d from the other parent, so they have a 50% of
being Dd and a 50% chance of being dd. But when genes are located together on
the same chromosome, they don’t undergo independent assortment. The result is
that we see them being transmitted together more often than not.
Ch. 5.1 Linkage and Recombination
 Genetic linkage is the tendency of genes located on the same chromosome
to be associated in inheritance more frequently than expected from their
independent assortment in meiosis. If two genes are always transmitted
together, they are said to exhibit complete linkage.

Some genes are linked on the same chromosome, but do not exhibit
complete linkage because of the occurrence of DNA crossover events
between homologous regions of homologous chromosomes. The crossover
events occur during prophase I of meiosis. This crossover is called
recombination, which involves the physical breakage of DNA in a
chromosome and reforming a connection to the DNA on the homologous
chromosome. The result of recombination is a new combination of alleles
in the gametes, different from the arrangement on the parental
chromosomes.
o In Drosophila, recombination only takes place in females, not in
males. In humans, males 60% of the recombination of females.

Parental types are allele arrangements which are identical to the
arrangements of alleles in the parents.

Recombinant types are allele arrangements different from the parental
types, due to recombination or crossovers.
The frequency of recombination is calculated as the number of offspring
with recombinant allele arrangements, divided by the total number. To
get a percent, multiply this frequency by 100%. A recombination
frequency of < 50% means that the genes are linked. A frequency of 50%


means that the genes are unlinked and undergo independent
assortment.
Each pair of linked genes has a characteristic recombination frequency.

Example 1: Calculation of recombination frequencies.
P
♀w y+ / w y+
x
♂w+ y /Y
♀w y+ / w+ y
x
♂w y+ /Y
F1
F2
males
w y+ /Y
4484
w+ y /Y
4413
w+ y+ /Y
76
w y /Y
53
parental types:
(4484 + 4413) / 9026 x 100 = 99%
Recombinant types:
(76 + 53) / 9026 x 100 = 1%
Recombination frequency: 1%
 Example 2:
Recombination frequency of w (white-eyes) and m (miniature wings)
which are both X-linked.
P
♀ w+ m+ / w+ m+
x
♂wm/Y
F1
♀ w+ m+ / w m
x
♂ w+ m+ / Y
F2 males:
412
w+ m+ / Y (parental)
389
w m / Y (parental)
206
w+ m / Y (recombinant)
185
w m+ / Y (recombinant)
Total: 1192
Recombination frequency= (206+185)/1192 x 1100% = 32.8%
 Example 3:
Autosomal genes also exhibit linkage:
P
♀ b c+ / b c+ x
♂ b+ c / b+ c
F1
all b c+ / b+ c
Test cross: ♀b c+ / b+ c
x
♂bc/bc
2934 b c+/ b c
2768 b+ c / b c
871
bc/bc
846
b+ c+ / b c
Total: 7419
Recombinant frequency= (871+846)/7419 x 100% = 23%

Terms for allele arrangement in heterozygote: BbCc
o Trans, or repulsion: means that mutant genes are on opposite
chromosomes:
o b c+ / b+ c
o Cis, or coupling: means that mutant genes are present on the same
chromosome: b+ c+ / b c

Using the numbers of offspring to compare observed and expected values,
the chi-square test is important for determining if recombination
frequencies are significant and due to linkage or simply an effect of
random sampling variation.
o If the chi-square value for recombinant vs. non-recombinant
offspring says the numbers are statistically significantly different,
i.e. the p value < 0.05, there is linkage.
5.2 Genetic mapping
 The recombination frequency is proportional to the distance between two
genes on a chromosome. For short distances, 1 map unit, “m.u.” equals 1%
recombination. 1 m.u. also equals 1cM, centimorgan. This is because a
greater distance between two linked genes means a greater chance for a
single crossover to occur between them. The frequencies can be used to
build a genetic map representing the linear order of linked genes and the
distances between them.

Genes located on the same chromosome are said to be syntenic, whether
or not they are linked (i.e. have a recombination frequency of < 50%). A
group of syntenic genes is called a linkage group. The number of linkage
group for an organism is equal to the haploid number of chromosomes.
5.3 Genetic mapping in a three-point cross
 Two point crosses are limited when genes are very close together or when
double crossovers affect the recombination freq.
 Three point crosses are more accurate in mapping genes
Example: a three point cross in corn
Looking at the linked genes:
 lz: lazy or prostrate growth
 gl: glossy leaf
 su: sugary endosperm
A cross is done using multiply heterozygous parental genotype:
LlGgSs x LlGgSs
Progeny from a testcross of the offspring:
Phenotype
Genotype
of testcross progeny
of gamete
Number
 Normal
Lz Gl Su
286
 Lazy
lz Gl Su
33
 Glossy
Lz gl Su
59
 Sugary
Lz Gl su
4
 Lazy, glossy
lz gl Su
2
 Lazy, sugary
lz Gl su
44
 Glossy, sugary
Lz gl su
40
 Lazy, glossy, sugary
lz gl su
272
Total: 740


In any genetic cross involving linked genes, no matter how complex, the
two most frequent types of gametes with respect to any pair of genes are
nonrecombinant: these provide the linkage phase (cis vs. trans) of the
alleles of the genes in the multiply heterozygous parent.
The double crossover gametes will be the least frequent types and can
indicate the order of the three genes on the chromosome. A double
crossover event will exchange the middle pair of alleles.  This testcross
suggests that the Su gene is in the middle of the other two.
Organize the data:
 Parental types:



 Normal
Lz Su Gl
 Lazy, glossy, sugary
lz su gl
Single crossover between lz and su:
 Glossy, sugary
Lz su gl
 Lazy
lz Su Gl
Single crossover between su and gl:
 Lazy, sugary
lz su Gl
 Glossy
Lz Su gl
Double crossover types
 (both lz x su and su x gl occurred)
 Sugary
Lz su Gl
 Lazy, glossy
lz Su gl
286
272
40
33
44
59
4
2
Recombination frequency between lz and su:
(40+33+4+2)/740 = 0.107
Recombination frequency between su and gl:
(44+59+4+2)/740 = 0.147
Build the map:
lz
gl
su
10.7 map units
14.7 map units
5.4 Genetic mapping in Human Pedigrees
Because human pedigrees must be used to determine linkage between human
genes, and the relative numbers of offspring for these will be small, statistics
must be utilized to determine linkage.
The standard in human genetics is to find an lod score for a pedigree or group of
pedigrees. Lod represents a “log of odds” or the logarithm of the likelihood ratio
between the likelihood of linkage and the likelihood of non-linkage. A frequency
of recombination, r, that maximizes the lod score is determined by iterative
calculations of the lod using different r’s. The binomial coefficient is calculated
for a given pedigree based on its number of outcomes (or offspring) that indicate
something about recombination between the two genes of interest. An lod score
of > 3 is considered statistically significant evidence of linkage. An lod < -2 is
significant evidence against linkage. A value -2 < lod < 3 is considered
uninformative and more data should be collected in order to draw a conclusion
about linkage.
5.5 Tetrad Analysis
Some species of fungus create haploid spores as a product of meiosis. The
genotype of these spores can be analyzed to determine linkage and gene
mapping. Yeast form four spores in an unordered tetrad called an ascus.
PD: parental ditype: the alleles have the same combination found in the parents,
only two different genotypes are present in the 4 spores of the tetrad.
NPD: nonparental ditype: there are two genotypes in the tetrad, and they are
not in the same allele combinations as the parents
TT: tetratype tetrad: all four possible allele arrangements are present in the four
spores in the tetrad