Genetics

GENETICS
CHAPTER 5
LINKED GENE INHERITANCE
Contents
 Concepts of linkage and recombination

 Linkage and Recombination between 2 genes
 Linkage and Recombination between 3 genes
 Linkage and gene mapping
1. Linkage and Recombination
• Morgan
• Genes are located on the same chromosome thus travel together
during meiosis
• Sturtevant
• Variation of length of linkage indicates how genes are positioned
along chromosome
• These genes are not obeyed Mendelian principles of inheritance
• Number of chromosome is limited while number of genes is more →
some genes must be on the same chromosome and could not assort
independently
• Genes located close together on the same chromosome are called
linked genes
2. Linkage and Recombinant between
two genes
- Genes on the same chromosome travel together
and arrive at the same destination
- Genes may switch from one to homologous
chromosome occasionally through crossing
over in meiosis
- crossing over produce recombination
- Genes on the same chromosome may exhibit the
independent assortment if they are far enough
- Linked genes are noted as, for example, Ab/aB,
where each pair A and b, a and B are on the
same chromosome
2.1 Complete linkage compared with
independent assortment
- test cross of linkage can be done with tomato plants

genes
- one pair of gene: M produces normal leave (dominant)
and m produces mottles leave (recessive)
- other pair of gene: D produces tall plant (dominant)
and d produces dwarf plant (recessive)
2.2 Crossing over of the linked genes
- linkage is rarely complete
- usually, there is crossing over between linked genes –
incomplete linkage, produce re-combinations of traits
- for closely linked genes, crossing over does not
usually take place in meiosis
Example
Calculation the recombinant frequency
The percentage of recombinant progeny produced in the
cross is called recombinant frequency
In the testcross above,
So 12% of progeny exhibit new combinations of traits

resulting from crossing over
Coupling and Repulsion
- the arrangement in which wildtype alleles found on one
chromosome and mutant alleles on other chromosome
is called coupling (cis configuration). Ex., a+a+/aa
- the arrangement in which each chromosome carry one
wild type and mutant allele is called repulsion (trans
configuration). Ex., a+a/a+a
- these arrangements critically important to determine the
outcome of the cross
Predicting the outcome of the cross with
linked genes
- arrangement of alleles on chromosome determines the

type of progeny
- the recombinant frequency helps to determine the
proportion of the progeny
Testing for independent assortment
In some cross, the nonrecombinants and recombinants

does not differ clearly
 For example, in the cross AaBb x aabb, the result shows: 54
AaBb, 56 aabb, 42 Aabb, and 48 aaBb
This ratio is quite similar to 1:1:1:1 ratio of independent
assortment
Testing for independent assortment is required to confirm
whether genes are linked.
For example
A test cross y+y cv+ cv X y y cv cv produces
Evaluate the result if two genes in this cross assort independently?
The result of the cross shows the ratio that closely near
1:1:1:1  assume that this cross follow the Mendel principle
To test these two gene independently assorted  require the
calculation of the 3 chi squared tests: test the independent
assortment at each locus and at two loci.
Brown Yellow Brown Yellow
Phenotypes
Straight Curved Curved Straight
Total 200
Observed 63 77 28 32
Expected 50 50 50 50
At first locus for gene body color, the cross between
heterozygote and homozygote (y+y X yy)  ½ y+y brown
and ½ yy yellow
The expected : 100 each
The observed: brown 63+28 = 91 brown, 77+32=109 yellow
The degree of freedom: 2-1 =1  0.2 < p < 0.3 >>0.05

The expected and observed are not significantly different
At second locus for gene wing length, the cross between
heterozygote and homozygote (cv+cv X cvcv)  ½ cv+cv
straight and ½ cvcv curved
The expected : 100 each
The observed: straight 63+32 = 95 , 77+28=105 curved
The degree of freedom: 2-1 =1  0.3 < p < 0.5 >>0.05

The expected and observed are not significantly different
 Testing ratio for the independent assortment:
 There are 4 phenotypes  df = 4 – 1 = 3  p<0.001  this

result shows that two values (expected and observed) are differed
significantly  the two genes are not assorted independently,
they are linked
3. Gene mapping with recombinant
frequencies
 Morgan and student’s idea
 Physical distances between genes on chromosome are
related to the recombinant frequencies
 Genes that lie far apart are more likely to undergo the
crossover than genes that are close together
 Recombinant frequencies could give the way to
determine the order of genes along chromosome and
estimate the distance between genes
 Chromosome maps
 Based on recombinant frequency is called
genetic map
 Based on the distance along chromosome is
called physical map
 Distance on genetic map is measured in map unit
(mu). One mu equals 1% recombination. One mu also
called centiMorgan (cM), 1 morgan equals 100 cM
 When constructing map using recombinant frequencies
 Recombinant frequency between 2 genes can not
exceed 50%. If this rate is 50% → these two genes
probably belong to different group of linked genes,
or far apart on chromosome, or on different
chromosomes
 The test cross for two genes that are far apart
relatively on chromosome is underestimated the true
recombination rate. The double crossover may take
place and influence the recombination rate.
Two point cross
 The cross between 2 genes is called 2 point cross
 Genetic map can be constructed by conducting series of
test cross between pairs of genes
 See book example (…........)
4. Linkage and Recombination
between 3 genes
 Three point test cross is cross between 3 genes
 Using 3 point cross to construct the genetic map of
chromosome
– Order of genes can be established in single set of
progeny, not necessary to carry out many 2point test
crosses
– Can detect double crossover
Test cross of ABC x abc with 2 crossovers
Gene mapping with 3 point test cross
- See test cross of 3 genes
- st+ / st : red eyes/ scarlet eyes
- e+ / e : gray body color / ebony body color
- ss+ / ss : normal bristle / small bristle (spineless)
With 2 classes of progeny possible for each of 3 loci,
there will be 2.2.2 =8 classes of phenotypes
Because the mutant parent has only the recessive
gamete, so we can define the genotype of other parent
in progeny
Genotype (no order phenotype Number of progeny
indicated)
283
St+ e+ ss+ normal
St e ss mutant 278
St+ e ss Ebony, spineless 50
St e+ ss+ scarlet 52
St+ e+ ss spineless 5
St e ss+ Scarlet, ebony 3
St+ e ss+ ebony 43
St e+ ss Scarlet, spineless 41
Determining the gene order
 Determine the nonrecombinant progeny – they will be the
most numerous class of progeny
 Identify the double crossover – there should be the least
numerous class of progeny, because the probability of
double cross over is less than single crossover
 Define the possible orders of genes to find the most
appropriate which indicate one gene in the middle
Determining the location of crossover
 Write the phenotype of progeny with the correct order of
genes
 Define the non-recombinant ones
 Compare the genotypes of single and double crossovers
with the non-recombinants
Calculating the recombinant frequencies
 Calculating the Recombinantions between pairs of genes
(st-ss, st-e, ss-e) includes both single and double
crossovers in total number of progeny
 In this example, the recombinant frequency of
 St-ss = (50+52+5+3)/755 = 14.6%
 St-e = {(50+52+43+41 +(2x5)+(2x3)}/755 = 26.8%
 Ss-e = (43+41+5+3)/755 = 12.2%
Interference and coefficient of coincidence
Interference: The degree to which one crossover interferes with additional crossovers
in the same region
For example:
genes st and ss on the third chromosome of D. melanogaster are separated by a distance of 14.6
m.u  14.6% of the gametes produced by a fly heterozygous at these two loci will be
recombinants.
Genes ss and e are separated by 12.2mu  12.2% of the gametes from a fly heterozygous for
will be recombinants
Proportion of double cross over is equal 12.2%x14.6% = 0.0178
 with total number of progenies produced as 755  number of offsprings with double cross
over is 0.0178*755 = 13.4
The real number observed is 8
Coefficient of coincidence: which is the ratio of observed double crossovers to

expected double crossovers
Then the coefficient of coincidence is 8/13.4 = 0.6
The interferance is 1-Coefficient of coincidence  the interferance is equal 1 - 0.6 = 0.4 
saying that 40% of progenies with double crossover were not expressed because of the
interference
Physical chromosome mapping
Deletion mapping
Somatic cell
hybridization
In situ hybridization
DNA sequencing

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 Concepts of linkage and recombination

- test cross of linkage can be done with tomato plants

In the testcross above,

So 12% of progeny exhibit new combinations of traits

- arrangement of alleles on chromosome determines the

In some cross, the nonrecombinants and recombinants

Evaluate the result if two genes in this cross assort independently?

The degree of freedom: 2-1 =1  0.2 < p < 0.3 >>0.05

The degree of freedom: 2-1 =1  0.3 < p < 0.5 >>0.05

 There are 4 phenotypes  df = 4 – 1 = 3  p<0.001  this

St+ e ss Ebony, spineless 50

St e ss+ Scarlet, ebony 3

St+ e ss+ ebony 43

Coefficient of coincidence: which is the ratio of observed double crossovers to

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