linkage and genetic mapping in eukaryotes. in eukaryotic species, each linear chromosome contains a...

LINKAGE AND GENETIC MAPPING IN EUKARYOTES

In eukaryotic species, each linear chromosome contains a long piece of DNA A typical chromosome contains many hundred

or even a few thousand different genes The term linkage has two related

meanings 1. Two or more genes can be located on the

same chromosome 2. Genes that are close together tend to be

transmitted as a unit

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LINKAGE AND CROSSING OVER

Chromosomes are called linkage groups They contain a group of genes that are linked together

The number of linkage groups is the number of types of chromosomes of the species For example, in humans

22 autosomal linkage groups An X chromosome linkage group A Y chromosome linkage group

Genes that are far apart on the same chromosome may independently assort from each other This is due to crossing-over

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Crossing Over May Produce Recombinant Phenotypes

In diploid eukaryotic species, linkage can be altered during meiosis as a result of crossing over

Crossing over Occurs during prophase I of meiosis at the

bivalent stage Non-sister chromatids of homologous

chromosomes exchange DNA segments

5-5Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display

Copyright © The McGraw-Hill Companies, Inc. Permission required for reproduction or display.

Diploid cell afterchromosome replication

Meiosis

Possible haploid cells(a) Without crossing over, linked alleles segregate together.

ba

ba

ba

BA

ba

BA

Diploid cell afterchromosome replication

Meiosis

Possible haploid cells(b) Crossing over can reassort linked alleles.

bA

BA

ba

Ba

BA

BA

BA

ba

5-7Figure 5.1

These haploid cells contain a combination of alleles NOT

found in the original chromosomes

These are termed parental or non-recombinant cells

This new combination of alleles is a result of

genetic recombination

These are termed nonparental or recombinant

cells

Bateson and Punnett Discovered Two Traits That Did Not Assort Independently

In 1905, William Bateson and Reginald Punnett conducted a cross in sweet pea involving two different traits Flower color and pollen shape

This is a dihybrid cross that is expected to yield a 9:3:3:1 phenotypic ratio in the F2 generation However, Bateson and Punnett obtained surprising

results


Figure 5.2

5-9

A much greater proportion of the two types found in the parental generation

Morgan Provided Evidence for the Linkage of Several X-linked Genes

The first direct evidence of linkage came from studies of Thomas Hunt Morgan

Morgan investigated several traits that followed an X-linked pattern of inheritance

Figure 5.3 illustrates an experiment involving three traits Body color Eye color Wing length


yy ww mm

y+y w+w m+m

F1 generation

x

y w m Y

x

y+ w+ m+ Y

F1 generation contains wild-typefemales and yellow-bodied,white-eyed, miniature-wingedmales.

5-13

Morgan observed a much higher proportion of the combinations of traits found in the parental generation

P Males

P Females

Morgan’s explanation: All three genes are located on the X chromosome Therefore, they tend to be transmitted together as a unit

1. Why did the F2 generation have a significant number of nonparental combinations?

2. Why was there a quantitative difference between the various nonparental combinations?


Morgan Provided Evidence for the Linkage of Several X-linked Genes


Gray body, red eyes 1,159

Yellow body, white eyes 1,017

Gray body, white eyes 17

Yellow body, red eyes 12

Total 2,205

Let’s reorganize Morgan’s data by considering the pairs of genes separately

Red eyes, normal wings 770

White eyes, miniature wings 716

Red eyes, miniature wings 401

White eyes, normal wings 318

Total 2,205

It was fairly common to get this nonparental combination

But this nonparental combination was rare

Morgan made three important hypotheses to explain his results 1. The genes for body color, eye color and

wing length are all located on the X-chromosome

They tend to be inherited together 2. Due to crossing over, the homologous X

chromosomes (in the female) can exchange pieces of chromosomes

This created new combination of alleles 3. The likelihood of crossing over depends on

the distance between the two genes Crossing over is more likely to occur between two

genes that are far apart from each other5-17

5-18

Figure 5.4

These parental phenotypes are the most common offspring

because the genes are far apart

These recombinant offspring are not uncommon

5-19

Figure 5.4

because the genes are very close together

These recombinant offspring are fairly uncommon

These recombinant offspring are very unlikely1 out of 2,205

This method is frequently used to determine if the outcome of a dihybrid cross is consistent with linkage or independent assortment


Chi Square Analysis

Parentalchromosomes

Nonparentalchromosomes

C Wx

c wx

c Wx

C wx

Crossing over

(b) Crossing over between normal and abnormal chromosome 9

Normalchromosome 9

Abnormalchromosome 9

Knob

(a) Normal and abnormal chromosome 9

Interchangedpiece fromchromosome 8

Creighton and McClintock ExperimentThey demonstrated physical evidence of cross-overs.

C = Coloredc = colorlessWx = Starchy endospermwx = waxy endosperm

5-30Figure 5.6

Interpreting the Data


Parent A Parent B

C wx (nonrecombinant)

c Wx (nonrecombinant)

C Wx (recombinant)

c wx (recombinant)

c Wx

c wx

By combining these gametes into a Punnett square, the following types of offspring can be produced

5-34

The colored, waxy phenotype (Cc wxwx) can occur only if Recombination did not occur in parent A

AND Parent A passed the knobbed, translocated

chromosome to its offspring This was the case, as shown in the data table

below

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5-35

The colorless, waxy phenotype (cc wxwx) can occur only if Recombination did occur in parent A

AND Parent A passed a chromosome 9 that had a

translocation but was knobless This was the case, as shown in the data table

below


The Data


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These observations were consistent with the idea that a cross over occurred between the C and wx genes

As stated by Creighton and McClintock: “Pairing chromosomes, heteromorphic in two

regions, have been shown to exchange parts at the same time they exchange genes assigned to these regions.”

Genetic mapping is also known as gene mapping or chromosome mapping

Its purpose is to determine the linear order of linked genes along the same chromosome

Figure 5.8 illustrates a simplified genetic linkage map of Drosophila melanogaster


GENETIC MAPPING IN PLANTS AND ANIMALS


Figure 5.8

Each gene has its own unique locus at a particular site

within a chromosome

Physical Maps

Use nucleotide sequences to map genes

5-45

Experimentally, the percentage of recombinant offspring is correlated with the distance between the two genes If the genes are far apart many recombinant offspring If the genes are close very few recombinant offspring

Map distance =


Number of recombinant offspring

Total number of offspringX 100

The units of distance are called map units (mu) They are also referred to as centiMorgans (cM)

One map unit is equivalent to 1% recombination frequency

5-47Figure 5.9

Chromosomes are the product of a crossover during

meiosis in the heterozygous parent

Recombinant offspring are fewer

in number than nonrecombinant

offspring

5-48

The data at the bottom of Figure 5.9 can be used to estimate the distance between the two genes

Map distance =


Number of recombinant offspring

Total number of offspringX 100

76 + 75

542 + 537 + 76 + 75X 100=

= 12.3 map units

The first genetic map was constructed in 1911 by Alfred Sturtevant He was an undergraduate who spent time in the

laboratory of Thomas Hunt Morgan Sturtevant wrote:

“In conversation with Morgan … I suddenly realized that the variations in the length of linkage, already attributed by Morgan to differences in the spatial orientation of the genes, offered the possibility of determining sequences [of different genes] in the linear dimension of the chromosome. I went home and spent most of the night (to the neglect of my undergraduate homework) in producing the first chromosome map, which included the sex-linked genes, y, w, v, m, and r, in the order and approximately the relative spacing that they still appear on the standard maps.”


Alfred Sturtevant’s Experiment

5-52Figure 5.10

The Data


Alleles Concerned

Number Recombinant/ Total Number

Percent Recombinant Offspring

y and w/w-e 214/21,736 1.0

y and v 1,464/4,551 32.2

y and r 115/324 35.5

y and m 260/693 37.5

w/w-e and v 471/1,584 29.7

w/w-e and r 2,062/6,116 33.7

w/w-e and m 406/898 45.2

v and r 17/573 3.0

v and m 109/405 26.9

Interpreting the Data


In some dihybrid crosses, the percentage of nonparental (recombinant) offspring was rather low For example, there’s only 1% recombinant offspring in

the crosses involving the y and w or w-e alleles This suggests that these two genes are very close

together Other dihybrid crosses showed a higher

percentage of nonparental offspring For example, crosses between the v and m alleles

produced 26.9% recombinant offspring This suggests that these two genes are farther apart


Sturtevant assumed that the map distances would be more accurate among genes that are closely linked. Therefore, his map is based on the following distances

y – w (1.0), w – v (29.7), v – r (3.0) and v – m (26.9) Sturtevant also considered map distances amongst

gene pairs to deduce the order of genes Percentage of crossovers between w and r was 33.7 Percentage of crossovers between w and v was 29.7 Percentage of crossovers between v and r was 3.0 Therefore, the gene order is w – v – r

Where v is closer to r than it is to w


Sturtevant collectively considered all these data and proposed the following genetic map

Sturtevant began at the y gene and mapped the genes from left to right


A close look at Sturtevant’s data reveals two points that do not agree very well with his genetic map The y and m dihybrid cross yielded 37.5% recombinants

But the map distance is 57.6 The w and m dihybrid cross yielded 45.2% recombinants

But the map distance is 56.6

So what’s up? As the percentage of recombinant offspring

approaches a value of 50 % This value becomes a progressively more

inaccurate measure of map distance Refer to Figure 5.11


When the distance between two genes is large The likelihood of multiple crossovers increases This causes the observed number of recombinant offspring

to underestimate the distance between the two genes

Figure 5.11


Trihybrid Crosses

Data from trihybrid crosses can also yield information about map distance and gene order

The following experiment outlines a common strategy for using trihybrid crosses to map genes In this example, we will consider fruit flies that differ in

body color, eye color and wing shape


Trihybrid Crosses

b = black body color b+ = gray body color

pr = purple eye color pr+ = red eye color

vg = vestigial wings vg+ = normal wings

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Step 1: Cross two true-breeding strains that differ with regard to three alleles.

Female is mutant for all three traits

Male is homozygous wildtype for all three

traits

The goal in this step is to obtain aF1 individuals that are heterozygous for all three genes

Order of genes not important here.


Step 2: Perform a testcross by mating F1 female heterozygotes to male flies that are homozygous recessive for all three alleles

During gametogenesis in the heterozygous female F1 flies, crossovers may produce new combinations of the 3 alleles


Step 3: Collect data for the F2 generation

Phenotype Number of Observed Offspring

Gray body, red eyes, normal wings

+ + +

411 parental

Gray body, red eyes, vestigial wings

+ + vg

61 pr/vg

Gray body, purple eyes, normal wings

+ pr +

2 b/pr and pr/vg

Gray body, purple eyes, vestigial wings

+ pr vg

30 b/pr

Black body, red eyes, normal wings

b + +

28 b/pr

Black body, red eyes, vestigial wings

B + vg 1 b/pr and pr/vg

Black body, purple eyes, normal wings

B pr +

60 pr/vg

Black body, purple eyes, vestigial wings

B pr vg

412 parental


The three genes exist as two alleles each Therefore, there are 23 = 8 possible combinations

of F2 offspring If the genes assorted independently, all eight

combinations would occur in equal proportions It is obvious that they are far from equal

In the offspring of crosses involving linked genes, Parental phenotypes occur most frequently Double crossover phenotypes occur least frequently Single crossover phenotypes occur with

“intermediate” frequency


The combination of traits in the double crossover tells us which gene is in the middle A double crossover separates the gene in the middle from

the other two genes at either end

In the double crossover categories, the recessive purple eye color is separated from the other two recessive alleles Thus, the gene for eye color lies between the genes for

body color and wing shape

Which are the double cross-overs?

The ones with the least amount.


Step 4: Calculate the map distance between pairs of genesNumber of recombs between pr and vg: 61 + 60+ 2 + 1 = 124Number of recombs between b and pr: 30 + 28 + 2 + 1 = 61Number of recombs between b and vg, all but double cross-overs: 61 + 60 + 30 + 28 = 178

Map Distance

pr/vg = 124/1005 x 100 = 12.3 b/pr = 61/1005 x 100 = 6 b and vg = 179/1005 x 100 = 17.8

_____6____________12.3____________ b pr vg

The distance between b and vg was found to be 17.8. The actual distance is 18.3 mu.

Interference The slightly smaller lower value was a

small underestimate because we did not consider the double crossovers in the calculation between b and vg.

The lower than expected value is due to a common genetic phenomenon, termed positive interference. The first crossover decreases the probability that a second crossover will occur nearby.

Much of our earliest understanding of genetic recombination came from the genetic analyses of fungi

Fungi may be unicellular or multicellular organisms They are typically haploid (1n) They reproduce asexually and, in many cases,

sexually

The sac fungi (ascomycetes) have been particularly useful to geneticists because of their unique style of sexual reproduction


GENETIC MAPPING IN HAPLOID EUKARYOTES

5-79

Meiosis produces four haploid cells,

termed spores

Figure 5.12

These are enclosed in a sac termed an ascus

The cells of a tetrad or octad are contained within a sac

In other words, the products of a single meiotic division are contained within one sac


The arrangement of spores within an ascus varies from species to species Unordered tetrads or octads

Ascus provides enough space for the spores to randomly mix together

Ordered tetrads or octads Ascus is very tight, thereby preventing spores from

randomly moving around


Types of Tetrads or Octads

5-82Figure 5.13


YeastUnicellular alga

Mold

Ascus provides space for spores to

randomly mix together

Tight ascus prevents mixing

of spores

Ordered tetrads or octads have the following key feature The position and order of spores within the ascus is

determined by the divisions of meiosis and mitosis In crosses of tan and black Neurospora cultures, the

spores appear tan or black in a certain order. All black spores or all tan spores indicate no

hybridization.


Ordered Tetrad Analysis

5-84Figure 5.13


Pairs of daughter cells are located

next to each other

All eight cells are arranged in a linear, ordered fashion

Non-crossovers

Cross-overs

Non cross-overs

Cross-overs

Non cross-overs

To calculate this distance, the experimenter must count the number of cross-over asci, as well as the total number of asci In cross-over asci, only half of the spores are actually the

product of a crossover Therefore

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(1/2) (Number of SDS asci)

Total number of asciX 100Map distance =


Genetics of Corn

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linkage and genetic mapping in eukaryotes. in eukaryotic species, each linear chromosome contains a...

Documents

x chromosome linkage

parental generation

term linkage

y x y w

y y w w

number of linkage groups

xlinked genes

generation x y w